Bleach-concentrated direct sputum smear microscopy procedure for diagnosis of pulmonary tuberculosis in poverty areas / Microscopia direta de amostra de escarro concentrado em água sanitária para diagnóstico de tuberculose pulmonar

ABSTRACT INTRODUCTION: Pulmonary tuberculosis caused by Mycobacterium tuberculosis is a serious public health problem affecting millions of people worldwide. The development of easy and low-cost diagnostic methods is crucial for disease control in rural remote and poverty areas and among vulnerable groups. OBJECTIVE: To evaluate the accuracy of laboratory methods for the diagnosis of Pulmonary tuberculosis. MATERIAL AND METHODS: Sputum samples from patients with clinical signs and symptoms were analyzed by microscopy after chemical treatment and spontaneous sedimentation and compared with methods employed routinely: direct sputum smear microscopy, culture, and GeneXpert®MTB/RIF. RESULTS: From the samples analyzed, 16% were positive by microscopy in the processed samples, 18% by both culture and Xpert®MTB/RIF, while 13% in the direct microscopy. The processed samples showed a 31% increase in positivity (57 samples) compared to conventional direct microscopy. In the analysis of the accuracy of the evaluated methods, all the results were statistically significant proving that they were not randomly positive or negative and confirming that there is a tendency for these results. CONCLUSION: Chemical treatment and spontaneous sedimentation of the sputum samples procedure represent an effective diagnostic tool in situations where more advanced technologies are not feasible. Besides the higher accuracy and greater detection of positive cases regarding the direct smear, the procedure strengthens biosafety by decreasing the risks of aerial contamination by Mycobacterium tuberculosis for laboratory professionals.

RESUMEN INTRODUCCIÓN: La tuberculosis pulmonar causada por Mycobacterium tuberculosis es un grave problema de salud pública que afecta millones de individuos en el mundo. El desarrollo de métodos de diagnóstico fáciles y de bajo costo es esencial para el control de la enfermedad en zonas rurales remotas y pobres y entre los grupos vulnerables. OBJETIVO: Evaluar la exactitud de métodos de laboratorio para el diagnóstico de tuberculosis pulmonar. MATERIAL Y MÉTODO: Las muestras del esputo de pacientes con signos y síntomas clínicos fueron analizadas por microscopía luego de tratamiento químico y sedimentación espontánea y comparados con métodos empleados ordinariamente: baciloscopía directa de esputo, cultivo y GeneXpert® MTB/RIF. RESULTADOS: Entre las muestras analizadas, 16% fueron positivas por microscopía en las muestras procesadas; 18% por cultivo y Xpert® MTB/RIF; y 13% por microscopía directa. Las muestras procesadas presentaran un aumento de 31% de positividad (57 muestras) con respecto a la microscopía directa convencional. En el análisis de los métodos, todos los resultados fueron estadísticamente significativos, comprobando que no eran aleatoriamente positivos o negativos y confirmando que hay una tendencia para esos resultados. CONCLUSIÓN: El tratamiento químico y la sedimentación espontánea de las muestras de esputo representan una herramienta diagnóstica eficaz en las situaciones en las cuales tecnologías más avanzadas no son viables. Además de la mayor precisión y mayor detección de casos positivos de lo que hace el frotis directo, el procedimiento fortalece la bioseguridad, disminuyendo los riesgos de contaminación del aire por Mycobacterium tuberculosis para el personal de laboratorio.

RESUMO INTRODUÇÃO: A tuberculose pulmonar causada por Mycobacterium tuberculosis é um grave problema de saúde pública que afeta mundialmente milhões de indivíduos. O desenvolvimento de métodos de diagnóstico fáceis e de baixo custo é essencial para o controle da doença nas áreas rurais remotas e de pobreza e entre os grupos vulneráveis. OBJETIVO: Avaliar a acurácia dos métodos laboratoriais para o diagnóstico de tuberculose pulmonar. MATERIAL E MÉTODOS: As amostras de escarro de pacientes com sinais e sintomas clínicos foram analisadas por microscopia após tratamento químico e sedimentação espontânea e comparadas com métodos empregados rotineiramente: baciloscopia direta do escarro, cultura e GeneXpert® MTB/RIF. RESULTADOS: Das amostras analisadas, 16% foram positivas por microscopia nas amostras processadas; 18%, por cultura e Xpert® MTB/RIF; e 13%, por microscopia direta. As amostras processadas apresentaram um aumento de 31% de positividade (57 amostras) em relação à microscopia direta convencional. Na análise dos métodos avaliados, todos os resultados foram estatisticamente significativos, comprovando que não eram positivos ou negativos aleatoriamente e confirmando que há uma tendência para esses resultados. CONCLUSÃO: O tratamento químico e a sedimentação espontânea das amostras de escarro representam uma ferramenta diagnóstica eficaz nas situações em que tecnologias mais avançadas não são viáveis. Além da maior precisão e maior detecção de casos positivos em relação ao esfregaço direto, o procedimento reforça a biossegurança, diminuindo os riscos de contaminação aérea por Mycobacterium tuberculosis para profissionais de laboratório

