K-mer applied in Mycobacterium tuberculosis genome cluster analysis

Abstract According to studies carried out, approximately 10 million people developed tuberculosis in 2018. Of this total, 1.5 million people died from the disease. To study the behavior of the genome sequences of Mycobacterium tuberculosis (MTB), the bacterium responsible for the development of tuberculosis (TB), an analysis was performed using k-mers (DNA word frequency). The k values ranged from 1 to 10, because the analysis was performed on the full length of the sequences, where each sequence is composed of approximately 4 million base pairs, k values above 10, the analysis is interrupted, as consequence of the program's capacity. The aim of this work was to verify the formation of the phylogenetic tree in each k-mer analyzed. The results showed the formation of distinct groups in some k-mers analyzed, taking into account the threshold line. However, in all groups, the multidrug-resistant (MDR) and extensively drug-resistant (XDR) strains remained together and separated from the other strains.

Abordagem bayesiana na avaliação da dissimilaridade em clones de batata-doce

A disponibilidade de variabilidade genética em bancos de germoplasma é fundamental para o sucesso de programas de melhoramento vegetal. A inferência bayesiana, aliada a técnicas multivariadas, permite identificar essas fontes de variabilidade, auxiliando nas tomadas de decisão no melhoramento de plantas. Logo, objetivou-se avaliar a dissimilaridade genética entre 24 clones de batata-doce por meio de dados qualitativos e quantitativos, utilizando a abordagem multivariada por meio da inferência bayesiana. Na caracterização morfológica, foram utilizados 24 descritores morfológicos e dados de produtividade de raízes e ramas. Para análise estatística foi utilizada a análise multivariada através da inferência bayesiana. Houve variabilidade genética entre os clones de batata-doce. Há grande dissimilaridade dos clones UFVJM05, UFVJM09, UFVJM31, UFVJM37, UFVJM40 com os demais. Esses clones divergentes podem ser utilizados em cruzamentos a fim de obter progênies com alta variabilidade genética. A abordagem multivariada por meio da inferência bayesiana foi eficiente na avaliação da dissimilaridade.

Suicide cases in developed and emerging countries: an analysis using wavelets

ABSTRACT Objective The aim of this study was to use a wavelet technique to determine whether the number of suicides is similar between developed and emerging countries. Methods Annual data were obtained from World Health Organization (WHO) reports from 1986 to 2015. Discrete nondecimated wavelet transform was used for the analysis, and the Daubechies wavelet function was applied with five-level decomposition. Regarding clustering, energy (variance) was used to analyze the clusters and visualize the clustering process. We constructed a dendrogram using the Mahalanobis distance. The number of groups was set using a specific function in the R program. Results The cluster analysis verified the formation of four groups as follows: Japan, the United States and Brazil were distinct and isolated groups, and other countries (Austria, Belgium, Chile, Israel, Mexico, Italy and the Netherlands) constituted a single group. Conclusion The methods utilized in this paper enabled a detailed verification of countries with similar behaviors despite very distinct socioeconomic, geographic and climate characteristics.

Evaluation of genome similarities using a wavelet-domain approach

INTRODUCTION

Tuberculosis is listed among the top 10 causes of deaths worldwide. The resistant strains causing this disease have been considered to be responsible for public health emergencies and health security threats. As stated by the World Health Organization (WHO), around 558,000 different cases coupled with resistance to rifampicin (the most operative first-line drug) have been estimated to date. Therefore, in order to detect the resistant strains using the genomes of Mycobacterium tuberculosis (MTB), we propose a new methodology for the analysis of genomic similarities that associate the different levels of decomposition of the genome (discrete non-decimated wavelet transform) and the Hurst exponent.

METHODS

The signals corresponding to the ten analyzed sequences were obtained by assessing GC content, and then these signals were decomposed using the discrete non-decimated wavelet transform along with the Daubechies wavelet with four null moments at five levels of decomposition. The Hurst exponent was calculated at each decomposition level using five different methods. The cluster analysis was performed using the results obtained for the Hurst exponent.

RESULTS

The aggregated variance, differenced aggregated variance, and aggregated absolute value methods presented the formation of three groups, whereas the Peng and R/S methods presented the formation of two groups. The aggregated variance method exhibited the best results with respect to the group formation between similar strains.

