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Chinese Journal of Biotechnology ; (12): 1432-1445, 2022.
Article in Chinese | WPRIM | ID: wpr-927791


Bacterial multi-drug resistance (MDR) is a global challenge in the fields of medicine and health, agriculture and fishery, ecology and environment. The cross-region spread of antibiotic resistance genes (ARGs) among different species is one of the main cause of bacterial MDR. However, there is no effective strategies for addressing the intensifying bacterial MDR. The CRISPR-Cas system, consisting of clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR associated proteins, can targetedly degrade exogenous nucleic acids, thus exhibiting high application potential in preventing and controlling bacterial MDR caused by ARGs. This review briefly introduced the working mechanism of CRISPR-Cas systems, followed by discussing recent advances in reducing ARGs by CRISPR-Cas systems delivered through mediators (e.g. plasmids, bacteriophages and nanoparticle). Moreover, the trends of this research field were envisioned, providing a new perspective on preventing and controlling MDR.

Anti-Bacterial Agents , Bacteriophages/genetics , CRISPR-Cas Systems , Drug Resistance, Bacterial/genetics , Plasmids/genetics
Braz. j. biol ; 81(4): 954-961, Oct.-Dec. 2021. tab, graf
Article in English | LILACS | ID: biblio-1153438


Abstract The aim of present study is to characterize the resistance and virulence profile of enterococci isolated from aquaculture excavated ponds and masonry tanks (6 samples) in southern Brazil. Samples were cultured in selective medium, 10 colonies were randomly selected from each sample, which were identified by MALDI-TOF and tested against 13 antimicrobials. The presence of resistance (tetL, tetM, tetS, ermB and msrC) and virulence (ace, esp, agg, cylA and gelE) genes were determined by PCR. A total of 79 enterococci were identified, and Entecococcus faecalis (44.3%) and E. casseliflavus (36.7%) were the most prevalent species isolated. Sixty-five strains (82.3%) were resistant to at least one of the antimicrobials tested, whereas 27 (34.2%) strains were multiresistant. The overall percentages of antimicrobial resistant isolates were: 58.2% to rifampicin, 40.5% to fluoroquinolones, 36.7% to erythromycin and 30.4% to tetracycline. The tetL and tetM genes were found in 57.7% of the tetracycline-resistant strains; and msrC in 31.01% of erythromycin-resistant strains. The most frequently detected virulence factors were ace and gelE genes. Although limited to a single farm, these data suggest that aquaculture may be a reservoir of resistant and virulent enterococci. This study is the first step towards enhancing our understandingof distribution, resistance and virulence profile in enterococci isolated from fish farming environments in the south Brazil.

Resumo O objetivo do estudo apresentado é caracterizar o perfil de resistência e virulência de enterococos isolados de viveiros escavados e tanques de alvenaria (6 amostras) de uma pisicultura no Sul do Brasil. As amostras foram cultivadas em meio seletivo, 10 colônias foram selecionadas aleatoriamente de cada amostra, que foram identificadas por MALDI-TOF e testadas contra 13 antimicrobianos. A presença de genes de resistência (tetL, tetM, tetS, ermB e msrC) e virulência (ace, esp, agg, cylA e gelE) foi determinada por PCR. Foram identificados 79 enterococos, sendo Entecococcus faecalis (44,3%) e E. casseliflavus (36,7%) as espécies mais frequentes isoladas. Sessenta e cinco cepas (82,3%) eram resistentes a pelo menos um dos antimicrobianos testados, enquanto 27 (34,2%) eram multirresistentes. As porcentagens gerais de isolados resistentes a antimicrobianos foram: 58,2% para rifampicina, 40,5% para fluoroquinolonas, 36,7% para eritromicina e 30,4% para tetraciclina. Os genes tetL e tetM foram encontrados em 57,7% das cepas resistentes à tetraciclina; e msrC em 31,01% das cepas resistentes à eritromicina. Os fatores de virulência mais comumente detectados foram ace e gelE. Embora limitados a uma única fazenda, esses dados indicam que a aquicultura pode ser uma fonte de enterococos resistentes e virulentos. Este estudo é o primeiro passo para melhorar nosso entendimento da distribuição, resistência e perfil de virulência em enterococos isolados de ambientes de piscicultura no sul do Brasil.

Animals , Enterococcus/genetics , Drug Resistance, Bacterial/genetics , Brazil , Microbial Sensitivity Tests , Agriculture
Arq. bras. med. vet. zootec. (Online) ; 73(2): 302-310, Mar.-Apr. 2021. tab
Article in English | LILACS, VETINDEX | ID: biblio-1248934


Bovine clinical mastitis caused by Staphylococcus spp. is a serious and widespread disease in the world of dairy farming. Antimicrobial therapy is of fundamental importance in the prevention and treatment of infectious mastitis, but the indiscriminate use of antimicrobials acts as a determining factor for the spread of the disease. The present study evaluated the resistance profiles of 57 Staphylococcus spp. isolated from bovine clinical mastitis to beta-lactams and gentamicin, relating characteristics of phenotype (in vitro susceptibility tests) and genotype (detection and expression of genes encoding resistance - mecA, mecALGA251, blaZ, femA, femB, and aacA-aphD - using PCR and RT-PCR, respectively). One or more genes coding for resistance to different antimicrobials were detected in 50 Staphylococcus spp. isolates. The femA and femB genes were the most frequent (75.4% for both). The observed expression of the genes was as follows: blaZ (60%), femA (39.5%), aacA-aphD (50%), femB (32.6%), mecA (8.3%), and mecALGA251 (0%). Considering the relevance of the genus Staphylococcus to bovine mastitis, this study aimed to elucidate aspects regarding the genotypic and phenotypic profiles of these microorganisms so as to contribute to the development of effective strategies for mastitis control.(AU)

