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Mem. Inst. Oswaldo Cruz ; 116: e200517, 2021. tab, graf
Article in English | LILACS | ID: biblio-1154877


Molecular-typing can help in unraveling epidemiological scenarios and improvement for disease control strategies. A literature review of Mycobacterium tuberculosis transmission in Brazil through genotyping on 56 studies published from 1996-2019 was performed. The clustering rate for mycobacterial interspersed repetitive units - variable tandem repeats (MIRU-VNTR) of 1,613 isolates were: 73%, 33% and 28% based on 12, 15 and 24-loci, respectively; while for RFLP-IS6110 were: 84% among prison population in Rio de Janeiro, 69% among multidrug-resistant isolates in Rio Grande do Sul, and 56.2% in general population in São Paulo. These findings could improve tuberculosis (TB) surveillance and set up a solid basis to build a database of Mycobacterium genomes.

Humans , Polymorphism, Restriction Fragment Length/genetics , Minisatellite Repeats/genetics , Mycobacterium tuberculosis/genetics , Brazil/epidemiology , Bacterial Typing Techniques , Molecular Epidemiology , Whole Genome Sequencing , Genotype , Mycobacterium tuberculosis/isolation & purification
J. bras. pneumol ; 46(2): e20190184, 2020. tab, graf
Article in English | LILACS | ID: biblio-1134864


ABSTRACT Objective: Nontuberculous mycobacteria (NTM) are a heterogeneous group of bacteria that are widely distributed in nature and associated with opportunistic infections in humans. The aims of this study were to identify NTM in patients with suspected tuberculosis who presented positive cultures and to evaluate the genetic diversity of strains identified as Mycobacterium avium. Methods: We studied pulmonary and extrapulmonary samples obtained from 1,248 patients. The samples that tested positive on culture and negative for the M. tuberculosis complex by molecular identification techniques were evaluated by detection of the hsp65 and rpoB genes and sequencing of conserved fragments of these genes. All strains identified as M. avium were genotyped using the eight-locus mycobacterial interspersed repetitive unit-variable-number tandem-repeat method. Results: We found that NTM accounted for 25 (7.5%) of the 332 mycobacteria isolated. Of those 25, 18 (72%) were M. avium, 5 (20%) were M. abscessus, 1 (4%) was M. gastri, and 1 (4%) was M. kansasii. The 18 M. avium strains showed high diversity, only two strains being genetically related. Conclusions: These results highlight the need to consider the investigation of NTM in patients with suspected active tuberculosis who present with positive cultures, as well as to evaluate the genetic diversity of M. avium strains.

RESUMO Objetivo: As micobactérias não tuberculosas (MNT) são um grupo heterogêneo de bactérias amplamente distribuídas na natureza e relacionadas com infecções oportunistas em seres humanos. Os objetivos deste estudo foram identificar MNT em pacientes com suspeita de tuberculose e culturas positivas e avaliar a diversidade genética de cepas identificadas como Mycobacterium avium. Métodos: Foram estudadas amostras pulmonares e extrapulmonares provenientes de 1.248 pacientes. As amostras que apresentaram resultado positivo em cultura e negativo para o complexo M. tuberculosis na identificação molecular foram avaliadas por meio da detecção dos genes hsp65 e rpoB e de sequenciamento de fragmentos conservados desses genes. Todas as cepas identificadas como M. avium foram genotipadas pelo método mycobacterial interspersed repetitive unit-variable-number tandem-repeat com oito loci. Resultados: Das 332 micobactérias isoladas, 25 (7,5%) eram MNT. Dessas 25, 18 (72%) eram M. avium, 5 (20%) eram M. abscessus, 1 (4%) era M. gastri e 1 (4%) era M. kansasii. As 18 cepas de M. avium apresentaram alta diversidade, e apenas duas eram geneticamente relacionadas. Conclusões: Esses resultados mostram a necessidade de considerar a investigação de MNT em pacientes com suspeita de tuberculose ativa e culturas positivas e de avaliar a diversidade genética de cepas de M. avium.