CONCLUSION

The evaluation of Hurst exponent associated with discrete non-decimated wavelet transform can be used as a measure of similarity between genome sequences, thus leading to a refinement in the analysis.

Wavelet-domain elastic net for clustering on genomes strains

We propose to evaluate genome similarity by combining discrete non-decimated wavelet transform (NDWT) and elastic net. The wavelets represent a signal with levels of detail, that is, hidden components are detected by means of the decomposition of this signal, where each level provides a different characteristic. The main feature of the elastic net is the grouping of correlated variables where the number of predictors is greater than the number of observations. The combination of these two methodologies applied in the clustering analysis of the Mycobacterium tuberculosis genome strains proved very effective, being able to identify clusters at each level of decomposition.

Bayesian analyses of genetic parameters for growth traits in Nellore cattle raised on pasture

This study was carried out to investigate (co)variance components and genetic parameters for growth traits in beef cattle using a multi-trait model by Bayesian methods. Genetic and residual (co)variances and parameters were estimated for weights at standard ages of 120 (W120), 210 (W210), 365 (W365), and 450 days (W450), and for pre- and post-weaning daily weight gain (preWWG and postWWG) in Nellore cattle. Data were collected over 16 years (1993-2009), and all animals were raised on pasture in eight farms in the North of Brazil that participate in the National Association of Breeders and Researchers. Analyses were run by the Bayesian approach using Gibbs sampler. Additive direct heritabilities for W120, W210, W365, and W450 and for preWWG and postWWG were 0.28 ± 0.013, 0.32 ± 0.002, 0.31 ± 0.002, 0.50 ± 0.026, 0.61 ± 0.047, and 0.79 ± 0.055, respectively. The estimates of maternal heritability were 0.32 ± 0.012, 0.29 ± 0.004, 0.30 ± 0.005, 0.25 ± 0.015, 0.23 ± 0.017, and 0.22 ± 0.016, respectively, for W120, W210, W365, and W450 and for preWWG and postWWG. The estimates of genetic direct additive correlation among all traits were positive and ranged from 0.25 ± 0.03 (preWWG and postWWG) to 0.99 ± 0.00 (W210 and preWWG). The moderate to high estimates of heritability and genetic correlation for weights and daily weight gains at different ages is suggestive of genetic improvement in these traits by selection at an appropriate age. Maternal genetic effects seemed to be significant across the traits. When the focus is on direct and maternal effects, W210 seems to be a good criterium for the selection of Nellore cattle considering the importance of this breed as a major breed of beef cattle not only in Northern Brazil but all regions covered by tropical pastures. As in this study the genetic correlations among all traits were high, the selection based on weaning weight might be a good choice because at this age there are two important effects (maternal and direct genetic effects). In contrast, W120 should be preferred when the objective is improving the maternal ability of the dams. Furthermore, selection for postWWG can be used if the animals show both heavier weaning weights and high growth rate after weaning because it is possible to shorten the time between weaning and slaughter based on weaning weight, postWWG, and desired weight at the time of slaughter.

Karyotype characterization and comparison of three hexaploid species of Bromus Linnaeus, 1753 (Poaceae)

Chromosome morphometry and nuclear DNA content are useful data for cytotaxonomy and to understand the evolutionary history of different taxa. For the genus Bromus Linnaeus, 1753, distinct ploidy levels have been reported, occurring from diploid to duodecaploid species. The geographic distribution of Bromus species has been correlated with chromosome number and ploidy level. In this study, the aims were to determine the nuclear genome size and characterize the karyotype of the South American Bromus species: Bromus auleticus Trinius ex Nees, 1829, Bromus brachyanthera Döll, 1878 and Bromus catharticus Vahl, 1791. The mean nuclear 2C value ranged from 2C = 12.64 pg for B. catharticus to 2C = 17.92 pg for B. auleticus, meaning a maximum variation of 2C = 5.28 pg, equivalent to 41.70%. Despite this significant difference in 2C value, the three species exhibit the same chromosome number, 2n = 6x = 42, which confirms their hexaploid origin. Corroborating the genome size, the chromosome morphometry (total, short- and long-arm length) and, consequently, the class differed among the karyotypes of the species. Based on the first karyograms for these Bromus species, some morphologically similar and several distinct chromosome pairs were found. Therefore, the karyotype characterization confirmed the hexaploid origin of the studied Bromus species, which differ in relation to the karyogram and the nuclear 2C value. Considering this, cytogenetics and flow cytometry can be used to discriminate Bromus species, contributing to taxonomy and systematic studies and providing information on the evolutionary history of this taxa.