A mastite clínica bovina causada por Staphylococcus spp. é uma doença grave e generalizada no mundo da pecuária leiteira. A terapia antimicrobiana é de fundamental importância na prevenção e no tratamento da mastite infecciosa, mas o uso indiscriminado de antimicrobianos atua como fator determinante para a disseminação da doença. O presente estudo avaliou os perfis de resistência de 57 Staphylococcus spp. isolados de mastite clínica bovina em relação ao uso de betalactâmicos e gentamicina, relacionando características do fenótipo (testes de suscetibilidade in vitro) e genótipo (detecção e expressão de genes que codificam resistência - mecA, mecALGA251, blaZ, femA, femB, e aacA-aphD - usando PCR e RT-PCR, respectivamente). Um ou mais genes que codificam resistência a diferentes antimicrobianos foram detectados em 50 Staphylococcus spp. isolados. Os genes femA e femB foram os mais frequentes (75,4% para ambos). A expressão observada dos genes foi a seguinte: blaZ (60%), femA (39,5%), aacA-aphD (50%), femB (32,6%), mecA (8,3%) e mecALGA251 (0%). Considerando-se a relevância do gênero Staphylococcus para a mastite bovina, este estudo teve como objetivo elucidar aspectos referentes aos perfis genotípico e fenotípico desses microrganismos, a fim de contribuir para o desenvolvimento de estratégias eficazes para o controle da mastite.(AU)

Staphylococcus/isolation & purification , Gene Expression/genetics , beta-Lactam Resistance/genetics , Drug Resistance, Bacterial/genetics , Mastitis, Bovine/microbiology , Gentamicins , Reverse Transcriptase Polymerase Chain Reaction
Article in Chinese | WPRIM | ID: wpr-888470


OBJECTIVE@#To study the drug resistance of @*METHODS@#BALF specimens were collected from 245 children with RMPP who were admitted to the Children's Hospital Affiliated to Zhengzhou University from March 2016 to December 2020. A rapid cultured drug sensitivity assay was used to detect the resistance of MP isolates to nine commonly used antimicrobial drugs. The real-time PCR was used to measure MP DNA. The direct sequencing was used to detect gene mutations in MP 23SrRNA V region central ring.@*RESULTS@#Among the 245 BALF specimens, 207 tested positive for MP DNA, with a positive rate of 84.5%. The results of drug susceptibility test showed that the children with RMPP had a resistance rate of > 70% to macrolide antimicrobial drugs, with the highest resistance rate to clarithromycin, followed by roxithromycin, clindamycin, acetylspiramycin, erythromycin, and azithromycin, and these children had a resistance rate of < 5% to quinolone antimicrobial drugs. Among the 207 MP DNA-positive specimens, 41 (19.8%) had no drug-resistance gene mutations and 166 (80.2%) had drug-resistance gene mutations, among which 154 (74.4%) had an A→G mutation at 2063 locus of 23SrRNA V region central ring, 7 (3.4%) had an A→G mutation at 2064 locus, and 5 (2.4%) had mutations in both 2063 and 2064 loci. Among the 166 specimens with point mutations of the MP 23SrRNA gene, 159 (95.8%) had point mutations at 2063 locus. The A→G point mutation at 2063 locus of 23SrRNA V region central ring had a great impact on resistance to macrolide antimicrobial drugs. There was a significant difference in the distribution of alleles at 2063 locus between the children with resistance to clarithromycin, roxithromycin, clindamycin, acetylspiramycin, erythromycin, and azithromycin (@*CONCLUSIONS@#MP in the BALF of children with RMPP has a relatively high resistance rate to macrolide antimicrobial drugs. Resistance to macrolide antimicrobial drugs is closely associated with the A→G point mutation in the 23SrRNA gene, and the point mutation at 2063 locus of 23SrRNA V region central ring may affect the drug-resistance mechanism of MP.

Anti-Bacterial Agents/pharmacology , Bronchoalveolar Lavage Fluid , Child , Drug Resistance, Bacterial/genetics , Humans , Mycoplasma pneumoniae/genetics , Pneumonia, Mycoplasma/drug therapy
Chinese Journal of Biotechnology ; (12): 2503-2512, 2021.
Article in Chinese | WPRIM | ID: wpr-887816


The purpose of this study is to provide a simple and reliable genetic typing approach for molecular drug susceptibility test of Mycobacterium tuberculosis, through the developing of fluorescence molecular marker of rifampicin resistance gene rpoB. Eleven fluorescent molecular markers of the rpoB gene were established by using the sequence difference between the amino acid positions 531, 526, 516, 511 and 513 of rpoB gene of rifampicin-resistant strains and the alleles of rifampicin-sensitive strains, combined with the PARMS technique (Penta-primer amplification refractory mutation system). We used 104 clinical isolates of Mycobacterium tuberculosis to validate this marker and it was verified by sequencing as 100% correct. These samples were also tested with proportional drug sensitivity test. The coincidence rate was 94.23%. The molecular markers had high reliability for genotyping of rpoB gene. It can also detect low-concentration drug-resistant samples (511/533 unit point mutations) whose phenotypic susceptibility cannot be detected. The eleven sets of fluorescent molecular markers could cover 92%-96% of rpoB gene mutation types of rifampicin-resistant strains, and provide new idea for rapid detection of rifampin-resistant Mycobacterium tuberculosis.

Bacterial Proteins/genetics , DNA-Directed RNA Polymerases/genetics , Drug Resistance, Bacterial/genetics , Microbial Sensitivity Tests , Mutation , Mycobacterium tuberculosis/genetics , Reproducibility of Results , Rifampin/pharmacology , Technology
Article in English | WPRIM | ID: wpr-887716


Objective@#This study was performed to compare the genetic diversity, virulence, and antimicrobial resistance of @*Methods@#A total of 38 clinical strains and 19 strains from healthy individuals were isolated from the samples collected in Ma'anshan City, Anhui Province. Their taxonomy was investigated using concatenated @*Results@#The 57 @*Conclusions@#The taxonomy, virulence properties, and antibiotic resistance of

Aeromonas/pathogenicity , Case-Control Studies , Drug Resistance, Bacterial/genetics , Genetic Variation , Humans , Virulence Factors/genetics
Braz. j. biol ; 81(2): 424-436, 2021. tab, ilus
Article in English | LILACS, VETINDEX | ID: biblio-1153346


