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PubMed2000

[Evaluation of the usefulness of selected virulence markers for identification of virulent Yersinia enterocolitica strains. II. Genotypic markers associated with the pYV plasmid].

Pathogenic strains of Yersinia enterocolitica bear virulence associated plasmid pYV. Unfortunately plasmid pYV is easily lost by these bacteria incubated at elevated temperatures (37 degrees C) or long stored at room temperatures. This sometimes makes difficult the detection of the virulence plasmid, especially by its isolation or biochemical tests. On the other hand, observations done by some authors suggest that polymerase chain reaction (PCR) could be useful for demonstration of the pYV plasmid of Yersinia strains. Accordingly to this observation the aim of the presented study was to check the usefulness of plasmid-localised genes virF and yadA, detected by PCR, for the identification of the virulent strains of Y. enterocolitica. In the presented study one hundred and fifty two clinical strains of Y. enterocolitica belonging to serogroup O3 were investigated by the PCR for the presence of genes virF and yadA. Bacterial strains were first tested for the presence of pYV plasmid. In addition the phenotypic features: calcium dependence, Congo red binding and autoagglutination were determined. In this way the virulence plasmid was found in 130 of 152 examined strains. For PCR studies also forty plasmid-cured strains of Y. enterocolitica and 32 non-Y. enterocolitica, Enterobacteriaceae strains were included. The obtained results show that the tested genes were present only in Yersinia strains possessing the pYV plasmid and no one non-specific PCR product was observed. The detection level of these genes in nested PCR permits to detect pathogenic Y. enterocolitica in suspension composed of 1 x 10(3) CFU/ml of pYV+ bacilli and 3 x 10(9) CFU/ml plasmid-cured, isogenic bacteria. In the study it was shown that genes virF and yadA were useful virulence markers, which could be helpful in clinical studies for the detection of the virulence plasmid in Y. enterocolitica strains long stored or incubated at elevated temperatures.

Adhesins, Bacterial↗

PubMed1999

Use of polymerase chain reaction to detect Proteus mirabilis and Ureaplasma urealyticum in urinary calculi.

In this study, we evaluated the efficacy of the polymerase chain reaction (PCR) in detecting urea-splitting microorganisms in desiccated urinary tract infection stones. Seventy-eight urinary tract stones were tested for the presence of Proteus mirabilis and Ureaplasma urealyticum by means of PCR with species-specific primers. Twenty-seven stone samples were composed of struvite and/or carbonate apatite (infection stone); 40 were calcium oxalate and/or calcium phosphate; seven were mixed, with struvite/carbonate apatite and calcium oxalate; and four were uric acid stones. PCR was performed with DNA extracted from pulverized stone pieces. Initial assays using the pulverized stone specimens spiked with microorganisms showed that PCR could not detect U. urealyticum at densities below 10(3) color changing units (CCU), or P. mirabilis at densities below 10(4) colony-forming units (CFU). PCR was negative for U. urealyticum and P. mirabilis in all metabolic stones from patients. P. mirabilis was detected by PCR in 10 of 34 patients with infection stones. Preoperative urine cultures grew P. mirabilis in three of these 10 patients, and were negative for P. mirabilis in the other seven. U. urealyticum was detected by PCR in stone samples from four patients, two of which were also PCR-positive for P. mirabilis. All four of these patients had infection stones: two had residual stones, and the other two had recurrence of urinary stones after their operations. These results demonstrate that microorganisms in urinary stones can be detected by PCR even when the voided urine culture is negative. Investigations into the role of bacterial infection in stone formation will require further improvements in the sensitivity of PCR assays for pathogen detection.

Adult↗

PubMed1995

Genital tract infections in sexually active women in Barbados.

Ninety-eight women attending three different clinics were prospectively studied for the presence of genital tract infections, including Chlamydia trachomatis. Of these 98 women, 35 were presenting to a polyclinic with symptoms of genital tract infection, 55 were attending an antenatal clinic for their first visit, and 8 referred to a colposcopy clinic because of an abnormal Papanicolaou smear were included. Gonorrhoea was detected in one patient, syphilis in two, and Trichomonas vaginalis in six. Candida albicans and Chlamydia trachomatis were each detected in 18 patients, while the most common condition was bacterial vaginosis, detected in 35 patients. The prevalence of these infections was lowest in patients referred for colposcopy and highest in the women attending the antenatal clinic. Chlamydia trachomatis was the most common sexually-transmitted pathogen detected in this population. These data emphasise the need for an aggressive approach to the diagnosis and treatment of chlamydial infection in females.