Comparative Genomics of Acinetobacter baumannii Clinical Strains From Brazil Reveals Polyclonal Dissemination and Selective Exchange of Mobile Genetic Elements Associated With Resistance Genes.

Acinetobacter baumannii is an opportunistic bacterial pathogen infecting immunocompromised patients and has gained attention worldwide due to its increased antimicrobial resistance. Here, we report a comparative whole-genome sequencing and analysis coupled with an assessment of antibiotic resistance of 46 Acinetobacter strains (45 A. baumannii plus one Acinetobacter nosocomialis) originated from five hospitals from the city of Recife, Brazil, between 2010 and 2014. An average of 3,809 genes were identified per genome, although only 2,006 genes were single copy orthologs or core genes conserved across all sequenced strains, with an average of 42 new genes found per strain. We evaluated genetic distance through a phylogenetic analysis and MLST as well as the presence of antibiotic resistance genes, virulence markers and mobile genetic elements (MGE). The phylogenetic analysis recovered distinct monophyletic A. baumannii groups corresponding to five known (ST1, ST15, ST25, ST79, and ST113) and one novel ST (ST881, related to ST1). A large number of ST specific genes were found, with the ST79 strains having the largest number of genes in common that were missing from the other STs. Multiple genes associated with resistance to ß-lactams, aminoglycosides and other antibiotics were found. Some of those were clearly mapped to defined MGEs and an analysis of those revealed known elements as well as a novel Tn7-Tn3 transposon with a clear ST specific distribution. An association of selected resistance/virulence markers with specific STs was indeed observed, as well as the recent spread of the OXA-253 carbapenemase encoding gene. Virulence genes associated with the synthesis of the capsular antigens were noticeably more variable in the ST113 and ST79 strains. Indeed, several resistance and virulence genes were common to the ST79 and ST113 strains only, despite a greater genetic distance between them, suggesting common means of genetic exchange. Our comparative analysis reveals the spread of multiple STs and the genomic plasticity of A. baumannii from different hospitals in a single metropolitan area. It also highlights differences in the spread of resistance markers and other MGEs between the investigated STs, impacting on the monitoring and treatment of Acinetobacter in the ongoing and future outbreaks.

A new recombinant F1 antigen as a cost and time-effective tool for plague diagnosis.

The Yersinia pestis capsular antigen F1 is widely used in plague laboratory diagnosis. Here, we describe the production of an F1 recombinant protein within reduced time and biosafety requirements. Its evaluation in hemagglutination tests indicated that the recombinant F1 can replace the conventional F1 protein for plague diagnosis.

A single introduction of Yersinia pestis to Brazil during the 3rd plague pandemic.

Yersinia pestis was introduced to Brazil during the third plague pandemic and currently exists in several recognized foci. There is currently limited available phylogeographic data regarding Y. pestis in Brazil. We generated whole genome sequences for 411 Y. pestis strains from six Brazilian foci to investigate the phylogeography of Y. pestis in Brazil; these strains were isolated from 1966 to 1997. All 411 strains were assigned to a single monophyletic clade within the 1.ORI population, indicating a single Y. pestis introduction was responsible for the successful establishment of endemic foci in Brazil. There was a moderate level of genomic diversity but little population structure among the 411 Brazilian Y. pestis strains, consistent with a radial expansion wherein Y. pestis spread rapidly from the coast to the interior of Brazil and became ecologically established. Overall, there were no strong spatial or temporal patterns among the Brazilian strains. However, strains from the same focus tended to be more closely related and strains isolated from foci closer to the coast tended to fall in more basal positions in the whole genome phylogeny than strains from more interior foci. Overall, the patterns observed in Brazil are similar to other locations affected during the 3rd plague pandemic such as in North America and Madagascar.