Pathogenic Yersinia enterocolitica (Y. enterocolitica) is one of the food-borne entero-pathogen responsible for yersiniosis in humans. The purpose of this research was to survey the prevalence, virulence-associated genes, and antimicrobial resistance of Y. enterocolitica isolated from meat and meat product samples in Egypt. Forty-one (5.9%) out of 700- samples of chicken meat, beef, ground beef, and sausage were positive Y. enterocolitica with a high prevalence in chicken meat (12%). Five virulence genes (ail, inv, ystA, ystB, and yadA) were characterized among 41 Y. enterocolitica isolates with variable frequencies. Among the strains tested, the ystB gene was detected with a high percentage (78.1%), followed by inv gene (70.7%), ail gene (14.6%), ystA gene (12.2%), and yadA gene (2.4%). A high resistance rate was estimated to amoxicillin-clavulanic acid (100%), followed by cefazolin (95%), ampicillin (65.9%), and doxycycline (51.2%), whilst a high sensitivity rate was observed to gentamicin and ciprofloxacin (97.6% each). Interestingly, the multidrug resistance was specified in the 70.7% of strains and showing 13 resistance patterns. Based on nucleotide sequence analysis of the 16s rRNA gene, the phylogenetic tree showed the genetic relatedness amongst Y. enterocolitica isolates. These findings highlighted the emergence of virulent and multidrug-resistant pathogenic Y. entrocolitica in retailed meat and meat products in Egypt.

A Yersinia enterocolitica patogênica (Y. enterocolitica) é um dos enteropatógenos de origem alimentar responsáveis pela yersiniose no ser humano. O objetivo desta pesquisa foi avaliar a prevalência, genes associados à virulência e resistência antimicrobiana de Y. enterocolitica isolada de amostras de carne e produtos à base de carne no Egito. Quarenta e um (5,9%) de 700 amostras de carne de frango, carne bovina, moída e linguiça foram Y. enterocolitica positivas, com alta prevalência em carne de frango (12%). Cinco genes de virulência (ail, inv, ystA, ystB e yadA) foram caracterizados entre 41 isolados de Y. enterocolitica com frequências variáveis. Entre as cepas testadas, o gene ystB foi detectado com uma alta porcentagem (78,1%), seguido pelo gene inv (70,7%), ail genes (14,6%), gene ystA (12,2%) e gene yadA (2,4%). Foi estimada uma alta taxa de resistência ao ácido amoxicilina-clavulânico (100%), seguida de cefazolina (95%), ampicilina (65,9%) e doxiciclina (51,2%), enquanto uma alta taxa de sensibilidade foi observada para gentamicina e ciprofloxacina (97,6% cada). Curiosamente, a resistência a múltiplas drogas foi especificada em 70,7% das cepas e mostrando 13 padrões de resistência. Com base na análise da sequência nucleotídica do gene rRNA 16s, a árvore filogenética mostrou a relação genética entre isolados de Y. enterocolitica. Esses achados destacaram o surgimento de Y. entrocolitica patogênica virulenta e multirresistente em carnes e produtos à base de carne no Egito.

Humans , Yersinia enterocolitica/genetics , Drug Resistance, Bacterial/genetics , Meat/microbiology , Meat Products/microbiology , Phylogeny , Virulence/genetics , RNA, Ribosomal, 16S , Egypt , Genotype , Anti-Bacterial Agents/pharmacology
Rev. Soc. Bras. Med. Trop ; 54: e05992020, 2021. tab
Article in English | LILACS | ID: biblio-1155526


Abstract INTRODUCTION: This study aimed to determine the role of genes encoding aminoglycoside-modifying enzymes (AMEs) and 16S rRNA methylase (ArmA) in Acinetobacter baumannii clinical isolates. METHODS: We collected 100 clinical isolates of A. baumannii and identified and confirmed them using microbiological tests and assessment of the OXA-51 gene. Antibiotic susceptibility testing was carried out using disk agar diffusion and micro-broth dilution methods. The presence of AME genes and ArmA was detected by PCR and multiplex PCR. RESULTS: The most and least effective antibiotics in this study were netilmicin and ciprofloxacin with 68% and 100% resistance rates, respectively. According to the minimum inhibitory concentration test, 94% of the isolates were resistant to gentamicin, tobramycin, and streptomycin, while the highest susceptibility (20%) was observed against netilmicin. The proportion of strains harboring the aminoglycoside resistance genes was as follows: APH(3′)-VIa (aphA6) (77%), ANT(2")-Ia (aadB) (73%), ANT(3")-Ia (aadA1) (33%), AAC(6′)-Ib (aacA4) (33%), ArmA (22%), and AAC(3)-IIa (aacC2) (19%). Among the 22 gene profiles detected in this study, the most prevalent profiles included APH(3′)-VIa + ANT(2")-Ia (39 isolates, 100% of which were kanamycin-resistant), and AAC(3)-IIa + AAC(6′)-Ib + ANT(3")-Ia + APH(3′)-VIa + ANT(2")-Ia (14 isolates, all of which were resistant to gentamicin, kanamycin, and streptomycin). CONCLUSIONS: High minimum inhibitory concentration of aminoglycosides in isolates with the simultaneous presence of AME- and ArmA-encoding genes indicated the importance of these genes in resistance to aminoglycosides. However, control of their spread could be effective in the treatment of infections caused by A. baumannii.

Acinetobacter baumannii/genetics , Bacterial Proteins , RNA, Ribosomal, 16S/genetics , Microbial Sensitivity Tests , Drug Resistance, Bacterial/genetics , Aminoglycosides/pharmacology , Methyltransferases , Anti-Bacterial Agents/pharmacology
Rev Bras Ginecol Obstet ; 42(8): 454-459, 2020. tab
Article in English | LILACS | ID: biblio-1137861