Population structure of jatropha and its implication for the breeding program

Jatropha (Jatropha curcas L.) has potential as an oilseed crop that requires the development of technology for its exploitation. The objective of this study was to assess the population structure and the genetic diversity in jatropha accessions at a global level using simple sequence repeat (SSR) molecular markers. Jatropha accessions (N = 109) from 10 countries were genotyped using 10 SSR markers. The results showed a low level of genetic diversity among 92 accessions originating from India, Mozambique, Ethiopia, Tanzania, Brazil, Honduras, and Indonesia, which were grouped in one cluster. In contrast, accessions from Mexico and Costa Rica showed high level of genetic variability. These accessions may be used to increase the genetic diversity of jatropha in the breeding populations. The study also showed the need of collecting activity from the center of diversity (Mexico and Costa Rica) to aggregate the genetic diversity in the international collections of jatropha.

Developing selection criteria based on an ontogenetic path analysis approach to improve grain yield in barley

We used correlation and path coefficient analysis based on an ontogenetic approach to develop selection criteria in barley (Hordeum vulgare L.) for an early production system in Ethiopia. A total of 100 genotypes using 10x10-simple lattices with two replications were used to perform the experiment at Ambo and Asasa. The combined analysis of the measured traits showed significant differences among genotypes for all traits. A positive correlation was observed between grain yield and spike/m2, kernel number/spike, and 1000-kernel weight. The path analysis showed that spike/m2, 1000-kernel weight, and kernel number per spike had significant positive direct effects on grain yield, which shows that these traits can be used as selection criteria to improve grain yield. The significant positive correlation of spike/ m2, 1000-kernel weight, and grain-filling period and the positive direct effect on grain yield indicated the potential of these traits as indirect selection criteria to improve grain yield in the early production system in Ethiopia. This study also showed that the path coefficient analysis based on an ontogenetic model was efficient and produced results that can be interpreted clearly.

Genetic diversity of Brazilian and introduced olive germplasms based on microsatellite markers

Olive trees have been grown since the beginning of civilization, and the consumption of olives and olive products is increasing worldwide, due to their health benefits and organoleptic qualities. To meet the growing market for olives, commercial cultivation of this species is expanding from traditional areas to new regions. Although the Brazilian olive industry has just begun to be established, breeding programs are already developing cultivars that are more adapted to local conditions. We used 12 microsatellite markers to evaluate 60 olive accessions, including several cultivars that were developed in Brazil. The analyses identified 72 distinct alleles; the largest number of alleles per locus were at the markers GAPU 101 and GAPU 71B, which contained 10 and 9 alleles, respectively. The largest allelic diversity and polymorphic information contents were also found at the GAPU 101 and GAPU 71B markers, with values of 0.8399/0.8203 and 0.8117/0.7863, respectively. Additionally, the 12 microsatellite markers generated a cumulative identity probability of 1.51 x 10(-10), indicating a high level of accuracy of accession identification. The set of markers that we used allowed the identification of 52 of the 60 olive genotypes, in addition to the recognition of several varietal synonyms. The components of a two-dimensional principal coordinate analysis explained 48.6% of the total genetic variation. The results obtained from the microsatellite markers showed a substantial degree of genetic diversity in the olive tree accessions used in Brazil.

