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PubMed2005

[Study of real-time PCR assays for rapid detection of food-borne pathogens].

A duplex real-time SYBR Green LightCycler PCR (LC-PCR) assay with DNA extraction using QIAamp DNA Stool Minikit was evaluated for detection of 8 of 19 species of food-borne pathogens, including Plesiomonas shigelloides, Providencia alcalifaciens, in five stool specimens. The time frame was within 2h or less. The protocol used the same LC-PCR with 22 pairs of specific primers. The rapid amplification and reliable detection of specific genes were determined by this LC-PCR assay from 10 cases of food-borne outbreaks in Shimane Prefecture from 2002 to 2005. These cases included Campylobacter jejuni (4), Clostridium perfringens (2), enteropathogenic Escherichia coli and astA positive E. coli (1), and astA positive E. coli, enterohemorrhagic E. coli 026, and Bacillus cereus (1 each). Rapid amplification and reliable detection of specific genes of food-or water-borne pathogenic bacteria in fecal samples should facilitate the diagnosis and management of food-borne outbreaks.

Base Sequence↗
PubMed2004

PCR-based detection of enterotoxigenic Staphylococcus aureus in the early stages of raw milk cheese making.

AIMS: To define PCR-based detectability of Staphylococcus aureus in raw milk and intermediate products of raw milk cheese making in the presence of a complex background microflora by targetting different specific genes harboured by a single strain. METHODS AND RESULTS: The strain Staph. aureus FRI 137 harbouring nuc, sec, seg, seh and sei genes was used in this study. Raw milk artificially contaminated by different concentrations of Staph. aureus FRI 137 was employed in dairy processing resembling traditional raw milk cheese making. Samples of milk and curds were PCR-analysed after DNA extraction by targetting all the above genes. The pathogen was detected when the initial contamination was 10(4) CFU ml(-1) by amplification of nuc and seh genes. 10(5) and 10(7) CFU ml(-1) were needed when seg or sei and sec genes were targetted, respectively. Enrichment cultures from raw milk and curd samples proved to increase the detection limit of 1 log on average. CONCLUSIONS: The direct detection of the pathogen in the raw material and dairy intermediates of production can provide rapid results and highlight the presence of loads of Staph. aureus potentially representing the risk of intoxication. However, every target gene to be used in the analysis has to be studied in advance in a system similar to the real case in order to determine the level of contamination potentially predictable. SIGNIFICANCE AND IMPACT OF THE STUDY: The detection in real dairy systems of significant loads of Staph. aureus by multiple targets PCR can be more accurate.

Animals↗
PubMed2004

Detection of PCR amplicons from bacterial pathogens using microsphere agglutination.

For rapid and inexpensive detection of polymerase chain reaction (PCR) amplicons, a novel microsphere agglutination assay has been developed. PCR is carried out using biotinylated forward and reverse primers, and the amplified DNA fragments are able to agglutinate streptavidin-coated microspheres (5.7 microm in diameter). Purification of PCR amplicons is unnecessary when initial primer concentrations are 250 nM. Agglutination can be identified visually within 2 min without any additional equipment or reagents. Using listeriolysin (lisA)-specific biotinylated primers, we have successfully detected and identified Listeria monocytogenes lisA+ cells among Salmonella typhimurium, Staphylococcus aureus, Campylobacter jejuni and Escherichia coli O157:H7 cells. The simplicity of this protocol considerably reduces the time and cost of diagnostic PCR experiments. This procedure is potentially useful for various studies and field applications.

Agglutination↗
PubMed1985

Clinical evaluation of lysis-centrifugation technique and a biphasic bottle system for blood culture.

The lysis centrifugation technique (Isolator, DuPont) for blood culture was compared with a system with biphasic medium in bottles. The Isolator was filled with 10 ml of blood once. One aerobic and one anaerobic bottle were injected 3 times with 2.5 ml of blood each. Organisms were detected in 90/748 blood cultures; 26 of which were contaminants. 34 pathogens were detected by both methods, 12 with the Isolator only and 18 with the 3 bottle pairs only. The first pair of bottles revealed 45/52 isolates, the second and third pairs gave an additional 6 and 1 isolate respectively. The contamination rate was 2.3% for the Isolator, which is lower than earlier reported, and 1.3% for the bottles. The most common pathogens were Escherichia coli, Pseudomonas aeruginosa and Streptococcus pneumoniae. The Isolator gave a faster diagnosis in 23 of the 34 cases. No decrease in the recovery rate was seen after 8 h, the longest recommended transport time for the Isolator tubes. One Isolator gave the same yield as the first pair of bottles and combining the methods increased the yield 25% compared to either method alone.