Humans , Nontuberculous Mycobacteria/isolation & purification , Mycobacterium avium/genetics , Mycobacterium Infections, Nontuberculous/diagnosis , Bacterial Proteins/genetics , Genetic Variation , Brazil , DNA-Directed RNA Polymerases/genetics , Bacterial Typing Techniques , Chaperonin 60/genetics , Mycobacterium avium/isolation & purification , Mycobacterium Infections, Nontuberculous/microbiology
Rev. argent. microbiol ; 51(4): 359-362, dic. 2019. graf
Article in English | LILACS | ID: biblio-1057401


Abstract Listeria monocytogenes is a foodborne pathogen. The recent alert for L. monocytogenes in vegetables from Argentina warns about the importance of reinforcing its isolation, characterization and subtyping in food, clinical and environmental samples. The aim of the present study was to compare the discriminatory power of enterobacterial repetitive interpower; genic consensus polymerase chain reaction (ERIC-PCR), automated ribotyping and pulsed-field gel electrophoresis (PFGE) to subtype strains of L. monocytogenes isolated from Argentine meat and environmental samples. Simpson's Diversity Index (DI) was calculated on the basis of based on the dendrograms obtained in the by cluster analysis, showing the following discriminatory power: ApaI-PFGE (0.980), AscI-PFGE (0.966), ribotyping (0.912), ERIC-PCR (0.886). The ID values between ApaI- and AscI-PFGE and between ribotyping and ERIC-PCR were not significantly different. Of the three techniques evaluated, PFGE showed the highest discriminatory power. However, the subtyping techniques should be accompanied by effective food monitoring strategies and reliable clinical and epidemiological studies.

Resumen Listeria monocytogenes es un patógeno alimentario. La reciente alerta por la presencia de L. monocytogenes en vegetales en Argentina advierte sobre la importancia de reforzar el aislamiento, la caracterización y la subtipificación de esta bacteria en muestras clínicas de alimentos y ambientales. El objetivo del presente estudio fue comparar el poder discriminatorio de enterobacterial repetitive intergenic consensus polymerase chain reaction (ERIC-PCR), la ribotipificación automatizada y la pulsed-field gel electrophoresis (PFGE) para subtipificar cepas de L. monocytogenes aisladas de carne y de muestras ambientales en Argentina. El índice de diversidad (ID) de Simpson, calculado a partir de los dendrogramas obtenidos en el análisis de agrupamiento, mostró los siguientes resultados: Apal-PFGE (0,980), AscI-PFGE (0,966), riboti-pado (0,912), ERIC-PCR (0,886). Los valores obtenidos no fueron significativamente diferentes al comparar entre Apal- y AscI-PFGE, ni entre ribotipadoy ERIC-PCR. De las técnicas evaluadas, la PFGE presentó el mayor poder discriminatorio. Sin embargo, las técnicas de subtipificación deberían acompañarse de estrategias de control de los alimentos efectivas y de estudios clínicos y epidemiológicos confiables.

Bacterial Typing Techniques/methods , Listeria monocytogenes/classification , Discriminant Analysis , Ribotyping/methods , Listeria monocytogenes/isolation & purification
Rev. Paul. Pediatr. (Ed. Port., Online) ; 37(2): 156-160, Apr.-June 2019. tab, graf
Article in English | LILACS | ID: biblio-1013279


ASTRACT Objective: To describe eight cases of invasive non-type b Haemophilus influenzae disease in children admitted to Hospital de Clínicas of Universidade Estadual de Campinas. Cases description: In 2015, there were eight cases of invasive non-type b H. influenzae disease. We tested the ampicillin sensitivity and beta-lactamase production of the strains identified and performed the genotyping. Molecular typing was determined by Pulsed-Field Gel Electrophoresis. Four patients were diagnosed with bacteremia; in two cases, H. influenzae was detected in the pleural fluid, and two patients had meningitis. Patients with comorbidities represented 37.5% of cases. Except for the strain of one patient - not sent to the reference laboratory -, all were ampicillin-sensitive and non-beta-lactamase-producing. Genotyping identified four non-capsular, one type c, and two type a strains. Molecular typing ruled out nosocomial transmission since all serotypes were distinct regarding genotype. Comments: The rise in cases of invasive non-type b H. influenzae infection was real. There was no nosocomial transmission, and we found no justification for the increase. These data indicate the need for surveillance to correctly diagnose, monitor, and understand the spectrum of non-type b H. influenzae disease.

