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1.
Infectio ; 24(1): 42-49, ene.-mar. 2020. tab, graf
Article in Spanish | LILACS, COLNAL | ID: biblio-1090542

ABSTRACT

Resumen Objetivo: Determinar los mecanismos de resistencia antibiótica y la epidemiología molecular de aislados clínicos de Klebsiella pneumoniae resistentes a carbapenémicos. Materiales y métodos: 30 aislados multirresistentes de K. pneumoniae fueron obtenidos a partir de: urocultivo, aspirado traqueal, secreción de herida, sonda vesical, hemocultivo, líquido peritoneal, punta de catéter, colección abdominal y secreción bronquial. Los aislados fueron colectados de noviembre de 2012 a abril de 2013. La identificación y susceptibilidad antibiótica fue determinada por el sistema automatizado VITEK 2. Para la amplificación de genes de resistencia se empleó PCR, la determinación de las Secuencias Tipo (ST) fue obtenida por tipificación multilocus de secuencias (MLST) y la relación clonal fue establecida por electroforesis en gel de campo pulsado (PFGE). Resultados: Todos los aislados mostraron fenotipos multirresistentes, excepto a colistina y tigeciclina. El 100% de los aislados fue productor de la carbapenemasa KPC-2. La determinación de la presencia de genes codificantes de β-lactamasas de Espectro Extendido mostró que el 67% de los aislados fue positivo para el gen blaCTX-M, el 100% fue positivo para el gen blaSHV y 93% fue positivo para el gen blaTEM. El análisis de la relación clonal de los 30 aislados agrupó a 20 en un mismo pulso tipo. El análisis por MLST demostró que la ST predominante fue ST258 presente en el 60% de la población, seguida de ST1199 presente en el 20% de la población analizada. Conclusiones: Los resultados obtenidos demuestran la importancia de implementar y combinar estudios epidemiológicos, clínicos y moleculares para comprender la distribución de la resistencia entre bacterias de interés clínico.


Abstract Objective: To determine the mechanism of antibiotic resistance and molecular epidemiology of carbapenem resistant isolates of Klebsiella pneumoniae. Materials and Methods: 30 multidrug resistant isolates of K. pneumoniae were obtained from urine culture, tracheal aspirate, wound secretion, bladder catheter, blood culture, peritoneal fluid, catheter tip, abdominal collection, and bronchial secretion. K. pneumoniae isolates were collected between November 2012 and April 2013. Identification and susceptibility were determined by the VITEK 2 system. Resistance genes were identified by PCR, sequence type (ST) was established by multilocus sequence typing (MLST), and clonal relationship was defined by pulsed field gel electrophoresis (PFGE). Results: All isolates were multidrug resistant and susceptible to colistin and tigecycline. 100% of isolates produced KPC-2 carbapenemase. This study detected Extended Spectrum β-Lactamases enconding genes. 67% of isolates were positive for blaCTX-M, 100% were positive for blaSHV, and 93% of isolates were positive for blaTEM. Analysis of the clonal relationship clustered 20 isolates in the same clonal complex. Multilocus sequence typing showed the predominant sequence type ST 258 in 60% of population. ST 1199 were present in 20% of bacterial population. Conclusion: Molecular epidemiology, clinical research and molecular biology studies improve understanding of mechanisms of resistance distribution among bacteria of clinical interest.


Subject(s)
Humans , Carbapenem-Resistant Enterobacteriaceae , Klebsiella pneumoniae , Drug Resistance, Microbial , Epidemiologic Studies , Gene Amplification , Multilocus Sequence Typing , Clinical Studies as Topic
2.
Braz. j. infect. dis ; 24(1): 7-12, Feb. 2020. tab, graf
Article in English | LILACS | ID: biblio-1089323

ABSTRACT

ABSTRACT Background: This study aims to explore the epidemiology, clinical profile and strain characteristics of cryptococcosis from 2013 to 2017 in a major teaching hospital in China. Methods: Trends in antifungal drug susceptibility of 217 consecutive non-repetitive cryptococcal isolates collected from patients of an university hospital in China were analyzed between 2013 and 2017. Of those, 98 isolates were conserved for identification by internal transcribed spacer (ITS) sequencing and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) system. Multilocus sequence typing (MLST) was used to designate molecular types. Clinical characteristics of the 98 patients with cryptococcosis during the period of 2013-2017 were retrospectively evaluated. Results: There was a trend for gradual increase in the MIC range of fluconazole was from 2013 to 2017. The conserved 98 clinical cryptococcal isolates included 97 C. neoformans and one C. gattii, and 90 (91.8%) isolates belonged to ST5 genotype VNI. Out of the 98 patients with cryptococcosis, 28 (28.6%) were HIV-infected and 32 (32.7%) had no underlying diseases. HIV-infected patients had higher mortality than HIV-uninfected patients (28.6% vs 14.3%, p = 0.147). Conclusions: Most of the patients with cryptococcosis were not HIV-infected in this study, while patients with HIV had a higher mortality. Reduced susceptibility to fluconazole was observed among C. neoformans isolates, most of them belonged to ST5 genotype VNI having an impact on the effective dose of fluconazole.