Adolescent↗

PubMed2001

Monitoring of microbial hazards at farms, slaughterhouses, and processing lines of swine in Korea.

This study was executed to investigate microbiological hazards at swine farms, slaughterhouses, dressing operations, and local markets for the application of the hazard analysis critical control point system in Korea by analyzing total aerobic plate count (APC) and presence of pathogens. Six integrated pig farms and meat packers were selected from six different provinces, and samples were collected from pig carcasses by swabbing and excision methods at the slaughterhouses, processing rooms, and local markets, respectively. APCs of water in water tanks were relatively low, 1.9 to 3.1 log10 CFU/ml; however, they were increased to 4.6 to 6.9 log10 CFU/ml when sampled from water nipples in the pigpen. APCs of feeds in the feed bins and in the pigpens were 4.4 to 5.4 and 5.2 to 6.7 log10 CFU/g, respectively. Salmonella spp., Staphylococcus aureus, and Clostridium perfringens were detected from water and feed sampled in pigpens and pigpen floors. S. aureus was the most frequently detected pathogenic bacteria in slaughterhouses and processing rooms. Listeria monocytogenes and Yersinia enterocolitica were also detected from the processing rooms of the Kyonggi, Kyongsang, and Cheju provinces. Even though APCs were maintained at the low level of 3.0 log10 CFU/g during slaughtering and processing steps, those of final pork products produced by the same companies showed relatively high numbers when purchased from the local market. These results indicated that the cold chain system for transporting and merchandising of pork products was deficient in Korea. Water supply and feed bins in swine farms and individual operations can be identified as critical control points to reduce microbiological hazards in swine farms, slaughterhouses, and processing plants.

Abattoirs↗

PubMedDate not supplied

Nonsevere community-acquired pneumonia: correlation between cause and severity or comorbidity.

BACKGROUND: Community-acquired pneumonia frequently constitutes a nonsevere infection manageable at home. However, for these low-risk episodes, the epidemiological features have not been carefully analyzed. OBJECTIVES: To determine the cause of nonsevere community-acquired pneumonia and to investigate if a correlation exists between cause and severity or comorbidity. METHODS: During a 3-year period, all patients with nonsevere community-acquired pneumonia, according to the Pneumonia Patient Outcome Research Team prognostic classification (patients in groups 1-3), were included in the study. Causes were investigated through the following procedures: cultures of blood, sputum, and pleural fluid; serologic tests; and polymerase chain reaction methods to detect Streptococcus pneumoniae DNA in whole blood or Mycoplasma pneumoniae and Chlamydia pneumoniae DNA in throat swab specimens. RESULTS: Of 317 initially included patients, 247 were eligible for the study. A microbial diagnosis was obtained in 162 patients (66%), and the main pathogens detected were S pneumoniae (69 patients [28%]), M pneumoniae (40 patients [16%]), and C pneumoniae (28 patients [11%]). For the 58 patients in prognostic group 1, M pneumoniae was the most prevalent cause, and atypical microorganisms constituted 40 (69%) of the isolated agents. In contrast, for patients in prognostic groups 2 and 3, S pneumoniae was the leading agent, and a significant reduction of M pneumoniae cases and a greater presence of other more uncommon pathogens were observed. The existence of comorbid conditions was not a determining factor for particular causes. CONCLUSIONS: Among low-risk patients with community-acquired pneumonia, there was a certain correlation between severity and cause. In contrast, the existence of a comorbidity did not have a predictive causative value.

Adult↗

PubMed2002

Porcine circovirus type 2 (PCV-2) coinfections in US field cases of postweaning multisystemic wasting syndrome (PMWS).