Adolescent↗
PubMed1994

Rapid biochemical screening for Salmonella, Shigella, Yersinia, and Aeromonas isolates from stool specimens.

Four screens for the rapid (4 to 6 h) biochemical detection of pathogens from enteric isolation media are described. The Salmonella screen consisted of Kligler iron agar (KIA), motility-indole-urea-tryptophan-deamination semisolid medium (MIU-TDA), and the o-nitrophenyl-beta-D-galactopyranoside (ONPG) test; the Shigella screen consisted of KIA, MIU-TDA, the ONPG test, and the lysine decarboxylation-indole test; the Yersinia screen consisted of a rhamnose broth; the Aeromonas screen consisted of a xylose agar plate. When tested on 2,102 fresh isolates and 71 stock strains, the screens correctly detected 212 enteric pathogens (sensitivity, 100%), with a specificity of 98.1%.

Aeromonas↗
PubMed2025

Rethinking the pathogenicity of intragenic DMD duplications detected by carrier screening: High prevalence of nontandem duplications revealed by long-read sequencing.

PURPOSE: The pathogenicity of intragenic duplications depends on their structural configuration. Tandem duplications often disrupt reading frames and cause gene loss of function, whereas interspersed (nontandem) duplications are largely benign. When the configuration cannot be determined, current guidelines presume a tandem structure, leading to some laboratories automatically classifying such variants as likely pathogenic or pathogenic. This study evaluates the validity of this presumption for DMD, in patients with and without clinical indications of dystrophinopathy. METHODS: We performed high-coverage long-read genome sequencing on 15 patients with intragenic DMD duplications. A total of 4 patients had clinically indicated dystrophinopathy testing, whereas in the remaining 11 patients, the duplications were detected without clear indications of dystrophinopathy (eg, through carrier screening). RESULTS: All 4 patients with clinical indications had tandem duplications. In contrast, 64% (7/11) of the cases without such indications had interspersed duplications, with 4 subsequently reclassified as likely benign, 2 (likely) pathogenic, and 1 uncertain. These duplications were often complex, involving coduplications or codeletions with other regions. CONCLUSION: Our findings challenge the presumption that intragenic DMD duplications are predominantly in tandem. This highlights the need for a cautious variant interpretation approach, particularly in carrier screening and other settings in which variants are identified without indications of dystrophinopathy.

Humans↗
PubMed1996

Comparative evaluation of BACTEC aerobic Plus/F and Septi-Chek Release blood culture media.

The BACTEC 9240 (Becton Dickinson, Sparks, Md.) automated blood culture system is based on the continuous monitoring of CO2 production by means of a fluorescent sensor attached to the bottom of culture vials. We compared the performance of the BACTEC aerobic Plus/F medium to that of the Septi-Chek Release medium (Becton Dickinson, Sparks, Md.), a manual biphasic blood culture system. Sets consisting of BACTEC aerobic Plus/F and Septi-Chek Release vials inoculated with similar volumes (7 +/- 2 ml) were evaluated. In the laboratory, systems were equipped and analyzed according to the manufacturer's recommendations. The BACTEC and Septi-Chek vials were incubated at 35 degrees C for 5 days. A total of 6,116 compliant sets were obtained from 1,972 adult patients (3.1 cultures per patient). Of these, 731 (12%) were culture positive, including 612 (10%) that yielded at least one pathogen, and 143 (2%) were considered to be contaminated. Of the 672 pathogenic organisms detected, 524 were isolated from the BACTEC aerobic Plus/F medium and 574 were isolated from the Septi-Chek Release medium, 428 organisms grew in both media, 96 organisms grew only in the BACTEC aerobic Plus/F medium, and 146 organisms grew only in the Septi-Chek Release medium (P = 0.001). Haemophilus spp. were isolated more often (P = 0.03) from the BACTEC aerobic Plus/F medium; however, more Streptococcus anginosus organisms (P = 0.02), members of the Enterobacteriaceae family (P < 0.03), and gram-negative anaerobes (P = 0.03) were isolated from the Septi-Chek Release medium. Pathogenic organisms were detected significantly earlier (P < 0.0001) with the BACTEC aerobic Plus/F medium in conjunction with the BACTEC 9240 instrument than with the Septi-Chek Release medium.

Adult↗
PubMed2004

Rapid detection and differentiation of human pathogenic orthopox viruses by a fluorescence resonance energy transfer real-time PCR assay.