ABSTRACT Objetivo: Descrever oito casos de doença invasiva por Haemophilus influenzae não tipo b em crianças internadas no Hospital de Clínicas da Universidade Estadual de Campinas. Descrição dos casos: Em 2015, ocorreram oito casos de doença invasiva por H. influenzae não tipo b. Nas cepas identificadas, testou-se a sensibilidade à ampicilina e a produção de betalactamase, e realizou-se a genotipagem. A tipagem molecular foi feita por Pulsed Field Gel Electrophoresis. Em quatro pacientes, o diagnóstico foi de bacteremia; em dois casos, H. influenzae foi identificado em líquido pleural, e dois pacientes tiveram meningite. Comorbidades foram encontradas em 37,5% dos pacientes. Com exceção da cepa de um dos pacientes (que não foi enviada ao laboratório de referência), todas eram sensíveis à ampicilina e não produtoras de betalactamase. A genotipagem identificou quatro cepas não capsulares, uma cepa tipo c e duas cepas tipo a. A tipagem molecular descartou a transmissão intra-hospitalar, já que todos os sorotipos eram distintos quanto ao genótipo. Comentários: O aumento dos casos de infecção invasiva por H. influenzae não tipo b foi real. Não houve transmissão intra-hospitalar e não foi encontrada justificativa para o aumento. Esses dados indicam a necessidade de vigilância para diagnosticar corretamente, monitorar e entender o espectro da doença causada por H. influenzae não tipo b.

Humans , Male , Female , Infant , Child, Preschool , Child , Microbial Sensitivity Tests , Pleural Effusion/diagnosis , Pleural Effusion/microbiology , Brazil/epidemiology , Haemophilus influenzae/isolation & purification , Haemophilus influenzae/classification , Haemophilus influenzae/genetics , Retrospective Studies , Bacterial Typing Techniques , Bacteremia/diagnosis , Bacteremia/microbiology , Haemophilus Infections/complications , Haemophilus Infections/microbiology , Haemophilus Infections/drug therapy , Haemophilus Infections/epidemiology , Meningitis, Haemophilus/diagnosis , Meningitis, Haemophilus/etiology
Afr. j. lab. med. (Online) ; 8(1): 1-10, 2019. ilus
Article in English | AIM, AIM | ID: biblio-1257322


Background: In sub-Saharan Africa, molecular epidemiological investigation of outbreaks caused by antimicrobial-resistant enteric bacterial pathogens have mostly been described for Salmonella species, Vibrio cholerae, Shigella species and Escherichia coli. For these organisms, I reviewed all publications describing the use of molecular subtyping methodologies to investigate outbreaks caused by multidrug-resistant (MDR) enteric bacterial infections.Objectives: To describe the use of molecular subtyping methodologies to investigate outbreaks caused by MDR enteric bacterial pathogens in sub-Saharan Africa and to describe the current status of molecular subtyping capabilities in the region. Methods: A PubMed database literature search (English language only) was performed using the search strings: 'Africa outbreak MDR', 'Africa outbreak multi', 'Africa outbreak multidrug', 'Africa outbreak multi drug', 'Africa outbreak resistance', 'Africa outbreak resistant', 'Africa outbreak drug', 'Africa outbreak antibiotic', 'Africa outbreak antimicrobial'. These search strings were used in combination with genus and species names of the organisms listed above. All results were included in the review. Results: The year 1991 saw one of the first reports describing the use of molecular subtyping methodologies in sub-Saharan Africa; this included the use of plasmid profiling to characterise Salmonella Enteritidis. To date, several methodologies have been used; pulsed-field gel electrophoresis analysis and multilocus sequence typing have been the most commonly used methodologies. Investigations have particularly highlighted the emergence and spread of MDR clones; these include Salmonella Typhi H58 and Salmonella Typhimurium ST313 clones. In recent times, whole-genome sequencing (WGS) analysis approaches have increasingly been used. Conclusion: Traditional molecular subtyping methodologies are still commonly used and still have their place in investigations; however, WGS approaches have increasingly been used and are slowly gaining a stronghold. African laboratories need to start adapting their molecular surveillance methodologies to include WGS, as it is foreseen that WGS analysis will eventually replace all traditional methodologies

Africa South of the Sahara , Bacterial Typing Techniques , Drug Resistance, Multiple, Bacterial , Salmonella Infections/epidemiology , Salmonella Infections/microbiology
Mem. Inst. Oswaldo Cruz ; 114: e180443, 2019. graf
Article in English | LILACS | ID: biblio-1040616


The presence of tRNA array, a region with high tRNA gene number and density, has been demonstrated in Mycobacterium genus. However, a recent phylogenomic study revealed the existence of five distinct monophyletic groups (genera) within this genus. Considering this new scenario, and based on in-silico analyses, we have identified and characterised the abundance and diversity of tRNA array units within Mycobacterium, Mycolicibacterium gen. nov., Mycolicibacillus gen. nov., and Mycobacteroides gen. nov. The occurrence and prevalence of tRNA arrays among the genera belonging to Actinobacteria indicate their possible role in the organismal fitness.