The prevalence of different pathogens detected in combination with porcine circovirus type 2 (PCV-2) was studied retrospectively in field cases of postweaning multisystemic wasting syndrome (PMWS) diagnosed at the Iowa State University Veterinary Diagnostic Laboratory, Ames, Iowa, between January 2000, and September 2001. The presence of PCV-2 antigen in lymphoid tissues and/or lung, demonstrated by immunohistochemistry, together with moderate to severe lymphoid depletion and/or granulomatous lymphadenitis, was used as the criteria for the diagnosis of PMWS. A total of 484 cases fulfilled these criteria. Most of the cases (294/369) of PMWS occurred in pigs between the ages of 8 and 18 weeks, with a peak at 10 weeks of age. Porcine reproductive and respiratory syndrome virus was detected in 51.9% of the cases, Mycoplasma hyopneumoniae in 35.5%, bacterial septicemia in 14.0%, bacterial pneumonia in 7.6%, swine influenza virus in 5.4%, and PCV-2 alone in 1.9%. In cases with bacterial septicemia the most frequently isolated pathogen was Streptococcus suis. In cases with bacterial pneumonia, Pasteurella multocida was the most prevalent.

Animals↗

PubMed1995

Evaluation of periodontal treatments using controlled-release tetracycline fibers: microbiological response.

In a 12-month multi-center study of 116 adult periodontitis subjects, six putative periodontal pathogens were monitored by DNA probe methods in a subset of 31 subjects. Monitored species included Porphyromonas gingivalis (Pg), Prevotella intermedia (Pi), Fusobacterium nucleatum (Fn), Eikenella corrodens (Ec), Campylobacter rectus (Cr), and Actinobacillus actinomycetemcomitans (Aa) with an average detection limit of 1.8 x 10(4) bacterial colony forming units/sample. The microbiological response to four periodontal treatments was studied, one treatment in each quadrant; scaling and root planing (S), scaling and root planing with tetracycline (TC) fiber (SF), a single application of TC fiber (F) and two serial applications of TC fiber (FF). Generally two sites were sampled in each quadrant, however, in some quadrants only one site was selected. These treatments were evaluated at baseline; immediately following therapy; and post-treatment at 1, 3, 6, and 12 months. The study was conducted with a split-mouth design with no maintenance therapy over a 12-month period. At baseline, 70.8% of sites had detectable Fn; 42.9% Pg; 63.5% Pi; 29.7% Ec; 28.3% Cr; and 5.5% Aa. No significant differences were seen in baseline proportions of these species between centers. Numbers and proportions of detectable pathogens (with the exception of Pg) exhibited a triphasic temporal response: a precipitous initial decrease immediately following therapy; a rise in proportions in the 1- to 3-month post-therapy period; and a spontaneous decline in the absence of therapy over the 3- to 12-month period.(ABSTRACT TRUNCATED AT 250 WORDS)

Adult↗

PubMed2002

[Acute Gastroenteritis in hospitalized children. 14-Year evolution].

OBJECTIVES: To analyze the etiology and evolution of patients with acute gastroenteritis hospitalized in our pediatric department and to study the clinical and laboratory differences between acute viral and bacterial gastroenteritis. PATIENTS AND METHODS: We studied the children with a diagnosis of acute gastroenteritis, aged between 0 and 14 years, who were consecutively admitted between 1987 and 2000. Differences were considered statistically significant if p < 0.05. RESULTS: A total of 2,613 patients diagnosed with acute gastroenteritis were hospitalized (10.4 % of hospital admissions). The most common pathogens isolated were rotaviruses (46.5 %), followed by Salmonella (32.6 %) and Campylobacter (19.3 %). Hospital admissions due to Salmonella (p < 0.0001), other bacteria (Escherichia coli and Shigella) (p < 0.002) and adenoviruses (p < 0.01) significantly decreased. Rotaviruses were the most frequently detected pathogens in winter and in children aged less than 1 year (p < 0.0001). The incidence of Salmonella spp was greater in summer and in children older than 2 years (p < 0.0001). The incidence of hyperthermia (rectal temperature higher than 38.5 degreeC) (p < 0.0001), dehydration (p < 0.0005) and fecal blood (p < 0.0001) was higher in bacterial diarrheas. Erythrocyte sedimentation rate (p < 0.001) and leukocyte counts were higher in bacterial gastroenteritis (p < 0.01). CONCLUSIONS: Rotaviruses were the most frequently isolated enteropathogens. The features that best distinguished between bacterial and viral diarrhea were hyperthermia and fecal blood. Hospital admissions due to Salmonella Shigella E. coli, and adenoviruses significantly decreased.