BACKGROUND: The orthopox viruses that are pathogenic for humans include variola major virus (VAR), monkeypox virus (MPV), cowpox virus (CPV), and to a lesser extent, camelpox virus (CML) and vaccinia virus (VAC). PCR is a powerful tool to detect and differentiate orthopox viruses, and real-time PCR has the further advantages of rapid turnaround time, low risk of contamination, capability of strain differentiation, and use of multiplexed probes. METHODS: We used real-time PCR with fluorescence resonance energy transfer technology to simultaneously detect and differentiate VAR, MPV, CPV/VAC, and CML. An internal control generated by cloning and mutating the PCR target gene facilitated monitoring of PCR inhibition in each individual test reaction. RESULTS: Strain differentiation results showed little interassay variability (CV, 0.4-0.6%), and the test was 100-fold more sensitive than virus culture on Vero cells. Low copy numbers of DNA could be detected with > or =95% probability (235-849 genome copies/mL of plasma). CONCLUSIONS: The real-time PCR assay can detect and differentiate human pathogenic orthopox viruses. The use of an internal control qualifies the assay for high sample throughput, as is likely to be needed in situations of suspected acts of biological terrorism, e.g., use of VAR.

Animals↗
PubMed2006

Enteric pathogens associated with diarrhea in children in Fayoum, Egypt.

In a cross-sectional study of children <60 months old from Fayoum, Egypt, presenting with diarrhea, 46% (162/356) had detectable enteric pathogens. Bacterial pathogens were identified in 25% (89/356), whereas rotavirus and Cryptosporidium were detected in 21% (54/253) and 15% (39/253), respectively. Cryptosporidium is an important pathogen in this region.

Chi-Square Distribution↗
PubMed2004

Etiology of community-acquired pneumonia in hospitalized school-age children: evidence for high prevalence of viral infections.

BACKGROUND: Community-acquired pneumonia (CAP) in young children is most commonly associated with viral infections; however, the role of viruses in CAP of school-age children is still inconclusive. METHODS: Seventy-five school-age children hospitalized with CAP were prospectively evaluated for the presence of viral and bacterial pathogens. Nasopharyngeal washes were examined by polymerase chain reaction for viruses and atypical bacteria. Antibody assays to detect bacterial pathogens in acute-phase and convalescent-phase serum samples were also performed. RESULTS: A viral infection was identified in 65% of cases. Rhinovirus RNA was detected in 45% of patients; infection with another virus occurred in 31%. The most common bacterial pathogen was Mycoplasma pneumoniae, which was diagnosed in 35% of cases. Chlamydia pneumoniae DNA was not detected in any patient; results of serological tests were positive in only 2 patients (3%). Mixed infections were documented in 35% of patients, and the majority were a viral-bacterial combination. CONCLUSIONS: The high prevalence of viral and mixed viral-bacterial infections supports the notion that the presence of a virus, acting either as a direct or an indirect pathogen, may be the rule rather than the exception in the development of CAP in school-age children requiring hospitalization.

Adolescent↗
PubMed1992

Serial doxycycline and metronidazole in prevention of recurrent periodontitis in high-risk patients.

The efficacy of metronidazole and doxycycline in preventing recurrent periodontitis was studied in 23 patients. After treatment in the previous 7 months with either bimonthly scaling and 3 weeks of systemic doxycycline (11 subjects) or scaling and placebo (12 subjects), patients were monitored for recurrent periodontitis and were scaled every 2 months. When either a periodontal abscess or greater than 2 mm loss of gingival attachment was observed, metronidazole was administered (250 mg every 8 hours) for 10 days. In the placebo plus metronidazole group, 5 patients (42%) exhibited recurrent periodontitis after the metronidazole regimen compared with only one (9%) in the doxycycline plus metronidazole group (P less than 0.096). Subgingival plaque samples at study and healthy control sites were screened for the presence of Actinobacillus actinomycetemcomitans, Porphyromonas gingivalis, Prevotella intermedia, Eikenella corrodens, and Fusobacterium nucleatum by immunofluorescence and for spirochetes using Ryu's stain. Presence/absence analysis of the sum of scores of the 6 individual pathogens demonstrated large reductions (P less than 0.005) in the frequency of detection of pathogens in the former doxycycline compared with the placebo plus metronidazole group at both study and control sites before and one month after metronidazole. By 7 months after metronidazole, there was no detectable difference between groups. These results indicate that prevention of recurrent periodontitis with metronidazole may be enhanced by previous treatment with doxycycline.