Subject(s)
Humans , Male , Female , Adult , Middle Aged , Cryptococcosis/microbiology , Cryptococcosis/epidemiology , Hospitals, University/statistics & numerical data , Time Factors , Microbial Sensitivity Tests , China/epidemiology , Cross-Sectional Studies , Retrospective Studies , Statistics, Nonparametric , Cryptococcosis/drug therapy , Cryptococcus neoformans/isolation & purification , Cryptococcus neoformans/drug effects , Cryptococcus neoformans/genetics , Cryptococcus gattii/isolation & purification , Cryptococcus gattii/drug effects , Cryptococcus gattii/genetics , Multilocus Sequence Typing , Genotype , Antifungal Agents/therapeutic use
3.
Chinese Medical Journal ; (24): 2573-2585, 2020.
Article in English | WPRIM | ID: wpr-877863

ABSTRACT

BACKGROUND@#Carbapenemase-producing Klebsiella pneumoniae (CP-Kp) poses distinct clinical challenges due to extensively drug resistant (XDR) phenotype, and sequence type (ST) 11 is the most dominant blaKPC-2-bearing CP-Kp clone in China. The purpose of this current retrospective study was to explore the genetic factors associated with the success of XDR CP-Kp ST11 strains circulated in the intensive care unit (ICU) of a Chinese tertiary hospital.@*METHODS@#Six ST11 XDR CP-Kp strains were identified between May and December 2014 and validated by minimum inhibitory concentration examination, polymerase chain reaction, and pyrosequencing. The six ST11 XDR CP-Kp, as well as three multi-drug resistant (MDR) and four susceptible strains, were sequenced using single-molecule real-time method. Comprehensively structural and functional analysis based on comparative genomics was performed to identify genomic characteristics of the XDR ST11 CP-Kp strains.@*RESULTS@#We found that ST11 XDR blaKPC-2-bearing CP-Kp strains isolated from inpatients spread in the ICU of the hospital. Functionally, genes associated with information storage and processing of the ST11 XDR CP-Kp strains were more abundant than those of MDR and susceptible strains, especially genes correlative with mobile genetic elements (MGEs) such as transposons and prophages. Structurally, eleven large-scale genetic regions taken for the unique genome in these ST11 XDR CP-Kp strains were identified as MGEs including transposons, integrons, prophages, genomic islands, and integrative and conjugative elements. Three of them were located on plasmids and eight on chromosomes; five of them were with antimicrobial resistance genes and eight with adaptation associated genes. Notably, a new blaKPC-2-bearing ΔΔTn1721-blaKPC-2 transposon, probably transposed and truncated from ΔTn1721-blaKPC-2 by IS903D and ISKpn8, was identified in all six ST11 XDR CP-Kp strains.@*CONCLUSION@#Our findings suggested that together with clonal spread, MGEs identified uniquely in the ST11 XDR CP-Kp strains might contribute to their formidable adaptability, which facilitated their widespread dissemination in hospital.


Subject(s)
Anti-Bacterial Agents , Bacterial Proteins , China , Electrophoresis, Gel, Pulsed-Field , Hospitals , Humans , Klebsiella Infections/drug therapy , Klebsiella pneumoniae/genetics , Microbial Sensitivity Tests , Multilocus Sequence Typing , Pharmaceutical Preparations , Retrospective Studies , beta-Lactamases/genetics
4.
Article in English | WPRIM | ID: wpr-820819

ABSTRACT

OBJECTIVES: We investigated the characteristics of Streptococcus mutans in the national culture collection from Korea. Twenty-nine (dental plaque, n=27; endodontic infections, n=1; blood, n=1) isolates were included in this study.METHODS: Antimicrobial susceptibilities were tested using the disk diffusion test. Multilocus sequence typing (MLST), serotyping, and collagen-binding genes were used for polymerase chain reaction (PCR) and direct sequencing. A collagen-binding (to assess the adhesion properties) assay was performed. S. mutans demonstrated high susceptibility to antimicrobial agents. Differences in collagen-binding abilities of the cnm-positive and -negative groups were compared using the Mann-Whitney U test (P<0.05).RESULTS: MLST analyses revealed 25 sequence types (STs), 17 of which (ST213-ST229) contained new alleles. The strains were classified into four serotypes with the c type encompassing 79.3% of all strains, while the e, f, and k types representing 6.9% each. Analysis of the cnm and cbm genes, which encode the two surface adhesin components of S. mutans, revealed three cnm-positive strains, each displaying greater adhesion ability than those of the cnm-negative strains.CONCLUSIONS: This study highlights the presence of a wide variety of S. mutans genotypes in Korea. These findings may provide useful information regarding the pathogenesis of infectious diseases, such as dental caries.


