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1.
Infect Genet Evol ; : 104362, 2020 May 15.
Artigo em Inglês | MEDLINE | ID: mdl-32422352

RESUMO

Determining the source and genetic characteristics of the imported pathogen is critical in the control of infectious diseases. Here, we reported the investigation of an imported cholera case in China in 2018 with a recent travel history in Nepal and India. Stool culture from the patient was identified as Vibrio cholerae serogroup O1, biotype El Tor, serotype Ogawa. The strain 2018HL24 possessed intact Vibrio seventh pandemic island I (VSP-I), Vibrio pathogenicity Island 1 and 2 (VPI-1, VPI-2). A VSP-II variant with a 13 kb deletion was also detected, which was identical to those observed in V. cholerae in Cluster "Nepal-4". Phylogenetic analysis based on core genome SNPs showed that the isolate was most closely related to the V. cholerae isolated in northern India not far from the border of Nepal in 2012 (16 SNPs). Combining the epidemiological data with phylogenetic analysis results, we speculate that the patient may got infected in Nepal-India region.

2.
Emerg Microbes Infect ; 9(1): 605-615, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32178586

RESUMO

The source of secondary lower respiratory tract bacterial infections in influenza patients is not fully understood. A case-control study was conducted during the 2017-2018 influenza epidemic period in Beijing, China. Nasopharyngeal swabs were collected from 52 virologically confirmed influenza patients and 24 healthy medical staff. The nasopharyngeal microbiota taxonomic composition was analysed using high-throughput sequencing of the 16S rRNA gene V3-V4 regions. The super-dominant pathobiontic bacterial genus (SDPG) was defined as that accounting for >50% of sequences in a nasopharyngeal swab. We attempted to isolate bacteria of this genus from both nasopharyngeal swabs and lower-respiratory tract samples and analyse their genetic similarities. We observed a significantly lower taxonomy richness in influenza cases compared with healthy controls. A SDPG was detected in 61% of severe cases but in only 24% of mild cases and 29% of healthy controls. In 10 cases, the species isolated from lower-respiratory tract infection sites were identified as belonging to the nasopharyngeal microbiota SDPG. Genetically identical strains were isolated from both nasopharyngeal swabs and lower-respiratory tract infection sites, including 23 Acinetobacter baumannii strains from six severe cases, six Klebsiella pneumoniae strains from two severe cases, five Pseudomonas aeruginosa strains from one severe and one mild case, and four Corynebacterium striatum strains from two severe cases. The SDPG in the nasopharyngeal microbiota are the likely cause of subsequent infection in influenza patients.


Assuntos
Infecções Bacterianas , Coinfecção , Influenza Humana , Microbiota , Nasofaringe/microbiologia , Adulto , Idoso , Infecções Bacterianas/complicações , Feminino , Humanos , Influenza Humana/complicações , Masculino , Pessoa de Meia-Idade
3.
Am J Infect Control ; 48(1): 26-32, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31358417

RESUMO

BACKGROUND: Increased percentage of Pseudomonas aeruginosa from bronchoalveolar lavage fluid of patients in June 2016 was observed. P aeruginosa were also obtained from flexible bronchoscope and rinse water in the microbiological surveillance in June 2016. METHODS: Reprocessing procedure of bronchoscope was assessed, and environmental samples were collected. P aeruginosa isolates recovered from bronchoalveolar lavage fluid of patients between May and September 2016 and environment were characterized using multilocus sequence typing and pulsed-field gel electrophoresis. RESULTS: A novel multilocus sequence type (ST) of P aeruginosa was defined as ST 2387. ST671 and ST 2387 were both cultured from bronchoscopes and connecting tube in manual reprocessing cleaning equipment. One strain from a patient was indistinguishable from the clones obtained from the bronchoscope and connecting tube revealed by pulsed-field gel electrophoresis. Two strains from 2 patients from the burn intensive care unit were identical, and highly related to 2 other strains from the burn intensive care unit. The persistence of P aeruginosa in bronchoscopes, connecting tubes, and final rinse water was terminated by replacement of the connecting tube. CONCLUSIONS: We report a pseudo-outbreak of P aeruginosa associated with bronchoscope, for which connecting tube was the hidden reservoir for contaminating bronchoscopes. This highlights that effective measures are needed to control the bacterial load in final rinsing water to protect reusable equipment from contamination in reprocessing and cleaning.

4.
Int J Med Microbiol ; 310(1): 151357, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31570247

RESUMO

Understanding the evolutionary path of M. catarrhalis from macrolide-susceptible to macrolide-resistant organism, is important for hindering macrolide resistance from propagation. Multilocus sequence typing (MLST), pulsed-field gel electrophoresis (PFGE) and whole genome SNP typing (WGST), as useful and practical typing tools, have both advantages and disadvantages. We studied the utility of these 3 typing methods, including the level of agreement, consistency and drawbacks, in characterizing M. catarrhalis clones and clonal complexes. We focused on four clonal complexes [CC224, CC363, CC449 (CCN10) and CC446 (CCN08)] and found that PFGE and WGST had a high level of agreement and a proper consistency of the same clone or very closely related clones, while MLST is less discriminatory for different clones. Furthermore, we also established an evolutionary distance cut-off value for "The same clone". Moreover, we detected macrolide-resistant M. catarrhalis in CC224, which had previously been considered as a macrolide-susceptible clonal complex. A higher number of isolates belonged to ST215 compared to ST446, implying that ST215 is more likely to be the primary founder. Our study also demonstrated that all the four clonal complexes belong to the M. catarrhalis lineage 1, which is considered to be related to increased virulence potential and serum resistance. We also observed that copB II was highly related to CC449 and LOS type B was mainly confined in CC224. In conclusion, these findings provide further insight into the evolutionary characteristics of M. catarrhalis.