Biomonitoring of antioxidant and oxidative stress responses in Perinereis gualpensis (Polychaeta: Nereididae) in Chilean estuarine regions under different anthropogenic pressure

This study aimed to analyze oxidative stress parameters, including levels of the antioxidant glutathione (GSH), activity of glutamate-cysteine ligase (GCL) and glutathione-S-transferase (GST), total antioxidant capacity and protein oxidation, in the polychaete Perinereis gualpensis (Nereididae) collected from the Biobío, Itata, Valdivia and Lingue estuaries in Chile, which present different degrees of anthropogenic pressure. Sampling sites were characterized considering a geographic information system and the physicochemical characteristics of water and sediment. Significant differences (p<0.05) were observed between the sampling sites for most of the responses (GSH, GCL, GST and antioxidant capacity), mainly related to human activities such as agriculture, industry, among others. Multivariate correlation analysis indicates a certain relationship of antioxidant responses with human activities, salinity, and worm weight, this last employed to standardize GST and antioxidant capacity. These results clearly indicate biomarker responses in P. gualpensis in Biobío and Valdivia estuaries, the more affected by human activities.

Anti-tumor necrosis factor-a for the treatment of steroid-refractory acute graft-versus-host disease

Allogeneic stem cell transplantation has been increasingly performed for a variety of hematologic diseases. Clinically significant acute graft-versus-host disease (GVHD) occurs in 9 to 50% of patients who receive allogeneic grafts, resulting in high morbidity and mortality. There is no standard therapy for patients with acute GVHD who do not respond to steroids. Studies have shown a possible benefit of anti-TNF-a (infliximab)for the treatment of acute GVHD. We report here on the outcomes of 10 recipients of related or unrelated stem cell transplants who received 10 mg/kg infliximab, iv, once weekly for a median of 3.5 doses (range: 1-6) for the treatment of severe acute GVHD and who were not responsive to standard therapy. All patients had acute GVHD grades II to IV (II = 2, III = 3, IV = 5). Overall, 9 patients responded and 1 patient had progressive disease. Among the responders, 3 had complete responses and 6 partial responses. All patients with cutaneous or gastrointestinal involvement responded, while only 2 of 6 patients with liver disease showed any response. None of the 10 patients had any kind of immediate toxicity. Four patients died, all of them with sepsis. Six patients are still alive after a median follow-up time of 544 days (92-600) after transplantation. Considering the severity of the cases and the bad prognosis associated with advanced acute GVHD, we find our results encouraging. Anti-TNF-a seems to be a useful agent for the treatment of acute GVHD.

Endovascular Pressure Measurements: Validation with a Pulsatile Flow Model and Haemodynamic Assessment of Brain AVMs

SUMMARY

Intravascular pressure measurements for several types of endovascular catheters were obtained in an in vitro model to validate the pressure readings obtained during the interventional procedures of brain AVM embolization. An experimental model was used where the beat rate, flow and pressures were as close as possible to the average human values of interest. It is shown that the corrections increase with the decreasing inner diameter of the catheter used and with increasing vascular pressure. We have also shown that there were no differences between measurements made with the catheter in the direction of flow or against it. An average pressure reading corrections for the various microcatheters to compensate the readings obtained during in vivo monitoring is presented. The haemodynamic assessment of 81 brain AVMs was performed using the endovascular measurement of arterial pressure in 389 feeding arteries during embolization. Mostly, the feeders' arterial median pressure was half the systemic arterial pressure but there was a wide variability of AV shunts in brain AVMs not only from one brain AVM to another but also within the same brain AVM. Measurement of arterial feeder pressure is an inexpensive, quick and accurate tool to evaluate the type of AV shunts within brain AVM.

Comparison of the mouse bioassay and enzyme-linked immunosorbent assay procedures for the detection of type A botulinal toxin in food

Samples of chili linked to a foodborne illness outbreak of type A botulism were examined for preformed type A botulinal toxin using two enzyme-linked immunosorbent assay (ELISA) procedures and the mouse bioassay. One of the samples was positive for type A botulinal toxin and three of the samples were negative for type A, B, E, and F botulinal toxins using the three methods. The mouse bioassay indicated that type A toxin was present at the 10,000 minimal lethal dose per gram (MLD per g) of product. The ELISA tests indicated a toxicity of 7,650 MLD per g with one method and 8,350 MLD per g with the other method. The sample toxicity determined by the ELISA was estimated by comparing samples to a standard curve generated with standard type A neurotoxin in casein buffer. The ELISA methods are more rapid than the mouse bioassay, since the toxin type can be determined in 1 day. The mouse bioassay is more sensitive than the ELISA but usually requires multiple assays to obtain the toxin type and toxicity. Type A culture isolates from the sample were also verified using one ELISA method.