Bacterial Typing Techniques , Mycobacterium/genetics , Phylogeny , RNA, Transfer/genetics , Mycobacterium/classification
Rev. Soc. Bras. Med. Trop ; 52: e20190243, 2019. tab
Article in English | LILACS | ID: biblio-1020442


Abstract INTRODUCTION In recent decades, the prevalence of carbapenem-resistant Acinetobacter isolates has increased, and the production of oxacillinase (OXA)-type carbapenemases is the main mechanism underlying resistance. We evaluated OXA production from 114 Acinetobacter isolates collected between March and December 2013 from different clinical specimens of patients in two hospitals (Hospital 1 [n = 61] and Hospital 2 [n = 53]) located in Niterói, Rio de Janeiro, Brazil. We also evaluated the genetic diversity of OXA-producing isolates. METHODS All the isolates were identified through the automated system Vitek II and matrix-assisted laser desorption ionization-time of flight mass spectrometry MALDI-TOF MS as belonging to the A. baumannii-A. calcoaceticuscomplex. Antimicrobial susceptibility profiles were verified through agar diffusion tests. The presence of OXA-encoding genes was confirmed by PCR. The genetic diversity of isolates positive for carbapenemase production was analyzed through pulsed-field gel electrophoresis. RESULTS There was a high rate of resistance to carbapenems in the isolates (imipenem: 96%; meropenem: 92%) from both hospitals. Moreover, a high percentage (95.6%) of OXA-23-positive isolates was observed for both hospitals, indicating that this was the main mechanism of carbapenem-resistance among the studied population. In addition, most isolates (96.5%) were positive for bla OXA-51. A high genetic diversity and a few major genotypes were found among the OXA-23-positive isolates analyzed. Only intra-hospital dissemination was observed. CONCLUSIONS The elevated dissemination of bla OXA-23-like observed among Acinetobacter isolates from both the studied hospitals highlights the need for continuous epidemiological surveillance in these institutions.

Humans , Acinetobacter/enzymology , beta-Lactamases/drug effects , Acinetobacter Infections/microbiology , Acinetobacter/drug effects , Acinetobacter/genetics , beta-Lactamases/biosynthesis , Brazil , DNA, Bacterial/genetics , Microbial Sensitivity Tests , Polymerase Chain Reaction , Bacterial Typing Techniques , Electrophoresis, Gel, Pulsed-Field , Hospitals, General , Anti-Bacterial Agents/pharmacology
Rev. Soc. Bras. Med. Trop ; 52: e20190257, 2019. tab, graf
Article in English | LILACS | ID: biblio-1057252


Abstract INTRODUCTION Mozambique is one of three countries with high prevalence of tuberculosis (TB), TB/human immunodeficiency virus coinfection, and multidrug-resistant TB. We aimed to describe Mycobacterium tuberculosis spoligotypes circulating among drug resistant (DR) strains from Beira, Mozambique comparing them with genotypes in the country. METHODS: We performed spoligotyping of 79 M. tuberculosis suspected of DR-TB compared all spoligotype patterns published on the international database and PubMed. RESULTS: Both in Beira and Mozambique (n=578), the main clades were Latin-American-Mediterranean, East-African-Indian, Beijing and T, with no extensively DR TB cases. CONCLUSIONS: Beira and Mozambique share the same population genetic structure of M. tuberculosis.

Humans , Genetic Variation/genetics , Tuberculosis, Multidrug-Resistant/microbiology , Mycobacterium tuberculosis/genetics , Phylogeny , Bacterial Typing Techniques , Genotype , Mozambique , Mutation/genetics
Biol. Res ; 52: 5, 2019. tab, graf
Article in English | LILACS | ID: biblio-1011408