Subject(s)
Alleles , Anti-Infective Agents , Bacteremia , Communicable Diseases , Dental Caries , Diffusion , Genotype , Inflammation , Korea , Molecular Epidemiology , Multilocus Sequence Typing , Polymerase Chain Reaction , Serogroup , Serotyping , Streptococcus mutans , Streptococcus
6.
Rev. Soc. Bras. Med. Trop ; 53: e20190422, 2020. tab, graf
Article in English | ColecionaSUS, LILACS, ColecionaSUS, SES-SP | ID: biblio-1136889

ABSTRACT

Abstract INTRODUCTION: The average annual incidence of cryptococcosis in Colombia is 0.23 cases per 100,000 inhabitants in the general population, and 1.1 cases per 1000 in inhabitants with Acquired Immune Deficiency Syndrome (AIDS). In addition, the causal fungus has been isolated from the environment, with serotypes A-B and C in different regions. This study aims to determine the genetic association between clinical and environmental isolates of C. neoformans/C. gattii in Colombia. METHODS: Multilocus sequence typing (MLST) was used to identify possible clones, providing information about the epidemiology, ecology, and etiology of this pathogen in Colombia. RESULTS: A total of 110 strains, both clinical (n=61) and environmental (n=49), with 21 MLST sequence types (ST) of C. neoformans (n=14STs) and C. gattii (n=7STs) were identified. The STs which shared clinical and environmental isolate sources were grouped in different geographical categories; for C. neoformans, ST93 was identified in six departments, ST77 in five departments; and for C. gattii, ST25 was identified in three departments and ST79 in two. CONCLUSIONS: High genetic diversity was found in isolates of C. neoformans/gattii by MLST, suggesting the presence of environmental sources harboring strains which may be sources of infection for humans, especially in immunocompromised patients; these data contribute to the information available in the country on the distribution and molecular variability of C. neoformans and C. gattii isolates recovered in Colombia.


Subject(s)
Humans , Cryptococcosis , Cryptococcus neoformans , Cryptococcus gattii , Genetic Variation , Mycological Typing Techniques , Colombia , Multilocus Sequence Typing , Genotype
7.
Mem. Inst. Oswaldo Cruz ; 115: e200371, 2020. tab, graf
Article in English | SES-SP, LILACS, SES-SP | ID: biblio-1135238

ABSTRACT

BACKGROUND Acinetobacter baumannii outbreaks have been associated with pandemic International Clones (ICs), but the virulence factors involved with their pathogenicity are sparsely understood. Pigment production has been linked with bacterial pathogenicity, however, this phenotype is rarely observed in A. baumannii. OBJECTIVES This study aimed to characterise the reddish-brown pigment produced by A. baumannii strains, and to determine its biosynthetic pathway by genomic approaches. METHODS Pigment characterisation and antimicrobial susceptibility were conducted by phenotypic tests. The clonal relationship was obtained by pulsed field gel electrophoresis (PFGE) and multi-locus sequence typing (MLST). The genome of an A. baumannii was obtained for characterisation of genes involved with pigment production. FINDINGS The pyomelanin was the pigment produced by A. baumannii. Strains were extensively drug resistant and belonged to the IC-5/ST79. The pyomelanin biosynthetic pathway was determined and presented a particular architecture concerning the peripheral (tyrB, phhB and hpd) and central (hmgB, hmgC and hmgR) metabolic pathway genes. The identification of a distant HmgA homologue, probably without dioxygenase activity, could explain pyomelanin production. Virulence determinants involved with adherence (csuA/BABCDE and a T5bSS-carrying genomic island), and iron uptake (basABCDEFGHIJ, bauABCDEF and barAB) were characterised. MAIN CONCLUSION There is a biosynthetic pathway compatible with the pyomelanin production observed in persistent A. baumannii IC-5 strains.


Subject(s)
Humans , Acinetobacter Infections/microbiology , Acinetobacter baumannii/drug effects , Acinetobacter baumannii/genetics , Biosynthetic Pathways/genetics , Melanins , beta-Lactamases , Microbial Sensitivity Tests , Electrophoresis, Gel, Pulsed-Field , Acinetobacter baumannii/isolation & purification , Multilocus Sequence Typing , Pandemics , Anti-Bacterial Agents/pharmacology
8.
Rev. chil. infectol ; 36(5): 585-590, oct. 2019. graf
Article in Spanish | LILACS | ID: biblio-1058084

ABSTRACT

Resumen Introducción: Listeria monocytogenes es un patógeno transmitido por alimentos que causa listeriosis, una enfermedad que puede presentarse como gastroenteritis febril o en una forma invasora que tiene altas tasas de mortalidad. Hasta el momento, ha sido poco estudiada la diversidad genética de cepas de L. monocytogenes aisladas desde pacientes, alimentos y fuentes ambientales en Chile. Objetivo: Caracterizar genéticamente cepas de L. monocytogenes de estos tres orígenes recibidas por el Instituto de Salud Pública de Chile (ISP) entre los años 2007 y 2014. Material y Métodos: Se seleccionaron 94 cepas de L. monocytogenes correspondientes a 94 pulsotipos diferentes identificados por electroforesis en gel de campo pulsado (PFGE), se extrajo ADN y se realizó serotipificación mediante reacción de polimerasa en cadena (RPC) y tipificación de secuencias multilocus (MLST). Resultados: El serotipo más común fue 4b (55,3%), seguido de 1/2a (25,5%), 1/2b (17%) y 1/2c (2,2%). Se identificaron 32 secuencias tipo (ST), de las cuales cuatro fueron nuevas, y las predominantes fueron ST1 (28,7%) y ST2 (13,8%). La totalidad de las cepas se agrupó en los Linajes I y II. Conclusiones: Se observó una gran variabilidad genética en las cepas de L. monocytogenes analizadas, siendo predominantes las secuencias tipo ST1 y ST2, ambas pertenecientes al Linaje I. Nuestros resultados contribuyen a conocer la estructura poblacional de este patógeno en Chile y su presencia en muestras clínicas, alimentos y el medio ambiente.