Detection of preformed type A botulinal toxin in hash brown potatoes by using the mouse bioasssay and a modified ELISA test

A foodborne illness caused by type A toxin-producing Clostridium botulinum was investigated by using the standard mouse bioassay and a rapid invitro test for toxin detection. The patient, who consumed improperly stored hash brown potatoes that contained the preformed toxin, was diagnosed with type A botulism. C. botulinum type A toxin was detected in the hash brown potatoes as well as in the tryptone-peptone-glucose-yeast extract (TPGY) medium subcultures of this food using the mouse bioassay and an amplified ELISA technique. The mouse bioassay revealed preformed toxin at 10,000 minimum lethal dose (MLD)/g uncooked product and the amplified ELISA an equivalent 50,000 MLD/g. The cultural toxin from the uncooked product killed mice at the 10(6) dilution and a modification of the ELISA procedure was positive at the 10(3) dilution. Cooked food obtained from the consumer's waste can contained 100 MLD/g and the ELISA was also positive at the same dilution of the product. The culture of the cooked product obtained from the waste can was lethal for mice at the 10(7) dilution and positive using the modified ELISA at the 10(4) dilution. The unmodified amplified ELISA method indicated a toxin level of approximately 1 ng/mL (equivalent to 5 x 10(5) MLD/mL) in diluted culture fluid from the uncooked food and the culture of cooked food obtained from the waste can. The hash brown potatoes were negative for types B, E, and F preformed and cultural botulinal toxins using both assays.

Nitric oxide production by murine peritoneal macrophages in vitro and in vivo treated with Phyllanthus tenellus extracts

Phyllanthus spp. are used traditionally for the treatment of viral, bacterial and parasitic infections. Macrophages may play a central role in innate and adaptive response against several infections. Nitric oxide (NO) can be induced during macrophage activation and may exert antimicrobial activity inhibiting the replication of several viruses or parasites. In the present study, we investigated the immunomodulatory role, both in vitro and in vivo, of aqueous extracts of fresh and dried Phyllanthus tenellus as well as an acetone/water extract of the dried plant. NO production by mouse peritoneal macrophages was detected in culture supernatants. Our results demonstrated that: (1) in vitro, a concentration of 100 microg/ml fresh extract stimulated significantly (P< or =0.05) NO production in all assays and the optimal production was achieved at 48-h incubation; (2) 10 and 50 mg/kg fresh extract injected twice intraperitonealy primed macrophages in vivo. Priming was detected by in vitro addition of a second stimulus with 100 microg/ml extract of the fresh plant. Thus, P. tenellus was able to pre-activate macrophages in vivo, and induce full activation in vitro. Further studies should be carried out to better evaluate the optimal dose schedules in terms of time/response for obtaining antiviral or other antimicrobial activity without host damage.

Comparison of amplified ELISA and mouse bioassay procedures for determination of botulinal toxins A, B, E, and F

The amplified enzyme-linked immunosorbent assay (amp-ELISA) was compared to the mouse bioassay for determination of botulinal neurotoxin types A, B, E, and F. Twelve different toxin-producing type A, 13 proteolytic type B, 9 nonproteolytic type B, 16 type E, 8 proteolytic type F, 5 nonproteolytic type F, and 6 nontoxigenic clostridial strains were tested. The cultures were inoculated into cooked meat medium (CMM) and tryptone-peptone-glucose-yeast extract (TPGY) medium, incubated for 5 days, and then examined for biological toxicity in mice and amp-ELISA endpoints. The amp-ELISA was less sensitive in detecting toxins produced by nonproteolytic than proteolytic strains of type B and F organisms. All of the toxin-producing strains tested were positive by the AOAC method and the amp-ELISA in either undiluted TPGY or CMM culture fluids regardless of mouse toxicity level, source, or strain. Cross-reactivity was observed between some but not all of the botulinal strains tested. None of the nontoxigenic strains were positive by the amp-ELISA. Purified botulinal toxins were also assayed using these 2 methods. The sensitivity of the amp-ELISA using purified neurotoxins was about 0.1 ng/mL for types A, B, and E and about 1.0 ng/mL for type F.