BACKGROUND: A moderately thermophilic, slightly halophilic, aerobic, Gram-stain negative, bacterial strain, SLM16, was isolated from a mixed of seawater-sand-sediment sample collected from a coastal fumarole located in Whalers Bay, Deception Island, Antarctica. The aim was to screen for thermophilic microorganisms able to degrade primary amines and search for amine transaminase activity for potential industrial application. RESULTS: Identification and partial characterization of the microorganism SLM16 were carried out by means of morphological, physiological and biochemical tests along with molecular methods. Cells of strain SLM16 were non-motile irregular rods of 1.5-2.5 µm long and 0.3-0.45 µm wide. Growth occurred in the presence of 0.5-5.5% NaCl within temperature range of 35-55 °C and pH range of 5.5-9.5, respectively. The DNA G+C composition, estimated from ftsY gene, was 66% mol. Phylogenetic analysis using de 16S rRNA gene sequence showed that strain SLM16 belongs to the marine bacterial genus Albidovulum. CONCLUSION: Strain SLM16 is a moderate thermophilic Gram negative microorganisms which belongs to the marine bacterial genus Albidovulum and is closely related to Albidovulum inexpectatum species based on phylogenetic analysis. Additionally, amine-transaminase activity towards the arylaliphatic amine α-methylbenzylamine was detected.

Seawater/microbiology , DNA, Bacterial/genetics , Rhodobacteraceae/isolation & purification , Rhodobacteraceae/enzymology , Transaminases/metabolism , Phylogeny , RNA, Ribosomal, 16S/genetics , Bacterial Typing Techniques , Sequence Analysis, DNA , Rhodobacteraceae/classification , Antarctic Regions
Braz. j. microbiol ; 49(4): 816-822, Oct.-Dec. 2018. tab, graf
Article in English | LILACS | ID: biblio-974289


ABSTRACT Fifty seven soil-borne actinomycete strains were assessed for the antibiotic production. Two of the most active isolates, designed as Streptomyces ST-13 and DK-15 exhibited a broad range of antimicrobial activity and therefore they were selected for HPLC fractionation against the most suppressed bacteria Staphylococcus aureus (ST-13) and Chromobacterium violaceum (DK-15). LC/MS analysis of extracts showed the presence of polyketides factumycin (DK15) and tetrangomycin (ST13). The taxonomic position of the antibiotic-producing actinomycetes was determined using a polyphasic approach. Phenotypic characterization and 16S rRNA gene sequence analysis of the isolates matched those described for members of the genus Streptomyces. DK-15 strain exhibited the highest 16S rRNA gene sequence similarity to Streptomyces globosus DSM-40815 (T) and Streptomyces toxytricini DSM-40178 (T) and ST-13 strain to Streptomyces ederensis DSM-40741 (T) and Streptomyces phaeochromogenes DSM-40073 (T). For the proper identification, MALDI-TOF/MS profile of whole-cell proteins led to the identification of S. globosus DK-15 (accession number: KX527570) and S. ederensis ST13 (accession number: KX527568). To our knowledge, there is no report about the production of these antibiotics by S.globosus and S. ederensis, thus isolates DK15 and ST13 identified as S. globosus DK-15 and S.ederensis ST-13 can be considered as new sources of these unique antibacterial metabolites.

Streptomyces/isolation & purification , Streptomyces/metabolism , Anti-Bacterial Agents/biosynthesis , Phylogeny , Pyridones/metabolism , Soil Microbiology , Streptomyces/classification , Streptomyces/genetics , Benz(a)Anthracenes/metabolism , DNA, Bacterial/genetics , Bacterial Typing Techniques
Braz. j. microbiol ; 49(4): 900-908, Oct.-Dec. 2018. tab, graf
Article in English | LILACS | ID: biblio-974290


ABSTRACT Matrix Assisted Laser Desorption/Ionization and Time of Flight mass spectrometry (MALDI-TOF MS) is a powerful tool for the identification of bacteria through the detection and analysis of their proteins or fragments derived from ribosomes. Slight sequence variations in conserved ribosomal proteins distinguish microorganisms at the subspecies and strain levels. Characterization of Leptospira spp. by 16S RNA sequencing is costly and time-consuming, and recent studies have shown that closely related species (e.g., Leptospira interrogans and Leptospira kirschneri) may not be discriminated using this technology. Herein, we report an in-house Leptospira reference spectra database using Leptospira reference strains that were validated with a collection of well-identified Brazilian isolates kept in the Bacterial Zoonosis Laboratory at the Veterinary Preventive Medicine and Animal Health Department at Sao Paulo University. In addition, L. interrogans and L. kirschneri were differentiated using an in-depth mass spectrometry analysis with ClinProTools™ software. In conclusion, our in-house reference spectra database has the necessary accuracy to differentiate pathogenic and non-pathogenic species and to distinguish L. interrogans and L. kirschneri.