Background: Listeria monocytogenes is a foodborne pathogen that causes listeriosis, a disease that can present as febrile gastroenteritis or as an invasive form that has high mortality rates. So far, the genetic diversity of strains of L. monocytogenes isolated from patients, foods and environmental sources in Chile has been poorly studied. Aim: To characterize genetically L. monocytogenes strains received by the Institute of Public Health of Chile (ISP) between 2007 and 2014. Methods: We selected 94 strains of L. monocytogenes corresponding to 94 different pulsotypes identified by pulsed field gel electrophoresis (PFGE), DNA was extracted and serotyping was performed by polymerase chain reaction (PCR) and multilocus sequence typing (MLST). Results: The most common serotype was 4b (55.3%), followed by serotypes 1/2a (25.5%), 1/2b (17%) and 1/2c (2.2%). 32 sequence-type (ST) were identified, of which 4 were new, and the predominant ones were ST1 (28.7%) and ST2 (13.8%). All the strains of L. monocytogenes were grouped in Lineages I and II. Conclusions: A great genetic variability was observed in the strains of L. monocytogenes analyzed, being predominant the ST1 and ST2, both belonging to Lineage I. Our results contribute to know the population structure of this pathogen in Chile and its presence in clinical samples, food and the environment.


Subject(s)
Humans , Listeria monocytogenes/isolation & purification , Listeria monocytogenes/genetics , Time Factors , Genetic Variation , Serotyping , Chile , Polymerase Chain Reaction , Electrophoresis, Gel, Pulsed-Field , Environmental Microbiology , Multilocus Sequence Typing , Food Microbiology , Listeriosis/microbiology
9.
Article in English | WPRIM | ID: wpr-741141

ABSTRACT

BACKGROUND: Molecular epidemiological typing of Neisseria gonorrhoeae is crucial for monitoring the spread of resistant strains. As reference strains can be used for laboratory internal quality control, we genetically characterised the American Type Culture Collection (ATCC) gonococcal strains by Neisseria gonorrhoeae multiantigen sequence typing (NG-MAST) and porB sequence typing using public multilocus sequence typing (PubMLST). METHODS: Eight ATCC gonococcal reference strains (ATCC 19424, ATCC 31426, ATCC 35541, ATCC 43069, ATCC 43070, ATCC 49226, ATCC 49926, and ATCC 49981) from Culti-Loops (Thermo Fisher Scientific, USA) were cultured. After DNA extraction, porB and tbpB were amplified and sequenced. Sequence types (STs) and allele numbers were each determined by NG-MAST (http://www.ng-mast.net) and porB sequence typing using PubMLST (http://pubmlst.org/neisseria/porB/). RESULTS: ATCC 19424 was identified as ST 266 by NG-MAST, and as Allele 946 by PubMLST. ATCC31426 was assigned a novel ST by NG-MAST, and was assigned Allele 958 with 1.2% mismatch by PubMLST. ATCC 35541 was identified as ST 12 by NG-MAST, and as Allele 624 by PubMLST. ATCC 43069 and ATCC 43070 were both identified as ST 681 by NG-MAST, and as Allele 984 by PubMLST. ATCC 49226 was identified as ST 1572 by NG-MAST, and as Allele 2110 by PubMLST. ATCC 49926 and ATCC 49981 were both identified as ST 16496 by NG-MAST, and as Allele 928 by PubMLST. CONCLUSIONS: The ST data obtained for ATCC gonococcal reference strains by NG-MAST and porB sequence typing using PubMLST can be used for quality assurance of molecular epidemiological typing in clinical microbiological laboratories.


Subject(s)
Alleles , DNA , Multilocus Sequence Typing , Neisseria gonorrhoeae , Neisseria , Quality Control
10.
Article in English | WPRIM | ID: wpr-739141

ABSTRACT

No study has described Streptococcus dysgalactiae subsp. equisimilis (SDSE) isolates that cause repetitive infections (recurrence and reinfection). We compared the microbiological characteristics of SDSE causing repetitive infections with those causing single infections. Three patients with invasive infections were identified based on their medical records, and multiple SDSE isolates were collected at intervals over three weeks, using a laboratory repository. Isolates from 12 patients with single-episode infections served as controls. Six isolates were collected from three patients with first and second episodes of infection. All isolates causing either repetitive or single-episode infection were subjected to emm typing, multilocus sequence typing (MLST), pulsed-field gel electrophoresis (PFGE), and random amplified polymorphic DNA (RAPD) analyses. Amplification of five virulence genes (sicG, prtF1, prtF2, lmb, and cbp), biofilm formation (BF), and cell invasion abilities (CIAs) were measured as virulent phenotypes. We observed close genetic similarities in the data obtained by emm typing, MLST, PFGE, and RAPD in four isolates from two patients, suggesting recurrence, whereas two isolates from one patient indicated genetic differences in these data, suggesting re-infection. The presence of the five virulence genes and the BF and CIA measurements appeared not to contribute to repetitive infections, compared with isolates causing single-episode infection. In conclusion, clinicians encountering patients with repetitive infections should be aware of both possibilities: recurrence with closely related strains and reinfection with different strains.