Abstract Objective Streptococcus agalactiae is an important pathogen in neonates and pregnant women. Neonatal invasive infections due to S. agalactiae are life-threatening and preventive strategies for this challenge of human have become a concern. The aim of the present study was to determine the prevalence of rectovaginal colonization, related risk factors and antibiotic resistance pattern of S. agalactiae among pregnant women in Iran. Methods The present study was performed on 240 pregnant women. Vaginal and rectal swabs were obtained from all of the women and then were transferred to the laboratory. The isolation and identification of S. agalactiae was performed by standard microbiological tests and polymerase chain reaction (PCR) assay. The antimicrobial susceptibility patterns of the isolates were determined by the Kirby-Bauer disk diffusion. Polymerase chain reaction was used to detect ermB and mefA genes in erythromycin-nonsusceptible isolates. Results Out of 240 pregnant women, 16 cases (6.7%) were colonized by S. agalactiae. There is no significant association between demographic-obstetric factors and maternal S. agalactiae colonization in the pregnant women. Linezolid, vancomycin and ampicillin were the most effective antibiotics against S. agalactiae. The ermB gene was present in 6 (35.29%) S. agalactiae isolates. However, the mefA gene was not detected in any of the isolates. Conclusion Given the relatively significant prevalence of S. agalactiae colonization in the pregnant women in the present study and the risk of serious neonatal infections, the screening of pregnant mothers for the bacteria seems necessary. Our findings highlight the importance of appropriate antibiotic prophylaxis during pregnancy for the prevention of early onset S. agalactiae-neonatal infection and comorbidity.

Humans , Female , Pregnancy , Adolescent , Adult , Young Adult , Rectum/microbiology , Streptococcal Infections/microbiology , Streptococcal Infections/epidemiology , Streptococcus agalactiae/drug effects , Vagina/microbiology , Streptococcus agalactiae/genetics , Carrier State/microbiology , Carrier State/epidemiology , Microbial Sensitivity Tests , Prevalence , Cross-Sectional Studies , Drug Resistance, Bacterial/genetics , Iran , Middle Aged , Anti-Bacterial Agents/pharmacology
Int. j. odontostomatol. (Print) ; 14(3): 448-456, 2020. tab, graf
Article in English | LILACS | ID: biblio-1114920


Enterococci are important nosocomial pathogens due to their intrinsic multiresistance and the acquisition of new antibiotic resistance genes (ARG). Enterococcus faecalis has been shown to be one of the main pathogens in persistent endodontic infections, therefore, the main objective of this study was to evaluate the phenotype and resistance genotype of strains of E. faecalis isolated from teeth with persistent endodontic lesions, to the most commonly prescribed antibiotics in dentistry. Thirteen strains of E. faecalis of different pulsotype were analyzed to evaluate the susceptibility to antibiotics, amoxicillin, amoxicillin/clavulanic acid, tetracycline, erythromycin and metronidazole, using the Epsilometer test (E- test) and the presence of beta-lactamases with nitrocefin test. Finally, the detection of ARG was performed with a molecular polymerase chain reaction (PCR) technique and confirmed by the sequencing of the amplification products. Fisher's exact test was used, using 95 % confidence. Regarding the phenotype of resistance, the evaluated strains, independent of the pulsotype, were totally resistant to the action of metronidazole. Antibiotics with higher minimum inhibitory concentration (MIC) after metronidazole include tetracycline and erythromycin. In contrast, lower MIC are applied to the combination of amoxicillin with clavulanic acid. The nitrocefin test was positive only in one strain. Genotypically, two genetically distant strains isolated from a single patient, presented a genotype of resistance to erythromycin, determined by the presence of the ermB gene. No statistically significant relationship was found between phenotypic resistance and the presence of ARG in relation to erythromycin (p> 0.05). It was concluded that isolates of E. faecalis from persistent endodontic infections showed phenotypes of resistance to several antimicrobial agents, all of which were susceptible to amoxicillin/clavulanic acid. Periodic evaluation of susceptibility to antibiotics is suggested as an important practice for the surveillance of antibiotic resistance in oral strains.

Los enterococos son importantes patógenos nosocomiales debido a su multi resistencia intrínseca y la adquisición de nuevos genes de resistencia a los antibióticos (ARG). Enterococcus faecalis es uno de los principales patógenos en infecciones endodónticas persistentes, por lo tanto, el objetivo principal de este estudio fue evaluar el fenotipo y el genotipo de resistencia de cepas de E. faecalis aisladas de dientes con lesiones endodóncicas persistentes, a los antibióticos comúnmente recetados en odontología. Se analizaron 13 cepas de E. faecalis de diferentes pulsotipos para evaluar la susceptibilidad a los antibióticos, amoxicilina, amoxicilina / ácido clavulánico, tetraciclina, eritromicina y metronidazol, utilizando la prueba de Epsilometría (E-test) y la presencia de beta-lactamasas con prueba de nitrocefina. Finalmente, la detección de ARG se realizó con una técnica molecular de reacción en cadena de la polimerasa (PCR) y se confirmó mediante la secuenciación de los productos de amplificación. Se utilizó la prueba exacta de Fisher, con un 95 % de confianza. En cuanto al fenotipo de resistencia, las cepas evaluadas, independientes del pulsotipo, fueron totalmente resistentes a la acción del metronidazol. Los antibióticos con los valores más altos de concentración mínima inibitoria (CMI) después del metronidazol incluyen tetraciclina y eritromicina. En contraste, las CMI mas bajas se aplican a la combinación de amoxicilina con ácido clavulánico. La prueba de nitrocefina fue positiva solo en una cepa. Genotípicamente, dos cepas distantes genéticamente, aisladas de un mismo paciente fueron positivas para el gen ermB. No se encontró una relación estadísticamente significativa entre la resistencia fenotípica y la presencia de ARG en relación con la eritromicina (p> 0,05). Se concluyó que los aislamientos de E. faecalis de infecciones endodónticas persistentes mostraron fenotipos de resistencia a varios agentes antimicrobianos, todos los cuales fueron susceptibles a amoxicilina / ácido clavulánico. Se sugiere una evaluación periódica de la susceptibilidad a los antibióticos como una práctica importante para la vigilancia de la resistencia a los antibióticos en las cepas orales.