Caracterização fenotípica e molecular de amostras de Burkholderia mallei isoladas na Região Nordeste do Brasil / Phenotypic and molecular characterization of Burkholderia mallei isolated in northeastern Brazil

Objetivou-se com este trabalho realizar o estudo bioquímico e molecular de amostras de Burkholderia mallei isoladas de eqüídeos com diagnóstico clínico e sorológico para o mormo e provenientes da Região Metropolitana do Recife-PE e Zona da Mata dos Estados de Alagoas e Pernambuco. Foram realizadas as técnicas microbiológicas para o isolamento e identificação fenotípica de B. mallei e as técnicas moleculares de ribotipagem-PCR e RAPD-PCR. Das oito amostras estudadas, quatro apresentaram pequenas variações fenotípicas. Nas técnicas moleculares, as amostras formaram quatro grupos de diferentes perfis ribotípicos, demonstrando também quatro perfis genotípicos. Houve associação nos resultados da Ribotipagem-PCR e RAPD-PCR. As variações nos perfis ribotípicos e genotípicos foram associadas às diferentes regiões estudadas. De acordo com os resultados obtidos, conclui-se que as pequenas variações bioquímicas não estão associadas aos diferentes perfis moleculares e que essas diferenças demonstram uma heterogeneidade que está associada à procedência das amostras, indicando que a infecção nos animais ocorre por clones diferentes das amostras analisadas.

The objective of this paper was to study the molecular performance and phenotypic characterization of Burkholderia mallei isolated from horses with clinical and serological diagnosis of glanders, originating from the Metropolitan District of Recife and Zona da Mata of Pernambuco and Alagoas. The isolation and biochemical identification of B. mallei was carried out by microbiological and molecular techniques of PCR-fingerprinting and RAPD-PCR. From the eight samples studied, four showed little phenotype variations. In the molecular tests, the samples formed 4 groups of different ribotype profiles and 4 genotype profiles. There was some association of PCR-fingerprinting with RAPD-PCR results. It was concluded that the slight biochemical variations were not associated with different molecular profiles. They also indicated that these differences show heterogeneity associated with the origin of the sample, indicating that the infection was caused by clones of different strains and that the polymorphism of DNA observed could make it difficult to choose one standard strain for an immune prophylactic treatment of glanders.

Prevalence of cagA and vacA genes in isolates from patients with Helicobacter pylori-associated gastroduodenal diseases in Recife, Pernambuco, Brazil.

Geographical differences in the prevalence of Helicobacter pylori genes and their association with disease severity have been identified. This study analyzes the prevalences of the cagA gene and alleles of the vacA gene in H. pylori-associated gastroduodenal diseases in isolates from Recife, PE, Brazil. Gastric biopsy of 61 H. pylori-positive patients were submitted to DNA extraction and gene amplification by polymerase chain reaction. Among the 61 patients, 21 suffered from duodenal ulcer (DU) and 40 from gastritis (GT). The prevalence of H. pylori strains harbouring the cagA gene was higher in the DU group (90.5%) than in the GT group (60%) (p=0.02). The vacA gene was amplified in 56 out of 61 biopsies, of which 43 (76.8%) contained bacteria carrying the s1 allele and 13 (23.2%) the s2. However, the prevalence of the vacA s1 genotyping was the same in either DU or GT group. The majority of the s1-typed strains, 39 (90.7%) out of 43, were subtype s1b. In resume there was a strong association between the H. pylori cagA+ gene and DU. However, there were no differences between the DU and GT groups in relation to the vacA s1 and s2 alleles distribution, albeit the subtype s1b was predominant.

Prevalence of cagA and vacA genes in isolates from patients with Helicobacter pylori-associated gastroduodenal diseases in Recife, Pernambuco, Brazil

Geographical differences in the prevalence of Helicobacter pylori genes and their association with disease severity have been identified. This study analyzes the prevalences of the cagA gene and alleles of the vacA gene in H. pylori-associated gastroduodenal diseases in isolates from Recife, PE, Brazil. Gastric biopsy of 61 H. pylori-positive patients were submitted to DNA extraction and gene amplification by polymerase chain reaction. Among the 61 patients, 21 suffered from duodenal ulcer (DU) and 40 from gastritis (GT). The prevalence of H. pylori strains harbouring the cagA gene was higher in the DU group (90.5 percent) than in the GT group (60 percent) (p = 0.02). The vacA gene was amplified in 56 out of 61 biopsies, of which 43 (76.8 percent) contained bacteria carrying the s1 allele and 13 (23.2 percent) the s2. However, the prevalence of the vacA s1 genotying was the same in either DU or GT group. The majority of the s1-typed strains, 39 (90.7 percent) out of 43, were subtype s1b. In resume there was a strong association between the H. pylori cagA+ gene and DU. However, there were no differences between the DU and GT groups in relation to the vacA s1 and s2 alleles distribution, albeit the subtype s1b was predominat