Subject(s)
Biofilms , DNA , Electrophoresis, Gel, Pulsed-Field , Humans , Medical Records , Multilocus Sequence Typing , Phenotype , Recurrence , Streptococcus , Virulence
12.
Rev. Soc. Bras. Med. Trop ; 52: e20180419, 2019. graf
Article in English | LILACS | ID: biblio-990432

ABSTRACT

Abstract We report the first case of cryptococcosis due to Cryptococcus decagattii in an immunocompetent pediatric patient from an indigenous community in Argentina with a successful outcome. Two isolates (blood, cerebrospinal fluid) were genotyped by restriction fragment length polymorphism of the orotidine monophosphate pyrophosphorylase (URA5) gene as VGIV and identified by multi-locus sequence typing as C. decagattii. Matrix-assisted laser desorption/ionization time of flight mass spectrometry identification indicated genotype VGIII. The minimum inhibitory concentration of amphotericin B, fluconazole, itraconazole, and voriconazole was determined (cerebrospinal fluid: 0.25, 16, 0.12, and 0.12, blood: 0.25, 4, 0.12, and 0.06, respectively, all in mg/L).


Subject(s)
Humans , Female , Child , Cryptococcosis/microbiology , Cryptococcus/genetics , Argentina , Cryptococcosis/diagnosis , Cryptococcus/isolation & purification , Cryptococcus/classification , Multilocus Sequence Typing , Genotype
13.
Braz. j. microbiol ; 49(4): 695-702, Oct.-Dec. 2018. tab, graf
Article in English | LILACS | ID: biblio-974298

ABSTRACT

ABSTRACT Antarctica harbors a great diversity of microorganisms, including bacteria, archaea, microalgae and yeasts. The Pseudomonas genus is one of the most diverse and successful bacterial groups described to date, but only eight species isolated from Antarctica have been characterized. Here, we present three potentially novel species isolated on King George Island. The most abundant isolates from four different environments, were genotypically and phenotypically characterized. Multilocus sequence analysis and 16S rRNA gene analysis of a sequence concatenate for six genes (16S, aroE, glnS, gyrB, ileS and rpoD), determined one of the isolates to be a new Pseudomonas mandelii strain, while the other three are good candidates for new Pseudomonas species. Additionally, genotype analyses showed the three candidates to be part of a new subgroup within the Pseudomonas fluorescens complex, together with the Antarctic species Pseudomonas antarctica and Pseudomonas extremaustralis. We propose terming this new subgroup P. antarctica. Likewise, phenotypic analyses using API 20 NE and BIOLOG® corroborated the genotyping results, confirming that all presented isolates form part of the P. fluorescens complex. Pseudomonas genus research on the Antarctic continent is in its infancy. To understand these microorganisms' role in this extreme environment, the characterization and description of new species is vital.


Subject(s)
Phylogeny , Pseudomonas/isolation & purification , Pseudomonas/classification , Phenotype , Pseudomonas/genetics , Soil Microbiology , DNA, Bacterial/genetics , DNA, Ribosomal/genetics , RNA, Ribosomal, 16S/genetics , Multilocus Sequence Typing , Islands , Genotype , Antarctic Regions
14.
Braz. j. microbiol ; 49(4): 891-899, Oct.-Dec. 2018. tab, graf
Article in English | LILACS | ID: biblio-974311

ABSTRACT

ABSTRACT This study examined the antimicrobial susceptibility patterns and clonal complex (CC) characteristics of serogroup 6 Streptococcus pneumoniae isolates collected from children in Beijing, China, between 1997 and 2016. Serotypes were determined using the Quellung reaction, and the antimicrobial susceptibility profiles of the isolates were determined using the disc-diffusion method or by E-test. Sequence types (STs) were assigned based on multilocus sequence typing. A total of 250 isolates were examined, with 55.2%, 30.0%, 12.8%, and 2.0% of isolates identified as serotypes 6A, 6B, 6C, and 6D, respectively. All of the isolates were susceptible to levofloxacin and vancomycin, and the non-suceptibitility rate to penicillin was 41.6%. Eighty-two distinct STs, assigned to 13 CCs and 28 singletons, were identified. CC982 was the most prevalent CC amongst serotype 6A isolates (34%), followed by CC9789 and CC3173. Amongst serotype 6B isolates, CC90 and CC4542 were the most common, accounting for 25.3% and 14.7% of isolates respectively. Over the study period, the prevalence of CC982, CC4542, and CC4536 isolates showing susceptibility to penicillin and cefuroxime decreased, and the proportion of CC3173, CC9789, CC855, and CC902 isolates showing non-susceptibility to these two antibiotics increased.