Acute Disease↗

PubMed2001

Identification of virulence attributes of gastrointestinal Escherichia coli isolates of veterinary significance.

The pathogenic strains of Escherichia coli recovered from the intestinal tract of animals fall into categories called enterotoxigenic, enteropathogenic, enterohemorrhagic and necrotoxigenic. The other two categories, enteroinvasive and enteroaggregative, have not been reported in animals. The pathogenicity of these strains is determined by the presence of certain genes that encode adhesins and toxins, are generally organized in large blocks in chromosomes, large plasmids or phages, and are often transmitted horizontally between strains. In this review, we summarize current knowledge of the virulence attributes that determine the pathogenic potential of E. coli strains and the methods available to assess the virulence of the strains. We also discuss the clinical symptoms, the gross and histological lesions, and the molecular diagnostic methods our laboratories have implemented for detecting pathogenic strains of E. coli that are isolated from the gastrointestinal tract of animals.

Adhesins, Escherichia coli↗

PubMed1999

[Study on etiology of nongonococcal urethritis].

One thousand one hundred and fifty-seven samples from urogenital tract were detected by isolating culture and immunofluorescence. The positive rates of Chlamydia trachomatis (CT), Ureaplasma Urealyticum (UU), Mycoplasma hominis (Mh), Candida (Cd), Staphylococcus aureus were 27.8%, 33.5%, 25.6%, 11.5%, 23% respectively. The rate of mixed infection caused by at least two pathogens was 19.8%. About 90% of the infected patients were from 20 to 40 years old. The related factors of pathogen detection were also studied.

Adolescent↗

PubMed1989

Diagnostic studies of nosocomial diarrhea in children: assessing their use and value.

During a 17-month period (01/11/85-05/31/86) 225 cases of nosocomial diarrhea were identified in a children's hospital. Diarrhea was considered to be nosocomial if it began at least 72 hours after the patient's hospital admission or within 3 days after discharge. One or more routine diagnostic studies for identification of a pathogen were performed in 195 (87%) cases. The most commonly performed test was the bacterial stool culture. None of these samples yielded a bacterial pathogen. The only pathogens detected by routine laboratory studies were rotavirus (61/137 [45%] samples were positive for rotavirus by ELISA) and Clostridium difficile (9/54 [17%] positive for toxin). Of the patients whose tests were positive for rotavirus 56 were younger than 2 years of age, and all were identified in the winter and spring. When multiple stool samples were tested by the diagnostic laboratory, rotavirus was identified in an additional 14 patients whose initial stool samples were negative for rotavirus. All patients whose tests were positive for C. difficile toxin had received antibiotics within the previous 3 months. Ova/parasites were not detected in 53 of the tested stools. We also identified enteric adenovirus in six patients. Viruses were identified in 95 (42%) of the 225 cases of nosocomial gastroenteritis. Nosocomial diarrhea is common in a children's hospital. Rotavirus is the most commonly identified pathogen. Rotavirus testing is valuable in children with nosocomial diarrhea who are younger than 2 years of age, especially in the winter and spring. Multiple samples may be necessary to identify rotavirus. C. difficile toxin assay should be considered for patients who are receiving or who have received antibiotics.(ABSTRACT TRUNCATED AT 250 WORDS)

Cross Infection↗

PubMed2002

Distribution patterns of Escherichia coli O157:H7 in ground beef produced by a laboratory-scale grinder.