Humans , Enterococcus faecalis/drug effects , Enterococcus faecalis/genetics , Dental Pulp Cavity/microbiology , Anti-Bacterial Agents/pharmacology , Tetracycline , Microbial Sensitivity Tests , Erythromycin , Polymerase Chain Reaction , Clavulanic Acid/pharmacology , Drug Resistance, Bacterial/genetics , Amoxicillin/pharmacology , Metronidazole
Mem. Inst. Oswaldo Cruz ; 115: e190407, 2020. tab
Article in English | LILACS | ID: biblio-1101275


BACKGROUND Early diagnosis of tuberculosis (TB) and identification of strains of Mycobacterium tuberculosis resistant to anti-TB drugs are considered the main factors for disease control. OBJECTIVES To standardise a real-time polymerase chain reaction (qPCR) assay technique and apply it to identify mutations involved in M. tuberculosis resistance to Isoniazid (INH) directly in Ziehl-Neelsen (ZN) stained slides. METHODS Were analysed 55 independent DNA samples extracted from clinical isolates of M. tuberculosis by sequencing. For application in TB diagnosis resistance, 59 ZN-stained slides were used. The sensitivity, specificity and Kappa index, with a 95% confidence interval (CI95%), were determined. FINDINGS The agreement between the tests was, for the katG target, the Kappa index of 0.89 (CI95%: 0.7-1.0). The sensitivity and specificity were 97.6% (CI95%: 87.7-99.9) and 91.7% (CI95%: 61.5-99.5), respectively. For inhA, the Kappa index was 0.92 (CI95%: 0.8-1.0), the sensitivity and specificity were 94.4% (CI95%: 72.7-99.8) and 97.3% (CI95%: 85.8-99.9), respectively. The use of ZN-stained slides for drug-resistant TB detection showed significant results when compared to other standard tests for drug resistance. MAIN CONCLUSIONS qPCR genotyping proved to be an efficient method to detect genes that confer M. tuberculosis resistance to INH. Thus, qPCR genotyping may be an alternative instead of sequencing.

Humans , Genetic Markers/genetics , Drug Resistance, Bacterial/genetics , Isoniazid/pharmacology , Mutation/genetics , Mycobacterium tuberculosis/genetics , Antitubercular Agents/pharmacology , DNA, Bacterial/genetics , Microbial Sensitivity Tests , Sensitivity and Specificity , Real-Time Polymerase Chain Reaction , Genotype , Mycobacterium tuberculosis/drug effects
Chinese Journal of Biotechnology ; (12): 2582-2597, 2020.
Article in Chinese | WPRIM | ID: wpr-878513


The discovery of antibiotics is a big revolution in human history, and its clinical application has saved countless lives. However, with the widespread and abuse of antibiotics, many pathogens have developed resistance, and even "Super Bacteria" resistance to multiple drugs have evolved. In the arms race between humans and pathogens, humans are about to face a situation where no medicine is available. Research on microbial antibiotic resistance genes, resistance mechanisms, and the spread of resistance has attracted the attention of many scientific researchers, and various antibiotic resistance gene databases and analysis tools have emerged. In this review, we collect the current databases that focus on antibiotics resistance genes, and discuss these databases in terms of database types, data characteristics, antibiotics resistance gene prediction models and the types of analyzable sequences. In addition, a few gene databases of anti-metal ions and anti-biocides are also involved. It is believed that this summary will provide a reference for how to select and use antibiotic resistance gene databases.

Anti-Bacterial Agents/pharmacology , Bacterial Infections , Drug Resistance, Bacterial/genetics , Drug Resistance, Microbial/genetics , Humans , Metals
Rev. chil. infectol ; 36(4): 455-460, ago. 2019. tab, graf
Article in Spanish | LILACS | ID: biblio-1042662


Resumen Introducción: El método de difusión de doble disco se presenta como una alternativa diagnóstica que permite identificar aislados de Staphylococcus aureus susceptibles a clindamicina, ante el aumento de resistencia a meticilina, reduciendo así la posibilidad de fallo en el tratamiento. Objetivo: Determinar la frecuencia de resistencia a clindamicina inducida por eritromicina en S. aureus resistentes a meticilina (SARM) aislados de niños paraguayos. Materiales y Métodos: Estudio observacional, descriptivo, de corte transversal. Se colectaron 145 aislados S. aureus que causaron infecciones de piel y tejidos blandos y osteo-articulares en pacientes pediátricos del Hospital Central del Instituto de Previsión Social en el período de diciembre-2012 a noviembre-2013. La resistencia a clindamicina se determinó por métodos automatizados y de difusión de doble disco. Se realizó reacción de polimerasa en cadena para genes ermA, ermB, ermC y msrA de aislados representativos. Resultados: La resistencia global a meticilina y clindamicina fue de 67 y 13%, respectivamente (11% atribuible al mecanismo de resistencia a clindamicina inducible). Los genes ermC y msrA fueron detectados individualmente en 25 y 17% de los aislados, respectivamente, mientras que un aislado presentó ambos genes en simultáneo. Discusión: La frecuencia de mecanismo de resistencia inducible a clindamicina señala la importancia de los métodos de difusión de doble disco en la práctica microbiológica, así como se encuentran en los límites de puntos de cortes considerados como aceptables para el uso de este antimicrobiano para infecciones cutáneas y osteo-articulares causadas por SARM.

Background: The double disc diffusion method is an alternative diagnostic that allows the identification of Staphylococcus aureus isolates apparently susceptible to clindamycin but that may develop resistance due to an induction phenomena, mainly asociated to the increase in resistance to methicillin, thus increasing the possibility of failure in the treatment. Aim: To determine the frequency of induced clindamycin resistance in methicillin-resistant S. aureus (MRSA) isolated from Paraguayan children. Materials and Methods: In this cross sectional study, we collected 145 S. aureus isolates that caused skin and soft tissue and osteoarticular infections in pediatric patients of the Central Hospital I.P.S. in the period from December-2012 to November-2013. Resistance to clindamycin was determined by automated methods and double disc diffusion. PCR was performed for ermA, ermB, ermC and msrA genes from representative isolates. Results: The global resistance to methicillin and clindamycin was 67 and 13%, respectively (11% attributable to the inducible mechanism). The ermC and msrA genes were detected individually in 25 and 17% of the isolates respectively while an isolate presented both genes simultaneously. Discussion: The frequency of inducible resistance to clindamycin indicates the importance of double disc diffusion methods in microbiological practice, as well as being within the cut off points considered acceptable for the use of this antibiotic for skin infections. and osteoarticular caused by MRSA.