Subject(s)
Humans , Male , Female , Child, Preschool , Child , Pneumococcal Infections/microbiology , Streptococcus pneumoniae/isolation & purification , Streptococcus pneumoniae/drug effects , Anti-Bacterial Agents/pharmacology , Penicillins , Phylogeny , Pneumococcal Infections/epidemiology , Streptococcus pneumoniae/classification , Streptococcus pneumoniae/genetics , Microbial Sensitivity Tests , China , Multilocus Sequence Typing , Beijing/epidemiology
15.
Braz. j. infect. dis ; 22(6): 487-494, Nov.-Dec. 2018. tab, graf
Article in English | LILACS | ID: biblio-984020

ABSTRACT

ABSTRACT Background: The rate of methicillin-resistant Staphylococcus aureus (MRSA) among the total of S. aureus isolates decreased to 35.3% in 2017 in China. It is unclear whether the molecular characteristics of S. aureus isolates have changed as the rate decreased. Objective: This study aimed to investigate the molecular characteristics and virulence genes profile of S. aureus isolates causing bloodstream infection and analyze the correlation between the prevalence rates of the common sequence types and MRSA. Methods: A total of 112 S. aureus strains from eight hospitals of four cities, including 32 MRSA isolates, were identified and evaluated through multilocus sequence typing, spa typing, and determination of virulence genes. Results: Twenty-five STs were identified, of which ST5 (21.4%) was the most prevalent, whereas the prevalence of ST239 correlated with the rate of MRSA among all S. aureus isolates. Forty-six spa types were identified, of which t2460 (14.3%) was the most common. clfa, hla, seb, fnbA and hlb were the prevailing virulence genes. 81.3% MRSA and 45.0% methicillin-sensitive S. aureus (MSSA) isolates harbored six or more tested virulence genes. ST5-t2460, seldom noted in bloodborne S. aureus isolates in China, was the most common clone. The prevalence of harboring six or more virulence genes in ST5-t2460 and ST188-t189 were 93.8% and 8.3%, respectively. Conclusion: ST5-t2460 was the most common clone in S. aureus causing bloodstream infection followed by ST188-t189, which had never been noted in China before. Moreover, ST5-t2460 harbored more virulence genes than ST188-t189, and the prevalence of ST239 clone decreased with the proportion of MRSA among all S. aureus isolates.


Subject(s)
Humans , Staphylococcus aureus/genetics , Staphylococcus aureus/pathogenicity , Virulence/genetics , Bacteremia/virology , Phenotype , Microbial Sensitivity Tests , Virulence Factors/genetics , Methicillin-Resistant Staphylococcus aureus/genetics , Methicillin-Resistant Staphylococcus aureus/pathogenicity , Molecular Typing , Multilocus Sequence Typing , Genotype
16.
J. pediatr. (Rio J.) ; 94(4): 380-389, July-Aug. 2018. tab, graf
Article in English | LILACS | ID: biblio-954633

ABSTRACT

Abstract Objective: Staphylococcus aureus is responsible for a large number of infections in pediatric population; however, information about the behavior of such infections in this population is limited. The aim of the study was to describe the clinical, epidemiological, and molecular characteristics of infections caused by methicillin-susceptible and resistant S. aureus (MSSA-MRSA) in a pediatric population. Method: A cross-sectional descriptive study in patients from birth to 14 years of age from three high-complexity institutions was conducted (2008-2010). All patients infected with methicillin-resistant S. aureus and a representative sample of patients infected with methicillin-susceptible S. aureus were included. Clinical and epidemiological information was obtained from medical records and molecular characterization included spa typing, pulsed-field gel electrophoresis (PFGE), and multilocus sequence typing (MLST). In addition, staphylococcal cassette chromosome mec (SCCmec) and virulence factor genes were detected. Results: A total of 182 patients, 65 with methicillin-susceptible S. aureus infections and 117 with methicillin-resistant S. aureus infections, were included in the study; 41.4% of the patients being under 1 year. The most frequent infections were of the skin and soft tissues. Backgrounds such as having stayed in day care centers and previous use of antibiotics were more common in patients with methicillin-resistant S. aureus infections (p ≤ 0.05). Sixteen clonal complexes were identified and methicillin-susceptible S. aureus strains were more diverse. The most common cassette was staphylococcal cassette chromosomemec IVc (70.8%), which was linked to Panton-Valentine leukocidin (pvl). Conclusions: In contrast with other locations, a prevalence of infections in children under 1 year of age in the city could be observed; this emphasizes the importance of epidemiological knowledge at the local level.


Resumo Objetivo: O Staphylococcus aureus é responsável por um grande número de infecções na população pediátrica; contudo, as informações sobre o comportamento dessas infecções nessa população são limitadas. O objetivo do estudo foi descrever as características clínicas, epidemiológicas e moleculares de infecções causadas por Staphylococcus aureus suscetíveis e resistentes à meticilina (MSSA-MSRA) em uma população pediátrica. Método: Um estudo transversal descritivo foi realizado em pacientes entre 0 e 14 anos de idade de três instituições de alta complexidade (2008-2010). Todos os pacientes infectados com S. aureus resistentes à meticilina e uma amostra representativa de pacientes infectados com S. aureus suscetíveis à meticilina foram incluídos. As informações clínicas e epidemiológicas foram obtidas de prontuários médicos, e a caracterização molecular incluiu tipagem spa, Eletroforese em Gel de Campo Pulsado (PFGE) e Tipagem de sequências multilocus (MLST). Além disso, o Cassete Cromossômico Estafilocócico mec (SCCmec) e genes de fatores de virulência foram detectados. Resultados: 182 pacientes, 65 com infecções por S. aureus suscetíveis à meticilina e 117 com infecções por S. aureus resistentes à meticilina, foram incluídos no estudo; 41,4% dos pacientes com menos de um ano de idade. As infecções mais frequentes foram da pele e dos tecidos moles. Os históricos como internações em centros de atendimento e o uso prévio de antibióticos foram mais comuns em pacientes com infecções por S. aureus resistentes à meticilina (p ≤ 0,05). Dezesseis complexos clonais foram identificados, e as cepas de S. aureus suscetíveis à meticilina foram mais diversificadas. O cassete mais comum foi o Cassete Cromossômico Estafilocócicomec IVc (70,8%), relacionado à leucocidina de panton-valentine (pvl). Conclusões: Em comparação a outros locais, observamos uma prevalência de infecções em crianças com menos de um ano de idade na cidade; o que enfatiza a importância de conhecer a epidemiologia em nível local.