Humans , Bacterial Typing Techniques/methods , Tandem Mass Spectrometry/methods , Leptospira/isolation & purification , Leptospirosis/microbiology , Brazil , DNA, Bacterial/genetics , RNA, Ribosomal, 16S/genetics , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods , Leptospira/classification , Leptospira/genetics , Leptospira/chemistry
Braz. j. microbiol ; 49(4): 801-807, Oct.-Dec. 2018. tab, graf
Article in English | LILACS | ID: biblio-974302


ABSTRACT The present study aimed to compare two MALDI-TOF identification methods [(a) direct sample identification after pre-incubation; or (b) use of bacteria isolated on pre-culture)] to standard, traditional bench microbiology. A total of 120 quarter milk samples from 40 Holstein lactating cows were screened based on culture-positive results obtained by microbiological culture (reference method) with the following numbers of quarters positive per cow: 4 cows with 1, 8 cows with 2, 12 cows with 3 and 16 cows with 4 infected quarters per cow. For direct identification method, quarter milk samples (n = 120) were skimmed by centrifugation (10,000 × g/10 min) and pre-incubated at 37 ºC for 12 h. After pre-incubation, quarter milk samples were submitted to total bacterial count by flow cytometry and for a preparation protocol for bacterial ribosomal protein extraction followed by MALDI-TOF MS analysis. The direct MALDI-TOF MS identification method compared to microbiological culture correctly identified isolates of coagulase-negative Staphylococci (27.2%), Streptococcus agalactiae (21.8%), Staphylococcus aureus (14.2%), and Streptococcus uberis (5.2%). The pre-incubation protocol of milk samples, associated to the direct identification method by MALDI-TOF MS, did not increase the identification at species level (score >2.0) of pathogens causing subclinical mastitis in comparison to the method without previous incubation.

Animals , Female , Infant , Cattle , Staphylococcus/isolation & purification , Streptococcus/isolation & purification , Bacterial Typing Techniques/methods , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods , Milk/microbiology , Mastitis, Bovine/microbiology , Staphylococcus/genetics , Staphylococcus/chemistry , Streptococcus/genetics , Streptococcus/chemistry , Milk/chemistry , Mastitis, Bovine/physiopathology
Braz. j. microbiol ; 49(3): 641-646, July-Sept. 2018. tab, graf
Article in English | LILACS | ID: biblio-951817


Abstract DNA genotyping of Mycobacterium tuberculosis has been widely applied in the understanding of disease transmission in many countries. The purpose of this study was to genotype the strains of M. tuberculosis isolated in patients with new tuberculosis (TB) cases in Minas Gerais, as well as to compare the similarity, discriminatory power, and agreement of the clusters between the IS6110 Restriction Fragment Length Polymorfism (RFLP) and 12 loci Variable Number Tandem Repeat - Mycobacterial Interspersed Repetitive Units (MIRU-VNTR) techniques. It was observed that 32% (66/204) of the isolated strains in the RFLP-IS6110 and 50.9% (104/204) of the isolated strains in the MIRU-VNTR presented a similarity of equal to or above 85%. The RFLP-IS6110 and MIRU-VNTR proved to contain a high discriminatory power. The similarity index resulting from the RFLP showed no recent transmission. Good agreement was observed between the techniques when clusters were detected; however, the best epidemiological relationship was found when using the RFLP-IS6110.

Humans , Tuberculosis/microbiology , Polymorphism, Restriction Fragment Length , Bacterial Typing Techniques/methods , Minisatellite Repeats , Amplified Fragment Length Polymorphism Analysis/methods , Mycobacterium tuberculosis/isolation & purification , Brazil , Mycobacterium tuberculosis/classification , Mycobacterium tuberculosis/genetics
Int. j. odontostomatol. (Print) ; 12(1): 113-119, Mar. 2018. tab, graf
Article in English | LILACS | ID: biblio-893310


ABSTRACT: Molecular techniques that provide valuable information about the epidemiology of oral strains. The purpose of this study was to determine the genetic relatedness of 83 Enterococcus faecalis strains isolated from treated root canals. These strains were obtained from patients who were treated for persistent endodontic infections. E. faecalis isolates were molecular typed by Pulsed Field Gel Electrophoresis using Smal. Ten clonal groups and 13 pulse types with 38.7 % similarity for the less related strains were identified. Genetic heterogeneity among strains from different patients and a high level of genetic homogeneity among intrapatient strains were observed. Therefore, restriction endonuclease fingerprinting of genomic DNA from E. faecalis strains confirmed the polyclonality of the isolates obtained from the root canals of patients diagnosed with persistent endodontic infections, compared with other reports. These results provide additional data for a better understanding of the epidemiological aspects of root canal infections by E. faecalis.