Humans , Infant, Newborn , Infant , Child, Preschool , Child , Adolescent , Staphylococcal Infections/microbiology , Clindamycin/pharmacology , Drug Resistance, Bacterial/genetics , Methicillin-Resistant Staphylococcus aureus/drug effects , Anti-Bacterial Agents/pharmacology , Paraguay , Polymerase Chain Reaction , Cross-Sectional Studies , Drug Resistance, Bacterial/drug effects , Disk Diffusion Antimicrobial Tests , Methicillin-Resistant Staphylococcus aureus/isolation & purification , Genes, Bacterial
Biomédica (Bogotá) ; 39(supl.2): 117-129, ago. 2019. tab, graf
Article in Spanish | LILACS | ID: biblio-1038833


Resumen Introducción. La claritromicina es el antibiótico de primera línea para el tratamiento de la infección por Helicobacter pylori. La resistencia bacteriana se produce principalmente por mutaciones puntuales del gen ARN ribosómico 23S (ARNr 23S). Objetivo. Determinar la frecuencia de las mutaciones puntuales A2143G y A2142G del gen ARNr 23S asociadas con la resistencia de H. pylori a la claritromicina en muestras de pacientes con manifestaciones dispépticas en Medellín, región noroccidental de Colombia. Materiales y métodos. Se extrajo ADN a partir de muestras de biopsia gástrica obtenidas de pacientes con manifestaciones dispépticas atendidos en una unidad de endoscopia entre el 2016 y el 2017. Mediante reacción en cadena de la polimerasa (PCR), se amplificaron las regiones s y m del gen vacA y una región del gen ARNr 23S bacteriano. La presencia de las mutaciones A2142G y A2143G se determinó por la técnica de polimorfismos de longitud de fragmentos de restricción (RFLP) con las enzimas BbsI y BsaI, respectivamente. Resultados. Se encontró una prevalencia de infección de 44,2 % (175/396), según el informe de histopatología. En 143 de estas 175 muestras positivas se amplificaron las tres regiones del genoma bacteriano. Se identificaron las mutaciones A2143G y A2142G en 27 muestras (18,8 %; 27/143), la mutación más frecuente fue la A2143G (81,5 %; 22/27). Conclusiones. Hubo una gran prevalencia de mutaciones asociadas con la resistencia de H. pylori a la claritromicina en la población de estudio. Se requieren estudios adicionales para establecer la resistencia bacteriana en la población colombiana y, así, determinar los tratamientos de primera línea y de rescate.

Abstract Introduction: Clarithromycin is the first-line antibiotic for the treatment of Helicobacter pylori infection. Bacterial resistance is mainly due to the presence of specific mutations in the 23S ribosomal RNA (rRNA) gene. Objective: To determine the frequency of A2143G and A2142G specific mutations in the 23S rRNA gene associated with clarithromycin resistance of H. pylori in samples from patients with dyspeptic manifestations in Medellín, northwestern Colombia. Materials and methods: DNA was extracted from gastric biopsy samples of patients with dyspeptic manifestations seen at an endoscopy unit in Medellín between 2016 and 2017. PCR was performed to amplify the bacterial s and m vacA regions, and a region in the 23S rRNA gene. The presence of the A2142G and A2143G mutations was determined using the restriction fragment length polymorphism (RFLP) technique with the BbsI and BsaI enzymes, respectively. Results: The prevalence of infection was 44.2% (175/396), according to the histopathology report. The positive samples were analyzed and the three regions of the bacterial genome were amplified in 143 of the 175 samples. The A2143G and A2142G mutations were identified in 27 samples (18.8%, 27/143). The most frequent mutation was A2143G (81.5%, 22/27). Conclusions: We found a high prevalence of H. pylori mutations associated with clarithromycin resistance in the study population. Further studies are required to determine the bacterial resistance in the Colombian population in order to define first line and rescue treatments.

Adult , Aged , Female , Humans , Male , Middle Aged , Young Adult , RNA, Bacterial/genetics , RNA, Ribosomal, 23S/genetics , Helicobacter pylori/genetics , Helicobacter Infections/microbiology , Point Mutation , Clarithromycin/pharmacology , Genes, rRNA , Mutation, Missense , Drug Resistance, Bacterial/genetics , Genes, Bacterial , Anti-Bacterial Agents/pharmacology , Prevalence , Cross-Sectional Studies , Helicobacter pylori/isolation & purification , Helicobacter pylori/drug effects , Helicobacter Infections/epidemiology , Colombia/epidemiology , Dyspepsia/microbiology , Dyspepsia/epidemiology , Gastritis/microbiology , Gastritis/epidemiology
Rev. argent. microbiol ; 51(2): 179-183, jun. 2019.
Article in English | LILACS | ID: biblio-1013370


Enterococci are intrinsically resistant to several antimicrobial classes and show a great ability to acquire new mechanisms of resistance. Resistance to β-lactam antibiotics is a major concern because these drugs either alone or in combination are commonly used for the treatment of enterococcal infections. Ampicillin resistance, which is rare in Enterococcus faecium occurs in most of the hospital-associated Enterococcus faecium isolates. High-level resistance to ampicillin in E. faecium is mainly due to the enhanced production of PBP5 and/or by polymorphisms in the beta subunit of this protein. The dissemination of high-level ampicillin resistance can be the result of both clonal spread of strains with mutated pbp5 genes and resistance horizontal gene transfer.

Los enterococos son intrínsecamente resistentes a varias clases de antimicrobianos y presentan una gran capacidad para adquirir mecanismos de resistencia. La resistencia a los antibióticos p-lactámicos es preocupante porque estos fármacos solos o combinados se usan comúnmente para el tratamiento de las infecciones enterocócicas. La mayoría de los aislamientos hospitalarios de Enterococcus faecium presentan resistencia a la ampicilina, la cual es rara en Enterococcus faecalis. El alto nivel de resistencia a la ampicilina en E. faecium se debe principalmente a la hiperproducción de PBP5 y/o a polimorfismos en la subunidad beta de esta proteína. La propagación de esta resistencia puede deberse tanto a la diseminación clonal de cepas con genes pbp5 mutados como a la transferencia horizontal de genes.