This study determined the distribution patterns of Escherichia coli O157:1H7 in ground beef when a contaminated beef trim was introduced into a batch of uncontaminated beef trims prior to grinding in a small-scale laboratory grinder. A beef trim (15.3 +/- 2 g) was inoculated with a rifampicin-resistant strain of E. coli O157:H7 (E. coli O157:H7rif) and introduced into a stream of noncontaminated beef (322 +/- 33 g) prior to grinding. Seven inoculum levels (6, 5, and 4 total log CFU [high]; and 3, 2, 1, and 0 total log CFU [low]) were studied in triplicate. E. coli O157:H7rif was not detected in 3.1 to 43% of the ground beef inoculated with the high levels or in 3.4 to 96.9% of the ground beef inoculated with the low levels. For all inoculum levels studied, the five ground beef fractions (each 7.8 +/- 0.6 g) with the highest pathogen levels accounted for 59 to 100% of the total pathogens detected. For all inoculum levels, there was a linear relationship between the quantity of ground beef containing E. coli O157:H7rif and the inoculum level. The quantity of E. coli O157:H7rif in the beef remaining in the grinder was proportional to the inoculum level and was related to the location in the grinder. Different components of the grinder accumulated E. coli O157:H7rif in different quantities, with the most significant accumulation being in the nut (collar) that attaches the die to the blade. This study determined specific distribution patterns of E. coli O157:H7rif after the grinding of a contaminated beef trim along with uncontaminated trims, and the results indicate that the grinding operation should be regarded as a means of distribution of microbial contamination in risk analyses of ground beef operations.

Animals↗

PubMed2003

Prevalence and pathogenic role of Cyclospora cayetanensis in a Venezuelan community.

The prevalence and pathogenic role of Cyclospora cayetanensis among 212 subjects (age range = two months to 70 years) in an impoverished community in Venezuela were assessed retrospectively. For identification of the coccidium, modified Ziehl-Neelsen carbolfuchsin staining of formalin-ether concentrates was used. For other pathogenic parasites, iron-hematoxylin-stained smears and formalin-ether concentrates were examined. Cyclospora infections were identified in 13 (6.1%) subjects with a high percentage of asymptomatic carriers (11 of 13, 84.6%). Only two (15.4%) infants had diarrhea and the coccidium as the single detectable pathogenic parasite. The findings suggest that Cyclospora infections are relatively common and often asymptomatic in this region.

Adolescent↗

PubMed1999

THE THREE DS OF PCR-BASED GENOMIC ANALYSIS OF PHYTOBACTERIA: Diversity, Detection, and Disease Diagnosis.

The advent of molecular biology in general and the polymerase chain reaction in particular have greatly facilitated genomic analyses of microorganisms, provide enhanced capability to characterize and classify strains, and facilitate research to assess the genetic diversity of populations. The diversity of large populations can be assessed in a relatively efficient manner using rep-PCR-, AFLP-, and AP-PCR/RAPD-based genomic fingerprinting methods, especially when combined with computer-assisted pattern analysis. Genetic diversity maps provide a framework to understand the taxonomy, population structure, and dynamics of phytobacteria and provide a high-resolution framework to devise sensitive, specific, and rapid methods for pathogen detection, plant disease diagnosis, as well as management of disease risk. A variety of PCR-based fingerprinting protocols such as rDNA-based PCR, ITS-PCR, ARDRA, T-RFLPs, and tRNA-PCR have been devised, and numerous innovative approaches using specific primers have been adopted to enhance both the detection and identification of phytobacteria. PCR-based protocols, combined with computer-based analysis, have provided novel fundamental knowledge of the ecology and population dynamics of bacterial pathogens, and present exciting new opportunities for basic and applied studies in plant pathology.

Journal Article↗

PubMed2003

Standardization of diagnostic PCR for the detection of foodborne pathogens.

In vitro amplification of nucleic acids using the polymerase chain reaction (PCR) has become, since its discovery in the 1980s, a powerful diagnostic tool for the analysis of microbial infections as well as for the analysis of microorganisms in food samples. However, despite its potential, PCR has neither gained wide acceptance in routine diagnostics nor been widely incorporated in standardized methods. Lack of validation and standard protocols, as well as variable quality of reagents and equipment, influence the efficient dissemination of PCR methodology from expert research laboratories to end-user laboratories. Moreover, the food industry understandably requires and expects officially approved standards. Recognizing this, in 1999, the European Commission approved the research project, FOOD-PCR (http://www.PCR.dk), which aims to validate and standardize the use of diagnostic PCR for the detection of pathogenic bacteria in foods. The present review focuses on the harmonization procedure and standardization criteria for detection of foodborne pathogens by PCR. The progress of standardization so far and future perspectives of diagnostic PCR are discussed.