Subject(s)
Humans , Male , Female , Infant, Newborn , Infant , Child, Preschool , Child , Adolescent , Skin Diseases, Infectious/microbiology , Staphylococcal Infections/microbiology , Soft Tissue Infections/microbiology , Virulence Factors/genetics , Methicillin-Resistant Staphylococcus aureus/genetics , Skin Diseases, Infectious/diagnosis , Staphylococcal Infections/diagnosis , Cross-Sectional Studies , Electrophoresis, Gel, Pulsed-Field , Soft Tissue Infections/diagnosis , Methicillin-Resistant Staphylococcus aureus/isolation & purification , Multilocus Sequence Typing
17.
Neotrop. ichthyol ; 16(1): e170157, 2018. tab, graf
Article in English | LILACS, VETINDEX | ID: biblio-895135

ABSTRACT

Although former studies on systematics and biogeography represent a progress on the knowledge of the tribe Glandulocaudini, none was grounded on molecular evidence. Thus, the first hypothesis of relationships for the tribe based on a multilocus analysis is presented, including all genera and most of the valid species. DNA sequences of Glandulocauda caerulea and Mimagoniates sylvicola were analyzed for the first time. A molecular clock analysis was used to estimate the origin of the Glandulocaudini and the approximate timing of cladogenetic events within the group. Glandulocaudini was recovered as monophyletic. No hypothesis recovered Glandulocauda as monophyletic, since G. melanopleura is sister to Lophiobrycon weitzmani while G. caerulea is closely related to Mimagoniates. The relationships within the latter genus were resolved. The molecular clock results indicate the origin of the Glandulocaudini during the Miocene with diversification in the group occurring from Neogene to Pleistocene. These results corroborated the hypothesis that its origin took place on the Brazilian crystalline shield with the subsequent occupation of the Atlantic Coastal drainages. Apparently, Pleistocene sea-level fluctuations might have shaped the distribution pattern of some species in Glandulocaudini.(AU)


Embora estudos prévios sobre sistemática e biogeografia representam um avanço no conhecimento da tribo Glandulocaudini, nenhum foi baseado em evidência molecular. Assim, a primeira hipótese de relações para a tribo com base em uma análise multilocus é apresentada, incluindo todos os gêneros e a maioria das espécies válidas. Sequências de DNA de Glandulocauda caerulea e Mimagoniates sylvicola foram analisadas pela primeira vez. Uma análise de relógio molecular foi utilizada para estimar a origem de Glandulocaudini e datas aproximadas de eventos cladogenéticos dentro do grupo. Glandulocaudini foi recuperada como monofilética. Nenhuma hipótese recuperou Glandulocauda como monofilético, uma vez que G. melanopleura é irmã de Lophiobrycon weitzmani e G. caerulea está proximamente relacionada a Mimagoniates. As relações dentro deste último gênero foram resolvidas. Os resultados do relógio molecular indicam que Glandulocaudini originou-se durante o Mioceno, com diversificação dentro do grupo ocorrendo desde o Neogeno até o Pleistoceno. Estes resultados corroboram a hipótese da sua origem no escudo cristalino brasileiro, com a subsequente ocupação das drenagens costeiras atlânticas. Aparentemente, as flutuações pleistocênicas do nível do mar podem ter moldado o padrão de distribuição de algumas espécies em Glandulocaudini.(AU)


Subject(s)
Animals , Characidae/genetics , Multilocus Sequence Typing/veterinary , Phylogeny , Drainage, Sanitary
18.
Article in English | WPRIM | ID: wpr-714436