Enterococcus faecium/drug effects , Enterococcus faecium/genetics , Drug Resistance, Bacterial/genetics , Ampicillin/antagonists & inhibitors , Ampicillin Resistance/genetics
Rev. chil. infectol ; 36(3): 304-311, jun. 2019. tab, graf
Article in Spanish | LILACS | ID: biblio-1013788


Resumen Introducción: La expresión de β-lactamasas CTX-M pertenecientes a los grupos 1 y 9 en Klebsiella pneumoniae produce grados altos de resistencia a ceftazidima, y presentan una amplia distribución mundial. Objetivo: Identificar y caracterizar los genes blaCTX-M-Grupo1 y blaCTX-M-Grupo9 en aislados de K. pneumoniae resistentes a ceftazidima en un hospital de San José de Cúcuta, Colombia. Material y Método: Se diseñaron partidores para la identificación de K. pneumoniae y los genes blaCTX-M mediante reacción de polimerasa en cadena (RPC). Posteriormente se realizó el análisis de la relación genética de estos aislados por medio de la RPC basada en secuencias repetitivas (RPC-REP). Resultados: Treinta y ocho por ciento de los 24 aislados identificados por RPC como K. pneumoniae presentaron los genes blaCTX-M-3, blaCTX-M-15 y blaCTX-M-32 (Grupo CTX-M-1) y 42% los genes blaCTX-M14, blaCTX-M-24 y blaCTX-M-27 (Grupo CTX-M-9). El análisis filogenético agrupó los aislados de K. pneumoniae en cuatro clusters, mostrando correlación en los clusters I, II y IV, al comparar los perfiles genéticos con el tipo de muestra y grupo de genes. Discusión: Se encontró una frecuencia similar de los genes blaCTX-M-Grupo1 y blaCTX-M-Grupo 9 en aislados de K. pneumoniae resistentes a ceftazidima. La correlación entre la RPC-REP con los grupos de CTX-M y el tipo de muestra reveló la presencia de tres patrones clonales.

Background: The expression of CTX-M β-lactamases belonging to groups 1 and 9 in Klebsiella pneumoniae produces high levels of resistance to ceftazidime, and they have a wide distribution worldwide. Aim: To identify and characterize the blaCTX-M-Group1 and blaCTX-M-Group9 genes in K. pneumoniae isolates resistant to ceftazidime in a hospital in San José de Cúcuta, Colombia. Material and Methods: Primers were designed for the identification of K. pneumoniae and blaCTX-M genes by PCR. Subsequently, the genetic relationship of these isolates was analyzed by REP-PCR. Results: A 38% of the 24 isolates identified by PCR as K. pneumoniae showed blaCTX-M-3. blaCTX-M-15 y blaCTX-M-32 genes (Group CTX-M-1) and 42% blaCTX-M14. blaCTX-M-24 y blaCTX-M-27 genes (Group CTX-M-9). The phylogenetic analysis grouped the K. pneumoniae isolates into 4 clusters, showing correlation in clusters I, II and IV, when comparing the genetic profiles with the type of sample and group of genes. Discussion: We found a similar frequency of blaCTX-M-Group 1 and blaCTX-M-Group 9 genes in isolates of K. pneumoniae resistant to ceftazidime. The correlation between the REP-PCR with the CTX-M groups and the type of sample revealed the presence of three clonal patterns.

Humans , Bacterial Proteins/genetics , beta-Lactamases/genetics , Drug Resistance, Bacterial/genetics , Molecular Typing , Klebsiella pneumoniae/genetics , Phylogeny , Bacterial Proteins/isolation & purification , beta-Lactamases/isolation & purification , Ceftazidime , Polymerase Chain Reaction , Colombia , Klebsiella pneumoniae/isolation & purification , Anti-Bacterial Agents
Rev. peru. med. exp. salud publica ; 36(2): 265-269, abr.-jun. 2019. tab, graf
Article in Spanish | LILACS | ID: biblio-1020777


RESUMEN Con el objetivo de reportar marcadores de resistencia plasmídica a quinolonas qnr en aislamientos clínicos de enterobacterias productoras de betalactamasas CTX-M, se realizó un estudio descriptivo, con aislamientos del cepario del proyecto TO-06/09 del Instituto Nacional de Salud del Niño. Se recuperaron 138 aislamientos. La susceptibilidad antimicrobiana se determinó por el método de disco difusión y la identificación de genes por reacción en cadena de la polimerasa. De los 138 aislados, 67 (48,5%) fueron positivos para proteínas qnr por el método genotípico. De los cuales 38 (56,7%) presentaron determinantes qnrB y 48 (71,6%) determinantes qnrS. Ningún aislado presentó determinantes qnrA. Se detectó determinantes qnr en aislamientos que presentaban betalactamasas CTX-M en una población no expuesta.

ABSTRACT Aimed at reporting markers of plasmid resistance to qnr quinolones in clinical isolates of CTX-M beta-lactamase-producing enterobacteria, a descriptive study was conducted with isolates from the strain repository of TO-06/09 project of the National Children´s Health Institute. 138 isolates were recovered. Antimicrobial susceptibility was determined by the diffusion disk method, and gene identification by polymerase chain reaction. Of the 138 isolates, 67 (48.5%) were genotypically positive for qnr proteins; of these, 38 (56.7%) had qnrB determinants and 48 (71.6%) had qnrS determinants. No isolate presented qnrA determinants. qnr determinants were detected in isolates containing CTX-M beta-lactamases in a non-exposed population.