RESUMEN: Las técnicas moleculares proporcionan información valiosa sobre la epidemiología de aislados orales. El propósito de este estudio fue determinar la relación genética de 83 cepas de Enterococcus faecalis aisladas de conductos radiculares tratados. Estas cepas se obtuvieron de pacientes que fueron tratados por infecciones endodónticas persistentes. Los aislados de E. faecalis se tipificaron molecularmente por electroforesis en gel de campo pulsado usando Smal. Se identificaron diez grupos clonales y 13 pulsotipos con un 38,7 % de similitud para las cepas menos relacionadas. Se observó heterogeneidad genética entre las cepas de diferentes pacientes y un alto nivel de homogeneidad genética entre las cepas intrapacientes. Por lo tanto, la toma de huellas dactilares a traves de restricción de ADN genómico de cepas de E. faecalis confirmó la policlonalidad de los aislados obtenidos de los conductos radiculares de pacientes diagnosticados con infecciones endodónticas persistentes, en comparación con otros informes. Estos resultados proporcionan datos adicionales para una mejor comprensión de los aspectos epidemiológicos de las infecciones del conducto radicular por E. faecalis.

Humans , Periapical Periodontitis/microbiology , Enterococcus faecalis/isolation & purification , Tooth Apex/microbiology , DNA, Bacterial/analysis , Bacterial Typing Techniques , Gram-Positive Bacterial Infections/microbiology , Electrophoresis, Gel, Pulsed-Field , Dental Pulp Cavity/microbiology
Salud pública Méx ; 60(1): 56-62, Jan.-Feb. 2018. tab, graf
Article in English | LILACS | ID: biblio-903842


Abstract: Objective: Due to the fact that K. variicola, K. quasipneumoniae and K. pneumoniae are closely related bacterial species, misclassification can occur due to mistakes either in normal biochemical tests or during submission to public databases. The objective of this work was to identify K. variicola and K. quasipneumoniae genomes misclassified in GenBank database. Materials and methods: Both rpoB phylogenies and average nucleotide identity (ANI) were used to identify a significant number of misclassified Klebsiella spp. genomes. Results: Here we report an update of K. variicola and K. Quasipneumoniae genomes correctly classified and a list of isolated genomes obtained from humans, plants, animals and insects, described originally as K. pneumoniae or K. variicola, but known now to be misclassified. Conclusions: This work contributes to recognize the extensive presence of K. variicola and K. quasipneumoniae isolates in diverse sites and samples.

Resumen: Objetivo: Identificar genomas mal clasificados de K. variicola, y K. quasipneumoniae en la base de datos del GenBank. Material y métodos: En el presente estudio se usaron tanto análisis filogenéticos usando rpoB como la identidad media de nucleótidos (ANI, por sus siglas en ingles) para identificar un número significativo de genomas del género Klebsiella. Resultados: Se reportó una actualización de genomas de K. variicola y K. quasipneumoniae correctamente clasificados y una lista de aquellos aislamientos obtenidos de seres humanos, plantas, animales e insectos, descritos originalmente como K. pneumoniae o K. variicola pero ahora se conoce que están mal clasificados. Conclusiones: Este trabajo contribuye a la presencia extensiva de aislamientos de K. variicola y K. quasipneumoniae en diversos sitios y muestras.