Bacteria↗
PubMed2005

[Towards bacterial detection in labile blood products].

Bacterial contamination of blood components represents today the highest infectious risk in blood transfusion, the risk is particularly high when it affects platelet concentrates. The prevention methods developed over the past ten years (donor selection, phlebotomy site preparation, first 30 ml diversion, systematic leuko-reduction...) which aimed at limiting the introduction of bacteria in donations and bacterial proliferation, has reduced the risk of transfusion reaction due to the bacterial contamination. Improving strategies for reducing the risks of bacterial contamination is one of the priorities of the French National Blood Transfusion Service (l'Etablissement français du sang - EFS). It is essential to improve existent prevention methods and develop the implication of all the actors (from donation to transfusion) involved in the prevention of this risk. Bacterial detection or pathogens inactivation are now available and are able to reduce (for detection) or prevent (for inactivation) the occurrence of reaction due to bacterial contamination of PC. Up to now, the choice is in favour of bacterial detection. Three methods (BacT/Alert, BioMerieux; eBDS, Pall; ScanSystem, Hemosystem) of detection of bacterial contamination in PC can be generalised now. Adaptations, need for their implementation are acceptable, especially concerning PC availability.

Automation↗
PubMed2002

Similarity of the oral microbiota of pre-school children with that of their caregivers in a population-based study.

This study evaluated the similarity between the oral microbiota of young children and that of their adult caregivers. Oral samples from children (174 dentate and 18 pre-dentate) aged 6-36 months and their caregivers in Saipan were assayed using a DNA probe assay. Many species including Streptococcus mutans, Streptococcus sobrinus, Actinomyces species, Campylobacter rectus, Fusobacterium nucleatum, Prevotella intermedia, and Porphyromonas gingivalis were detected in dentate and pre-dentate children, whereas Bacteroides forsythus was detected only in dentate children. A higher percentage of children were positive for the detection of an individual species if the caregiver was also positive. There were significant relative risks of species detection between dentate children and their caregivers. By logistic regression, there were significant positive associations between species detection in caregiver and in child, but not between species detection and child age or maternal education level. In conclusion, dental pathogens were detected in young, including pre-dentate, children. The microbial profiles of children were strongly associated with the microbiota of their caregivers.

Actinomyces↗
PubMed2005

A randomized, multicenter, double blind, double dummy trial of single dose azithromycin versus high dose amoxicillin for treatment of uncomplicated acute otitis media.

BACKGROUND: High dose amoxicillin is recommended for the initial treatment of children with acute otitis media (AOM), particularly patients at risk for having drug-resistant Streptococcus pneumoniae. Single dose azithromycin (30 mg/kg) is considered an alternative agent for the treatment of AOM. OBJECTIVE: To compare the clinical efficacy and safety of single dose azithromycin with that of high dose amoxicillin among children with uncomplicated AOM. METHODS: This was a double blind, double dummy, multinational, clinical trial in which children (6-30 months of age) with AOM were randomized to treatment with single dose azithromycin (30 mg/kg) or high dose amoxicillin (90 mg/kg/d, in 2 divided doses) for 10 days. Tympanocentesis was performed at baseline and clinical responses were assessed at days 12-14 (end of therapy) and at days 25-28 (end of study). RESULTS: The study enrolled 313 patients, and 83% of the patients were < or =2 years of age. A total of 158 patients in the azithromycin group and 154 in the amoxicillin group were considered clinical modified intent-to-treat patients. A middle ear pathogen was detected for 212 patients (68%). Haemophilus influenzae was the most common pathogen (isolated for 96 patients), followed by S. pneumoniae (92 patients), Moraxella catarrhalis (23 patients) and Streptococcus pyogenes (23 patients). beta-Lactamase production was observed for 17% of H. influenzae isolates and 100% of M. catarrhalis isolates. Thirty-five (38%) S. pneumoniae isolates were penicillin-nonsusceptible and 24 (26%) isolates were macrolide-resistant. At the end of therapy, clinical success rates for azithromycin and amoxicillin were comparable for all patients (84 and 84%, respectively) and for children < or =2 years of age (82 and 82%, respectively). At the end of therapy and end of study, clinical efficacies among all microbiologic modified intent-to-treat evaluable subjects were comparable for patients treated with azithromycin (80%) and patients treated with amoxicillin (83%). The rates of treatment-related adverse events for azithromycin and amoxicillin were 20% and 29%, respectively (P = 0.064). Diarrhea was more common in the amoxicillin group than in the azithromycin group (17.5 and 8.2%, respectively) (P = 0.017). Compliance, defined as completion of > or =80% of the study medication, was higher in the azithromycin group (100%) than in the amoxicillin group (90%) (P = 0.001). CONCLUSIONS: In this study, single dose azithromycin was as effective as high dose amoxicillin for the treatment of children with AOM, whereas rates of adverse events were lower and compliance improved with the simplified single dose regimen.