Humans , beta-Lactamases/genetics , Quinolones/pharmacology , Enterobacteriaceae Infections/epidemiology , Anti-Bacterial Agents/pharmacology , Peru/epidemiology , Plasmids/genetics , Bacterial Proteins/genetics , Microbial Sensitivity Tests , Drug Resistance, Bacterial/genetics , Enterobacteriaceae/isolation & purification , Enterobacteriaceae/genetics , Enterobacteriaceae Infections/microbiology
Rev. peru. med. exp. salud publica ; 36(2): 270-274, abr.-jun. 2019. tab, graf
Article in Spanish | LILACS | ID: biblio-1020780


RESUMEN Con el objetivo de evaluar la susceptibilidad antimicrobiana y detectar mutaciones puntuales en el gen ARNr 23S en cepas de Helicobacter pylori se realizó un estudio transversal que incluyó a 95 pacientes con dispepsia atendidos en una clínica privada de Lima. Mediante endoscopía se colectaron biopsias de antro para el aislamiento de cepas de Helicobacter pylori para la evaluación de la susceptibilidad antimicrobiana empleando la técnica de microdilución en caldo. La detección de mutaciones puntuales se desarrolló mediante PCR-RFLP. El porcentaje de infección por Helicobacter pylori fue de 46,3%, se observaron valores de resistencia de 52,3% a claritromicina, 29,6% a metronidazol, 45,5% a levofloxacino y 4,6% a amoxicilina. El porcentaje de mutaciones puntuales A2142G y A2143G asociados a resistencia a claritromicina fue 43,5%. En conclusión, encontramos que las tasas de resistencia antimicrobiana y el porcentaje de cepas de Helicobacter pylori circulantes en una clínica privada de Lima fueron elevadas.

ABSTRACT In order to evaluate antimicrobial susceptibility and detect specific mutations in the 23S rRNA gene in Helicobacter pylori strains, a cross-sectional study was performed on 95 patients with dyspepsia treated in a private clinic in Lima. Antrum biopsies were collected by endoscopy for isolation and evaluation of antimicrobial susceptibility using the broth microdilution method. The detection of specific mutations was developed by PCR-RFLP. The percentage of infection by Helicobacter pylori was 46.3%. Resistance values of 52.3% to clarithromycin, 29.6% to metronidazole, 45.5% to levofloxacin, and 4.6% to amoxicillin were observed. The percentage of specific A2142G and A2143G mutations associated with clarithromycin resistance was 43.5%. In conclusion, we found that antimicrobial resistance rates and the percentage of Helicobacter pylori strains circulating in a private clinic in Lima were high.

Humans , Helicobacter pylori/isolation & purification , Helicobacter Infections/epidemiology , Dyspepsia/microbiology , Anti-Bacterial Agents/pharmacology , Peru , RNA, Ribosomal, 23S/genetics , Microbial Sensitivity Tests , Cross-Sectional Studies , Helicobacter pylori/drug effects , Helicobacter pylori/genetics , Helicobacter Infections/microbiology , Drug Resistance, Bacterial/genetics , Mutation
Rev. Soc. Bras. Med. Trop ; 52: e20180460, 2019. tab
Article in English | LILACS | ID: biblio-1041512


Abstract INTRODUCTION: The objective of this study was to characterize genes of aminoglycoside modifying enzymes (AMEs) in colonizing and infecting isolates of E. aerogenes harboring bla KPC from patients at a public hospital in Recife-PE, Brazil. METHODS: We analyzed 29 E. aerogenes clinical isolates resistant to aminoglycosides. AMEs genes were investigated by PCR and sequencing. RESULTS: Colonizing and infecting isolates mainly presented the genetic profiles aac(3)-IIa/aph(3')-VI or ant(2")-IIa/aph(3')-VI. This is the first report of aph(3')-VI in E. aerogenes harboring bla KPC in Brazil. CONCLUSIONS: The results highlight the importance in establishing rigorous methods for the surveillance of resistance genes, especially in colonized patients.

Humans , Enterobacter aerogenes/genetics , Drug Resistance, Bacterial/genetics , Enterobacteriaceae Infections/microbiology , Aminoglycosides/genetics , Anti-Bacterial Agents/pharmacology , Phenotype , Brazil , Microbial Sensitivity Tests , Polymerase Chain Reaction , Enterobacter aerogenes/isolation & purification
West Indian med. j ; 67(3): 226-228, July-Sept. 2018.
Article in English | LILACS | ID: biblio-1045848


ABSTRACT The main mechanism of quinolone resistance in Klebsiella (K) pneumoniae is caused by mutation of porin-related proteins and efflux pumps. This study aimed to investigate the prevalence of ciprofloxacin-resistant K pneumoniae in burns patients and to understand the role of the AcrAB multidrug efflux system on minimal inhibitory concentration (MIC) of ciprofloxacin. For this reason, 52 K pneumoniae samples were collected from burns patients and evaluated for the mechanism of ciprofloxacin resistance. The results demonstrated that 40 isolates of K pneumoniae were ciprofloxacin-resistant and 35 showed the mutation on gyrA locus. By inhibition of the efflux system, the MIC yield showed a significant decrease. Therefore, it could be concluded that the high rate of mutation on the gyrA locus in combination with quinolone resistance was responsible for ciprofloxacin resistance and by inhibition of AcrA, the resistance rate showed a significant decrease in K pneumoniae isolated from burns patients.

RESUMEN El principal mecanismo de resistencia a la quinolona en las Klebsiella (K) Pneumoniae tiene como causa la mutación de las porinas y las bombas de eflujo. Este estudio tuvo por objetivo investigar la prevalencia de las K pneumoniae resistentes a la ciprofloxacina en pacientes con quemaduras, así como entender el papel del sistema de eflujo multidroga AcrAB en la concentración inhibitoria mínima (CIM) de la ciprofloxacina. Por esta razón, se recogieron 52 muestras de K pneumoniae de pacientes con quemaduras, a fin de evaluar el mecanismo de resistencia a la ciprofloxacina. Los resultados mostraron que 40 aislados de K pneumoniae eran resistentes a la ciprofloxacina y 35 mostraron la mutación en el locus gyrA. Con la inhibición del sistema de eflujo, el rendimiento de CIM tuvo una disminución significativa. Por lo tanto, se pudo concluir que la alta tasa de mutación en el locus gyrA en combinación con la resistencia a la quinolona era responsable de la resistencia a la ciprofloxacina, y por la inhibición de AcrA, la tasa de resistencia mostró una disminución significativa en las K pneumoniae aisladas de los pacientes con quemaduras.

Humans , Male , Female , Burns/microbiology , Ciprofloxacin/pharmacology , Drug Resistance, Bacterial/genetics , Klebsiella pneumoniae/drug effects , Klebsiella pneumoniae/genetics , Mutation/genetics , Microbial Sensitivity Tests