Animals , Plants/microbiology , Ursidae/microbiology , Klebsiella Infections/microbiology , Bacterial Typing Techniques , Genome, Bacterial , Insecta/microbiology , Klebsiella/classification , Phylogeny , DNA, Bacterial , Sequence Analysis, DNA
Frontiers of Medicine ; (4): 23-33, 2018.
Article in English | WPRIM | ID: wpr-772731


Two decades have passed since the first bacterial whole-genome sequencing, which provides new opportunity for microbial genome. Consequently, considerable genetic diversity encoded by bacterial genomes and among the strains in the same species has been revealed. In recent years, genome sequencing techniques and bioinformatics have developed rapidly, which has resulted in transformation and expedited the application of strategy and methodology for bacterial genome comparison used in dissection of infectious disease epidemics. Bacterial whole-genome sequencing and bioinformatic computing allow genotyping to satisfy the requirements of epidemiological study in disease control. In this review, we outline the significance and summarize the roles of bacterial genome sequencing in the context of bacterial disease control and prevention.We discuss the applications of bacterial genome sequencing in outbreak detection, source tracing, transmission mode discovery, and new epidemic clone identification. Wide applications of genome sequencing and data sharing in infectious disease surveillance networks will considerably promote outbreak detection and early warning to prevent the dissemination of bacterial diseases.

Bacteria , Genetics , Bacterial Infections , Epidemiology , Microbiology , Bacterial Typing Techniques , Disease Outbreaks , Genome, Bacterial , Genotype , Humans , Population Surveillance , Whole Genome Sequencing
J. appl. oral sci ; 26: e20170141, 2018. graf
Article in English | LILACS, BBO | ID: biblio-893685


Abstract Objective Staphylococcus aureus strains can be disseminated during dental treatments and occasionally lead to the contamination and infection of patients and dentists, which is an important public health problem. The dynamics of the airborne propagation and the genetic diversity of S. aureus isolated in an academic dental clinic environment were investigated using isoenzyme typing. Material and Methods The isoenzymes of 44 previously reported isolates were obtained from fresh cultures and extracted using glass beads. Nine isoenzymes were investigated using multilocus enzyme electrophoresis (MLEE). The genetic diversity and relationship among the strains (electrophoretic type - ET) were determined using statistics previously described by Nei25 (1972) and the SAHN grouping method (UPGMA algorithm). Results Clonal pattern analyses indicated a high level of genetic polymorphism occurring among the 33 ETs, which were grouped into five taxa. Each taxon presented one or more clusters that were moderately related and that contained two or more identical/highly related isolates, revealing seasonal airborne propagation in these dental clinic environments. Conclusions These data suggest the occurrence of active microevolutionary processes in S. aureus as well as the possibility of environmental propagation during a 14-month time span. Such findings are important to show that multiuser academic dental clinics can retain certain strains that are spreadable to different niches.

Seasons , Staphylococcus aureus/isolation & purification , Staphylococcus aureus/genetics , Dental Clinics/statistics & numerical data , Polymorphism, Genetic , Reference Values , Staphylococcal Infections/microbiology , Staphylococcus aureus/enzymology , Time Factors , Genetic Variation , Cluster Analysis , Cross Infection/microbiology , Equipment Contamination , Bacterial Typing Techniques/methods , Multilocus Sequence Typing/methods , Isoenzymes/isolation & purification
Braz. j. infect. dis ; 21(6): 656-659, Nov.-Dec. 2017. graf
Article in English | LILACS | ID: biblio-1039207


ABSTRACT Vancomycin-resistant Enterococcus faecium (VREfm) has emerged as an important global nosocomial pathogen, and this trend is associated with the spread of high-risk clones. Here, we determined the genetic and phenotypic features of 93 VREfm isolates that were obtained from patients in 13 hospitals in Vitória, Espírito Santo, Brazil, during 2012-2013. All the isolates were vancomycin-resistant and harbored the vanA gene. Only 6 (6.5%) of the VREfm isolates showed the ability to form biofilm. The 93 isolates analyzed belong to a single pulsed-field gel electrophoresis lineage and presented six subtypes. MLST genotyping showed that all VREfm belonged to ST412 (the high-risk clone, hospital-adapted). The present study describes the dissemination of ST412 clone in the local hospitals. The clonal spread of these ST412 isolates in the area we analyzed as well as other hospitals in southeastern Brazil supports the importance of identifying and controlling the presence of these microorganisms in health care-related services.

Humans , Cross Infection/microbiology , Gram-Positive Bacterial Infections/microbiology , Enterococcus faecium/genetics , Vancomycin-Resistant Enterococci/genetics , Bacterial Proteins , Brazil , Microbial Sensitivity Tests , Bacterial Typing Techniques , Enterococcus faecium/drug effects , Electrophoresis, Gel, Pulsed-Field , Multilocus Sequence Typing , Vancomycin-Resistant Enterococci/drug effects , Anti-Bacterial Agents/pharmacology