Activities of the Pharmaceutical Technology Institute of the Oswaldo Cruz Foundation with medicinal, insecticidal and insect repellent plants

In addition to original research, Far-Manguinhos, the Pharmaceutical Division of the Brazilian Ministry of Health's Oswaldo Cruz Foundation (FIOCRUZ), devotes major attention to the finalising of products for use in public health campaigns or, under contract, for private industrial development. Emphasis is on standardisation, adequate supply, safety in use and efficacy. Among the products discussed in this summary of some of its activities in the chemical and pharmaceutical fields are medicinal plants Bidens pilosa, Cymbopogon citratus, Copaifera species, Mentha crispa, Phyllanthus tenellus Roxb. and other Phyllanthus species, insecticidal plants, Lonchocarpus urucu and Quassia amara, and the insect antifeedant plants Carapa guianensis and Pterodon emarginatus.

High prevalence of GB virus C in Brazil and molecular evidence for intrafamilial transmission

The prevalence of GB virus C (GBV-C) in candidate Brazilian blood donors with normal and elevated alanine aminotransferase levels was found to be 5.2% (5 of 95) and 6.5% (5 of 76), respectively. Among Brazilian patients, GBV-C was found in 9.5% (13 of 137) of cases of hepatitis not caused by hepatitis A virus (HAV), HBV, HCV, HDV, or HEV (non-A-E hepatitis) and in 18.2% (8 of 44) of individuals infected with HCV. Molecular characterization of GBV-C by partial sequencing of the NS3 region showed clustering between members of a single family, implying intrafamilial transmission. In conclusion, these results together suggest that contagion mechanisms which facilitate intrafamilial transmission of GBV-C may partially explain the high prevalence of viremic carriers worldwide.

Detection of Clostridium botulinum type F using the polymerase chain reaction

The polymerase chain reaction (PCR) was used to amplify a portion of the Clostridium botulinum type F toxin gene. An 1137-bp fragment was amplified from 11 different strains of type F C. botulinum with primers derived from the published sequence of type F strain no. 202. This fragment was not amplified from the DNA of C. botulinum types A, B and E, or from other clostridial organisms examined. When used as a hybridization probe, the 1137-bp PCR-generated fragment generated from one of the type F strains (the proteolytic strain type F Langeland) hybridized to the PCR products from all other type F toxin-producing strains tested. Portions of fragments amplified from the type F Langeland strain were sequenced. The sequence of this strain was found to exhibit approximately 3% variation from the published sequence of the non-proteolytic type F strain no. 202. Primers designed to pair with the regions of maximum sequence variation between strain 202 and the Langeland strain gave amplification products only with DNA from type F strains that exhibited the same proteolytic properties as the strain from which the primer sequences were derived. These findings underscore the need to consider variations in sequence when designing oligonucleotide probes and PCR primers in order to avoid false negative results.

Detection of type A, B, and E botulism neurotoxin genes in Clostridium botulinum and other Clostridium species by PCR: evidence of unexpressed type B toxin genes in type A toxigenic organisms

We studied the effectiveness of the PCR in detecting the type A, B, and E botulism neurotoxin genes in 209 strains of Clostridium botulinum and 29 strains of other Clostridium spp. All 79 strains that produced type A toxin, 77 strains that produced type B toxin, and 51 organisms that produced type E toxin (46 C. botulinum and 5 C. butyricum) were PCR positive in reactions with primers targeting sequences specific for their respective toxin genes. The PCR for type A toxin was positive for one type B toxin-producing strain that produced a small amount of type A toxin in addition to a large amount of type B toxin. Surprisingly, the type B toxin gene was detected in addition to the type A toxin gene in 43 type A toxin-producing strains, only 1 of which could be shown by bioassay to produce biologically active type B toxin in culture. The type B gene was also detected in two strains of C. subterminale, which were determined to be nontoxigenic by bioassay. While the PCR was sensitive and specific in detecting the neurotoxin genes, the discovery of unexpressed toxin genes indicates that PCR results may not be adequate for establishing type B neurotoxigenicity.