Conventional and molecular typing of Salmonella typhi strains from Brazil

Phenotypic and genotypic characteristics of Salmonella Typhi were studied in 30 strains, isolated in different years, from some areas in Brazil. Conventional typing methods were performed by biochemical tests, Vi phage-typing scheme, and antimicrobial susceptibility test. Molecular typing methods were performed by analysis of plasmid DNA and by random amplified polymorphic DNA (RAPD-PCR). For the latter, an optimization step was performed to ensure the reproducibility of the process in genetic characterization of S. Typhi. The predominance of 76.7 percent of biotype I (xylose +, arabinose -) was noticed in all studied areas. Three phage types were recognized, with prominence for the phage types A (73.3 percent) and I+IV (23.3 percent). All the strains were susceptible to the drugs used. However, 36.7 percent of the strains contained plasmids, with predominance of the 105 Kb plasmid. RAPD was capable of grouping the strains in 8 genotypic patterns using primer 784, in 6, using primer 787 and in 7, using primer 797. Conventional phenotypic typing methods, as well as the DNA plasmid analysis, presented nonsignificant discriminatory power; however, RAPD-PCR analysis showed discriminatory power, reproducibility, easy interpretation and performance, being considered as a promising alternative typing method for S. Typhi

Conventional and molecular typing of Salmonella typhi strains from Brazil.

Phenotypic and genotypic characteristics of Salmonella Typhi were studied in 30 strains, isolated in different years, from some areas in Brazil. Conventional typing methods were performed by biochemical tests, Vi phage-typing scheme, and antimicrobial susceptibility test. Molecular typing methods were performed by analysis of plasmid DNA and by random amplified polymorphic DNA (RAPD-PCR). For the latter, an optimization step was performed to ensure the reproducibility of the process in genetic characterization of S. Typhi. The predominance of 76.7% of biotype I (xylose +, arabinose -) was noticed in all studied areas. Three phage types were recognized, with prominence for the phage types A (73.3%) and I+IV (23.3%). All the strains were susceptible to the drugs used. However, 36.7% of the strains contained plasmids, with predominance of the 105 Kb plasmid. RAPD was capable of grouping the strains in 8 genotypic patterns using primer 784, in 6, using primer 787 and in 7, using primer 797. Conventional phenotypic typing methods, as well as the DNA plasmid analysis, presented nonsignificant discriminatory power; however, RAPD-PCR analysis showed discriminatory power, reproducibility, easy interpretation and performance, being considered as a promising alternative typing method for S. Typhi.

Molecular analysis of clinical isolates of Providencia alcalifaciens.

In an attempt to elucidate the virulence factors and the pathogenic mechanisms of Providencia alcalifaciens, 36 isolates identified in 1994-1995 in Recife city, Brazil were analysed by PCR to investigate the presence of DNA sequences homologous to virulence genes described in other invasive enterobacteria, as well as their ability to invade HeLa cells, their plasmid profiles and antibiotic resistance patterns. The genetic diversity of the isolates was also analysed by RAPD-PCR. No homologous sequences of virulence genes were observed with any of the P. alcalifaciens isolates studied. Ten isolates had no plasmid and 26 harboured one-to-five plasmids of 147-<6.9 kb. Invasion of HeLa cells was observed in only 10 isolates. No correlation between the plasmid content of the strains, their invasion of HeLa cells or their resistance to antimicrobial drugs could be established. The isolates could be distributed into 10 genotypic groups by RAPD-PCR. Considering the genotypic profile and ability to invade HeLa cells, 7 of the 10 invasive isolates belonged to the same genotypic group. The presence of invasive isolates in the same or a related genotypic group suggests the existence of a clonal lineage responsible for the invasiveness.

Diagnosis of plague and identification of virulence markers in Yersinia pestis by multiplex-PCR

We have developed a procedure for the rapid diagnosis of plague that also allows the identification of prominent virulence markers of Y. pestis strains. This procedure is based upon the use of a single polymerase chain reaction with multiple pairs of primers directed at genes present in the three virulence plasmids as well as in the chromosomal pathogenicity island of the bacterium. The technique allowed the discrimination of strains which lacked one or more of the known pathogenic loci, using as template total DNA obtained from bacterial cultures and from simulated blood cultures containing diluted concentration of bacteria. It also proved effective in confirming the disease in a blood culture from a plague suspected patient. As the results are obtained in a few hours this technique will be useful in the methodology of the Plague Control Program.