ABSTRACT

BACKGROUND: The molecular characterization of Streptococcus dysgalactiae subsp. equisimilis (SDSE) has not yet been performed in Korea. This study aimed to find the differences or similarities in the clinical features, molecular epidemiological findings, and antimicrobial resistance patterns of SDSE from two countries (Korea and Japan). METHODS: SDSE isolates were collected from Korea (N=69) from 2012–2016 and Japan (N=71) from 2014–2016. Clinical characteristics, emm genotypes, and sequence types (STs) were compared. Microdilution tests were performed using different antimicrobials, and their resistance determinants were screened. RESULTS: Median ages were 69 years in Korea and 76 years in Japan. The most common underlying diseases were diabetes and malignancy. Blood-derived isolates comprised 36.2% and 50.7% of Korean and Japanese isolates, respectively; mortality was not different between the two groups (5.8% vs 9.9%, P=0.53). Among Korean isolates with 20 different combined ST-emm types, ST127-stG245 (N=16), ST128-stG485 (N=10), and ST138-stG652 (N=8) were prevalent. Among Japanese isolates with 29 different combined types, ST17-stG6792 (N=11), ST29-stG485 (N=7), and ST205-stG6792 (N=6) were prevalent. Resistance rates to erythromycin, clindamycin, and minocycline were 34.8%, 17.4%, and 30.4% in Korea and 28.2%, 14.1%, and 21.4% in Japan, respectively. CONCLUSIONS: SDSE infections commonly occurred in elderly persons with underlying diseases. There was a significant difference in the distribution of ST-emm types between the two countries. Antimicrobial resistance rates were comparable with different frequencies of resistance determinants in each country.


Subject(s)
Aged , Asian Continental Ancestry Group , Clindamycin , Erythromycin , Genotype , Humans , Japan , Korea , Minocycline , Mortality , Multilocus Sequence Typing , Streptococcus
19.
Article in English | WPRIM | ID: wpr-714434

ABSTRACT

BACKGROUND: Enterococcus faecium, especially vancomycin-resistant E. faecium (VREfm), is a major concern for patients with hematologic diseases. Exposure to antibiotics including fluoroquinolone, which is used as a routine prophylaxis for patients with hematologic (MH) diseases, has been reported to be a risk factor for infection with vancomycin-resistant eneterocci. We compared the characteristics of E. faecium isolates according to their vancomycin susceptibility and patient group (MH vs non-MH patients). METHODS: A total of 120 E. faecium bacteremic isolates (84 from MH and 36 from non-MH patients) were collected consecutively, and their characteristics (susceptibility, multilocus sequence type [MLST], Tn1546 type, and the presence of virulence genes and plasmids) were determined. RESULTS: Among the vancomycin-susceptible E. faecium (VSEfm) isolates, resistance to ampicillin (97.6% vs 61.1%) and high-level gentamicin (71.4% vs 38.9%) was significantly higher in isolates from MH patients than in those from non-MH patients. Notably, hyl, esp, and pEF1071 were present only in isolates with ampicillin resistance. Among the VREfm isolates, ST230 (33.3%) and ST17 (26.2%) were predominant in MH patients, while ST17 (61.1%) was predominant in non-MH patients. Plasmid pLG1 was more prevalent in E. faecium isolates from MH patients than in those from non-MH patients, regardless of vancomycin resistance. Transposon analysis revealed five types across all VREfm isolates. CONCLUSIONS: The antimicrobial resistance profiles and molecular characteristics of E. faecium isolates differed according to the underlying diseases of patients within the same hospital. We hypothesize that the prophylactic use of fluoroquinolone might have an effect on these differences.


Subject(s)
Ampicillin , Ampicillin Resistance , Anti-Bacterial Agents , Enterococcus faecium , Enterococcus , Gentamicins , Hematologic Diseases , Humans , Multilocus Sequence Typing , Plasmids , Risk Factors , Vancomycin , Vancomycin Resistance , Virulence
20.
Article in English | WPRIM | ID: wpr-715910

ABSTRACT

BACKGROUND: From January 2014 to December 2015, 69 clones of Enterobacter cloacae showing multidrug resistance to six classes of antimicrobial agents were collected from two medical centers in Korea. METHODS: Minimum inhibitory concentrations were determined using the E-test method, and 17 genes were detected using polymerase chain reaction (PCR). The epidemiological relatedness of the strains was identified using repetitive element sequence-based PCR and multilocus sequence typing. RESULTS: The 69 E. cloacae clones produced extended spectrum β lactamase (ESBL) and AmpC and showed multidrug resistance to cefotaxime, ceftazidime, and aztreonam. We identified the following sequence types: ST56 of type VI for ESBL SHV (N=12, 17.4%); ST53, ST114, ST113, and ST550 of types I, IV, VI, and VII, respectively, for CTX-M (N=11, 15.9%); and ST668 of type III for the carbapenemase NDM gene (N=1, 1.5%). The AmpC DHA gene (N=2, 2.89%) was confirmed as ST134, although its type was not identified, whereas EBC (MIR/ACT; N=18, 26.1%) was identified as ST53, ST24, ST41, ST114, ST442, ST446, ST484, and ST550 of types V, I, III, IV, VII, and VI, respectively. The formed subclasses were bla CTX-M-3 and bla CTX-M-22 by CTX-M-1, bla CTX-M-9 and bla CTX-M-125 by CTX-M-9, bla DHA-1 by DHA, and bla MIR-7 and bla ACT-15,17,18,25,27,28 by EBC (MIR/ACT). CONCLUSIONS: There were no epidemiological relationships between the gene products and the occurrence of resistance among the strains.


Subject(s)
Anti-Infective Agents , Aztreonam , Cefotaxime , Ceftazidime , Cloaca , Clone Cells , Drug Resistance, Multiple , Enterobacter cloacae , Enterobacter , Korea , Methods , Microbial Sensitivity Tests , Multilocus Sequence Typing , Polymerase Chain Reaction
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