Monoclonal antibody to type F Clostridium botulinum toxin

Hybridomas synthesizing monoclonal antibodies (MAbs) against type F Clostridium botulinum toxin were developed. MAb from one stable hybridoma, hybridoma 223, consisted of kappa light chains and an immunoglobulin G subclass 2a heavy chain. This MAb was used in a double-sandwich enzyme-linked immunosorbent assay to detect type F toxin in foods, culture fluids, and purified toxin preparations. The sensitivity of the double-sandwich enzyme-linked immunosorbent assay was approximately 10 mouse lethal doses of toxin per ml of toxic fluid.

[Hospital infection at a private hospital in Ribeirão Preto, São Paulo, Brazil]

The aim of this work is to prospectively evaluate the incidence of infection, from June 1986 to June 1987, in 640 patients submitted to surgical treatment at the São Francisco Hospital, in Ribeirão Preto, São Paulo, Brazil. The overall incidence of infection was 10.31%. The incidence of wound abscess was 6.25%, and urinary infection 5.75%. In the surgical procedures considered as clean, the infection rate was 8.62%, in the clean-contaminated 14.81%, in the contaminated 8.33%, and in the dirty 16.94%. The antimicrobian drugs contributed to increase the infection rate. The hospital infection rate for the patients at infirmaries was 10.88%, and for the patients at private rooms 4.92%. The mortality rate due to hospital infection was 12.12%. The authors stress that a constant attention with the hospital infection is needed to verify the infection rate to be able to make a control program of the asepsis, antisepsis and sterilization methods, as well as to improve the operative techniques and the patient's management during the pre, per and postoperative period.

Monoclonal antibody for the detection of Clostridium botulinum type A toxin

Hybridomas producing monoclonal antibodies against type A Hall strain Clostridium botulinum toxin were generated by fusing mouse myeloma cell line P3-X63-Ag8.653 with spleen cells of Balb/c mice immunized with C. botulinum type A toxoid. The monoclonal antibody from one hybridoma, identified as No. 424, was selected from 61 others for its high antibody titre. This monoclonal antibody was used in a double-sandwich enzyme-linked immunosorbent assay (ELISA) system to detect type A toxin in culture fluids and in foods. The monoclonal antibody did not react with either C. botulinum toxin types B, C, D, E and F or with other clostridial species tested. This particular monoclonal antibody (No. 424) did not neutralize type A toxin in the mouse bioassay procedure but detected approximately 10 mouse lethal doses of type A toxin/ml culture fluid. Monoclonal antibody and rabbit antitoxin to type A C. botulinum toxin were useful in a double-sandwich ELISA for the rapid and specific detection of type A toxic fluids in culture and in food samples.

Probability of recovering pathogenic Escherichia coli from foods

The probability of recovering pathogenic Escherichia coli from food by the Bacteriological Analytical Manual method was determined by the effects of several factors: the number of strains per food, the ability of pathogenic strains to survive enrichment, and the frequency of plasmid loss during enrichment. Biochemical patterns indicated the presence of about six E. coli strains per food sample. About half of the strains isolated from humans did not survive enrichment. Among those which grew, plasmid loss, as determined by gel electrophoresis and DNA colony hybridization, ranged from 20 to 95%. The combined effects of failure to survive enrichment and plasmid loss decreased the relative numbers of these strains and reduced the chance of detecting pathogens. To counteract this tendency and obtain a 90 to 95% probability off recovering a given pathogenic strain, 40 to 50 colonies per food sample should be picked during the routine testing of foods.

Detection of Escherichia coli Enterotoxins by Using Mouse Adrenal Cell and Suckling Mouse Assays: Collaborative Study

The ability of 10 Escherichia coli strains to produce heat-stable enterotoxin (ST) and heat-labile enterotoxin (LT) was determined by 8 analysts in a collaborative study. The suckling mouse model and the mouse adrenal cell line (Y-l) tests were used to detect ST and LT, respectively. Cultures for assay were grown 24 h in casamino acid-yeast extracttrace salts broth at 37°C in a shaker incubator at 250 rpm. Cell-free culture broth prepared by centrifugation and filtration was divided into 2 portions: One was heated for 30 min and used both for ST assay and as a heated control for LT assay; the other was used unheated for LT assay. Results were expressed as positive for ST, positive for LT, positive for ST and LT, or negative for both ST and LT; percent of correct estimates was calculated for each culture for each analyst. At the 95% confidence interval, the overall correct results were 96.3 ± 2.9 and 95.0 ± 3.4% for ST and LT, respectively. The test performances thus were satisfactory for detecting ST and LT produced in vitro by E. coli. The method has been adopted official first action.