Bacteria↗

PubMed1994

[Etiology, diagnosis and course of infectious diarrhea in the Liestal canton hospital (5-year retrospective study)].

Between 1987 and 1991 219 patients (1.3% of all hospitalized patients) with acute infectious diarrhea were investigated retrospectively. 52% of the patients were hospitalized and 48% were outpatients. In 55% the inducing diarrhea microorganism could be identified. The most frequently detected pathogens were endemic Salmonella sp. and Campylobacter jejuni (65%). Imported diarrheas (Shigella sp. and parasites) were rare, as only 15% of the patients had a history of travel. All Clostridium difficile infections were associated with antibiotic treatment. The stool examinations for bacteria were positive in 92/160 patients (57%). Stool examinations for occult blood or fecal leukocytes were highly useful in detecting the infectious agent. In 70% of the patients with positive occult blood test or 81% of the patients with fecal leukocytes, an infectious agent in the stool was found. All patients recovered with few complications. 31% of the patients were treated by antibiotics because of septic disease or pathogenic parasites.

Adolescent↗

PubMed2025

Versatile wastewater monitoring of pathogens and antimicrobial resistance enabled by metatranscriptomics and long-read metagenomics.

Widespread interest in the development of population-wide pathogen and antimicrobial resistance (AMR) monitoring has revealed wastewater's microbial footprint as a marker of public health. Near-source wastewater remains a difficult sample type for microbiome analyses but represents a closer link to human health than the downstream products of its treatment. Few studies integrate methods for non-targeted monitoring applications, and critically, current methods cannot connect AMR genes to species, nor resolve full genomes. We address these challenges by developing a pipeline that enables untargeted metagenomics, metatranscriptomics, and novel long-read metagenomics (LRG). We achieve untargeted pathogen detection, limited by highly abundant resident species, while retaining microbial information with near-source sampling. Furthermore, LRG identifies antibiotic resistance gene-containing microbes and enables assembly of culture-independent genomes with previously unreported AMR genes. We establish an integrated approach to broadly monitor pathogens in wastewater, while demonstrating the importance of LRG to illuminate microbial AMR at the species level.

Journal Article↗

PubMed1988

[The place of 67Ga scintigraphy in the primary diagnosis and follow-up evaluation of opportunistic pneumonia in patients with AIDS].

Opportunistic pneumonias are a life-threatening complication in patients with AIDS. Early diagnosis and therapy is necessary to improve prognosis. This study was designed to assess the value of 67Ga scintigraphy in the primary detection and follow-up of these special pneumonias. 67Ga scintigraphy was performed in 40 patients: 10 normal controls and 30 HIV-positive patients with AIDS or AIDS-related complex (ARC). 67Ga scan results were compared with current chest radiographs and the results of pathogen detection. The evaluation of positive scans was based on a quantification of the pulmonary uptake, expressed as a pulmonary/soft-tissue uptake ratio. Only 8/30 patients had a normal scan, 22/30 showed diffuse (13/22) or focal (9/22) increases of pulmonary uptake. In 7/8 patients with normal scans the chest radiograph was negative as well. The one patient with negative scan but positive chest radiograph had pulmonary Kaposi's sarcoma. In 11/22 patients the 67Ga scan and chest radiograph were positive simultaneously. In the other 11/22 patients with positive scans chest radiographs were initially negative but showed pathology in 5 cases within 1-2 weeks. The reason for positive scans in most cases was an opportunistic lung infection; other forms of pneumonia were only observed in two cases. The defined uptake ratio demonstrated to be a highly sensitive parameter for monitoring pneumonia and the effects of therapy in follow-up studies. In conclusion, quantitative 67Ga scintigraphy proved to be a reliable and highly sensitive method for primary detection and follow-up of opportunistic pneumonias in patients with AIDS.

Acquired Immunodeficiency Syndrome↗