RAPD-PCR typing of Yersinia enterocolitica (enterobacteriaceae) O: 3 serotype strains isolated from pigs and humans

Foram utilizados três "primers" aleatórios para caracterizar pela técnica RAPD-PCR 16 cepas de Yersinia enterocolitica do sorotipo O:3, isoladas de suínos sadios do Rio de Janeiro. Pelos resultados dos padröes de amplificaçäo, as 16 cepas dos suínos e as 4 cepas humanas usadas como referência (sorotipos O:4, O:5, O:6 e O:13) foram agrupadas em 5 perfis genotípicos. Quinze cepas de suínos apresentaram um padräo de amplificaçäo idêntico (perfil genotípico 1) e somente uma apresentou um perfil de amplificaçäo diferente (perfil genotípico 2). O mesmo padräo de amplificaçäo do perfil genotípico 1 foi também observado em uma cepa humana do sorotipo O:6. As cepas humanas dos sorotipos O:4 e O:13 exibiram perfis de amplificaçäo semelhantes com 2 "primers", porém com o terceiro "primer" cada uma apresentou um perfil próprio. Essas duas cepas foram enquadradas, cada uma, em um tipo de perfil (perfis genotípicos 3 e 4, respectivamente). A cepa humana do sorotipo O:5 apresentou um perfil de amplificaçäo com cada "primer" completamente diferente dos observados nas outras cepas (perfil genotípico 5). A presença ou ausência de plasmídios nas cepas estudadas näo interferiu nos resultados das amplificaçöes. Esses resultados mostram que dentro de um mesmo sorotipo podem existir modificaçöes genéticas e que cepas de sorotipos diferentes apresentam o mesmo perfil de amplificaçäo com alguns "primers", comprovando que RAPD-PCR é uma ferramenta eficaz para reagrupamento de cepas e poderá ser útil em estudos epidemiológicos para rastreamento de uma cepa e assim acompanhar a disseminaçäo de Y. enterocolitica.

Marcadores de patogenicidade em Yersinia enterocolitica O: 3 isoladas de suínos do Rio de Janeiro / Genetic markers of pathogenicity in Yersinia enterocolitica O: 3 isolated from healthy pigs from Rio de Janeiro

Foi realizada a caracterização genotípica e fenotípica de fatores de patogenicidade em 16 amostras de Yersinia enterocolitica O:3 isoladas de suínos sadios do Rio de Janeiro. Foi observado que apenas 6 cepas possuíam o plasmídio de virulência, pYV (+ 70 kb) e apresentavam dependência ao cálcio no meio MOX a 37C. Um plasmídio críptico de cerca de 8,6 kb foi encontrado em uma cepa. Doze cepas revelaram sensibilidade à pesticina enquanto que apenas três se revelaram capazes de hidrolisar a esculina. Através de PCR com "primers" específicos, foi constatada a presença dos genes ail em 14 cepas, irp2, em 1 cepa e a ausência de psaA em todas as cepas analisadas. Quanto aos quimioterápicos, a quase totalidade das cepas mostrou-se ao mesmo tempo resistente à ampicilina e carbenicilina e sensível ao sulfazotrin e à cefoxitina. As respostas foram variadas frente ao cloranfenicol, tetraciclina, kanamicina, gentamicina e ácido nalidíxo

Survey of the irp2 gene among Yersinia pestis strains isolated during several plague outbreaks in northeast Brazil

The irp2 gene codes for a 190 kDa protein (HMWP2) synthesidez when highly pathogenic Yersinia are grown under conditions of iron starvation. In this work, the presence of irp2 in strains of Y. pestis isolated from different hosts during several plague outbreaks in the foci of Northeast Brazil wasstudied. For this purpose, 53 strains were spotted onto nylon filters and their DNA was hybridized with the A13 probe which is a 1 kb fragment of the irp2 coding sequence. All strains except two hybridized with the probe. However, when the initial stock culture of these two strains were analyzed, they both proved to bepositive with the A13 probe, indicating that the locus was lost after subculturein vitro but was always present in vivo. To examine the degree of conservation of the chromosomal fragment carrying irp2 among Brazilian strains, the hybridization profiles of 15 strains from different outbreaks, different hosts and different foci were compared. The hybridization profiles of these strains were all identical when their DNA was digested with either EcoRI, EcorRV or AvaII, indicatingthat the restriction sites surrounding the irp2 locus are very well conserved among Northeast Brazilian strains of Y. pestis. Altogether, these results suggest that the irp2 chromosomal region should be of prime importance for the bacteria during their multiplication in the host