Genetic methods for the detection of microbial pathogens. Identification of enterotoxigenic Escherichia coli by DNA colony hybridization: collaborative study

Enteropathogenic Escherichia coli strains may produce a cholera-like, heat-labile enterotoxin (LT) as a virulence factor. The gene that codes for LT can be purified by recombinant DNA techniques and used as a genetic probe for DNA hybridization. These probes detect enterotoxigenic strains as well as strains that may not manifest toxin production but carry the genetic information to do so. In this study, 13 laboratories tested 3 known and 25 unknown (10 positive and 15 negative) cultures of E. coli for the presence of the LT gene. The isolates had been tested and classified by the mouse Y-1 adrenal cell test and an enzyme-linked immunosorbent assay. Cultures were spotted on nitrocellulose filters on MacConkey agar and incubated. Colonies were lysed in situ and their DNA was hybridized to 32P-labeled, purified LT gene DNA (provided to the collaborators). Positive colonies were identified by autoradiography. Of 325 samples, 315 (96.9%) were identified correctly and 10 were misclassified; there were 6 false negative and 4 false positive identifications. Chi-square values indicated that the method agreed with the previous classification and was equally efficient in distinguishing positive and negative samples (95.7 and 98.1%, respectively). The method has been adopted official first action.

Genetic Methods for the Detection of Microbial Pathogens. Identification of Enterotoxigenic Escherichia coli by DNA Colony Hybridization: Collaborative Study

Enteropathogenic Escherichia coli strains may produce a cholera-like, heat-labile enterotoxin (LT) as a virulence factor. The gene that codes for LT can be purified by recombinant DNA techniques and used as a genetic probe for DNA hybridization. These probes detect enterotoxigenic strains as well as strains that may not manifest toxin production but carry the genetic information to do so. In this study, 13 laboratories tested 3 known and 25 unknown (10 positive and 15 negative) cultures off. coli for the presence of the LT gene. The isolates had been tested and classified by the mouse Y-l adrenal cell test and an enzyme-linked immunosorbent assay. Cultures were spotted on nitrocellulose filters on MacConkey agar and incubated. Colonies were lysed in situ and their DNA was hybridized to 32P-labeled, purified LT gene DNA (provided to the collaborators). Positive colonies were identified by autoradiography. Of 325 samples, 315 (96.9%) were identified correctly and 10 were misclassified; there were 6 false negative and 4 false positive identifications. Chi-square values indicated that the method agreed with the previous classification and was equally efficient in distinguishing positive and negative samples (95.7 and 98.1%, respectively). The method has been adopted official first action.

Immunodiffusion method for detection of type A Clostridium botulinum

A simple gel immunodiffusion agar procedure was developed for detecting toxigenic strains of Clostridium botulinum type A. The method consisted of overlaying colonies grown on thin-layer tryptone-peptone-glucose-yeast extract agar with gel diffusion agar containing desired levels of C. botulinum type A antitoxin. Concentric precipitin zones formed around colonies of C. botulinum type A. Strains of C. botulinum type A were detected by this procedure. However, C. botulinum type B reacted to a lesser degree with this system. No reaction was noted with types E, F, Langeland, F8G, Clostridium perfringens, or with strains of nontoxigenic Clostridium sporogenes. Thickness of the plating medium, incubation time and temperature, environmental growth conditions, and levels of both agar an antitoxin were important factors affecting the efficiency of the procedure, whereas the age of the culture (used as inoculum) was not critical. Thin agar medium (5 ml per plate [15 by 100 mm]) containing 1.5% agar gave consistent results, but more agar limited diffusion, and lower levels encouraged spreaders. The optimal concentration of antitoxin incorporated in to the gel diffusion agar overlay was 1.2 IU/ml gel diffusion agar. Rabbit type A antitoxin prepared with purer immunizing agent gave similar reactions. The addition of type A antitoxin in tryptone-peptone-glucose-yeast extract agar medium before inoculation with type A C. botulinum showed promising results.