Amoxicillin↗
PubMed1996

Chlamydia pneumoniae pneumonia in hospitalized patients. Clinical characteristics and diagnostic value of polymerase chain reaction detection in BAL.

STUDY OBJECTIVE: To evaluate the incidence and clinical characteristics of Chlamydia pneumoniae infection as detected by polymerase chain reaction (PCR) and culture of BAL in hospitalized patients with pneumonia, HIV-infected persons, and control subjects. DESIGN: Prospective, comparative clinical study. SETTING: University hospital medical center. PATIENTS: Fifty-seven hospitalized patients with acute lower respiratory tract infection (group 1); 47 HIV-positive patients (group 2); 100 patients with noninfectious bronchopulmonary disorders (group 3). INTERVENTIONS: BAL was performed in all patients at hospital admission for diagnostic purposes. In addition to semiquantitative bacterial and fungal culture, isolation and detection of C pneumoniae were performed by cell culture and PCR of the lavage fluid. MEASUREMENTS AND RESULTS: C pneumoniae was detected in 16% of group 1, 13% of HIV-positive persons, and 0% of control subjects. The sensitivity of chlamydial culture was much lower as compared with PCR (4 vs 15 cases). In contrast to group 1, in the HIV-positive patients, acute respiratory symptoms were not always present, and in 3 of 6 cases, copathogens were found in the BAL. BAL differential cell counts disclosed a significant lymphocyte elevation mostly due to the CD8 subset (group 1: 15% vs 5%; group II: 18.5% vs 4%; C pneumoniae positive vs negative cases, respectively). CONCLUSIONS: C pneumoniae is frequently detected in the BAL of hospitalized patients with pneumonia as sole pathogen. PCR detection is highly specific and far more sensitive than cell culture. Asymptomatic carriage seems to be uncommon in immunocompetent patients, but does occur in HIV-positive patients. A lymphocytic alveolitis is frequently found by BAL cytologic study and may represent a T-cell response to chlamydial infection in the lower respiratory tract.

AIDS-Related Opportunistic Infections↗
PubMed2026

Real-world pathogen spectrum, clinical actionability, and host correlates of first-time mNGS testing in hospitalized patients with hematologic diseases.

BACKGROUND: Patients with hematologic diseases are highly susceptible to infection. Conventional tests often have low sensitivity. Metagenomic next-generation sequencing (mNGS) can detect many pathogens at once, but its clinical value depends on how the results are interpreted. It is often hard to tell true infection from colonization or contamination. METHODS: We retrospectively studied hospitalized hematologic patients Only adult patients (&#x2265;18 years) who received mNGS for the first time. Detected organisms were reclassified using a clinical actionability system. We also analyzed the relationships between mNGS findings, host characteristics, and short-term outcomes. RESULTS: A total of 134 patients were included. At least one organism was detected in 87.3% of patients, but only 58.2% had highly actionable results. Bacteria were the most common findings, followed by viruses and fungi. Mixed detections were frequent. Actionable results were seen more often in respiratory specimens than in blood specimens. Viral detection was associated with immune status. Pathogen read counts were only weakly related to inflammatory markers and did not independently predict adverse outcomes. Age was the only independent risk factor for adverse outcome. CONCLUSION: mNGS had a high detection rate in hematologic patients, but not all positive findings were clinically important. Result interpretation should take specimen type and host status into account. Pathogen read counts alone were not useful for predicting short-term outcome.

Humans↗
PubMed2006

Mucosal interplay among commensal and pathogenic bacteria: lessons from flagellin and Toll-like receptor 5.

Toll-like receptors (TLR) detect pathogen-associated molecular patterns (PAMP) and play a crucial role in triggering immunity. Due to their large surfaces in direct contact with the environment, mucosal tissues are the major sites of PAMP-TLR signalling. How innate and adaptive immunity are triggered through flagellin-TLR5 interaction is the main focus of the review. In view of recent reports on genetic polymorphism, we will summarize the impact of TLR5 on the susceptibility to mucosal infections and on various immuno-pathologies. Finally, the contribution of TLRs in the induction and maintenance of mucosal homeostasis and commensal discrimination is discussed.

Bacterial Physiological Phenomena↗