5.
Emerg Infect Dis ; 25(11): 2021-2030, 2019 11.
Artigo em Inglês | MEDLINE | ID: mdl-31600132

RESUMO

Invasive group B Streptococcus (GBS) remains a leading cause of illness and death among infants globally. We conducted prospective and retrospective laboratory-based surveillance of GBS-positive cultures from infants <3 months of age in 18 hospitals across China during January 1, 2015-December 31, 2017. The overall incidence of GBS was 0.31 (95% CI 0.27-0.36) cases/1,000 live births; incidence was 0-0.76 cases/1,000 live births across participating hospitals. The case-fatality rate was 2.3%. We estimated 13,604 cases of GBS and 1,142 GBS-associated deaths in infants <90 days of age annually in China. GBS isolates were most commonly serotype III (61.5%) and clonal complex 17 (40.6%). Enhanced active surveillance and implementation of preventive strategies, such as maternal GBS vaccination, warrants further investigation in China to help prevent these infections.

6.
Artigo em Inglês | MEDLINE | ID: mdl-31570405

RESUMO

Colistin is a drug of last resort for the treatment of many multidrug resistant Gram-negative bacteria, including Klebsiella pneumoniae However, bacteria readily acquire resistance to this antibiotic via lipopolysaccharide modifications caused by spontaneous mutations or from enzymes acquired by lateral gene transfer. The fitness cost associated with these modifications remains poorly understood. In this study, we show that colistin-resistant K. pneumoniae are more susceptible to killing by a newly isolated lytic phage than the colistin sensitive parent strain. We observe this behavior for colistin-resistance conferred by a horizontally transferred mcr-1 containing plasmid and also from the inactivation of the chromosomal gene mgrB By measuring zeta potentials, we found that the phage particles were negatively charged at neutral pH and that colistin-resistant bacteria had less negative zeta potentials than did wildtype. These results suggest that the decreased negative surface charge of colistin-resistant cells lowers the electrostatic repulsion between the phage and bacteria, thereby promoting phage adherence and subsequent infection. To further explore this, we tested the effect of phage treatment on K. pneumoniae growing in several different environments. We found that colistin-resistant cells were more susceptible to phage than were the wildtype cells when growing in biofilms or infected moth larvae and when colonizing the mammalian gut. A better understanding of these fitness costs may lead to new treatment approaches that minimize the emergence and spread of colistin-resistant pathogens in human and environmental reservoirs.

7.
BMC Infect Dis ; 19(1): 812, 2019 Sep 18.
Artigo em Inglês | MEDLINE | ID: mdl-31533652

RESUMO

BACKGROUND: Invasive group B Streptococcus (GBS) disease in Chinese infants has gradually gained attention in recent years, but the molecular epidemiology of the pathogen is still not well known. METHODS: This multicenter study retrospectively investigated distribution of capsular serotypes, sequence types (STs), and hypervirulent GBS adhesin gene (hvgA) in clinical GBS isolates that caused invasive disease in infants aged < 3 months of age in southern mainland China between January 2013 and June 2016. Genes for antibiotic resistance to tetracycline, erythromycin, and clindamycin were also examined. RESULTS: From a total of 93 GBS isolates taken from 34 early-onset disease (EOD, 0-6 days after birth) and 59 late-onset disease (LOD, 7-89 days after birth) cases, four serotypes were identified: serotypes III (79.6%), Ib (12.9%), Ia (4.3%), and V (3.2%). Serotype III accounted for 73.5% of EOD and 83.1% of LOD and was responsible for 75.5% of cases involving meningitis. Fifteen STs were found, with the majority being ST17 (61.3%), ST12 (7.5%), ST19 (7.5%), and others (23.7%). 96.8% of STs belonged to only five clonal complexes (CCs): CC17 (64.5%), CC10 (12.9%), CC19 (9.7%), CC23 (6.5%), and CC1 (3.2%). The hvgA gene was detected in 66.7% of GBS isolates and 95% of CC17 isolates, all of which were serotype III except one serotype Ib/CC17 isolate. A large proportion of GBS isolates were found to be resistant to tetracycline (93.5%), clindamycin (65.5%), and erythromycin (60.2%). Genes of tetO (74.7%) and tetM (46.0%) were found in tetracycline resistant isolates, linB (24.6%) in clindamycin resistant isolates, and ermB (87.5%) and mefA (3.6%) in erythromycin resistant isolates. CONCLUSION: Our results reveal higher prevalence of serotype III, ST17, CC17, hvgA expressing, and antibiotic resistant GBS isolates than previously reported in southern mainland China. This study provides guidance for appropriate measures of prevention and control to be taken in the future.


Assuntos
Infecções Estreptocócicas/diagnóstico , Streptococcus agalactiae/isolamento & purificação , Adesinas Bacterianas/genética , Antibacterianos/farmacologia , Antibacterianos/uso terapêutico , China/epidemiologia , DNA Bacteriano/química , DNA Bacteriano/metabolismo , Farmacorresistência Bacteriana/efeitos dos fármacos , Humanos , Lactente , Recém-Nascido , Tipagem de Sequências Multilocus , Prevalência , Estudos Retrospectivos , Sorogrupo , Infecções Estreptocócicas/tratamento farmacológico , Infecções Estreptocócicas/epidemiologia , Infecções Estreptocócicas/patologia , Streptococcus agalactiae/genética
8.
Artigo em Inglês | MEDLINE | ID: mdl-31448241

RESUMO

Approximately 85% of cases of Legionnaires' disease are caused by Legionella pneumophila serogroup 1. In this study, we analyzed the distribution of lag-1 alleles, ORF 7 and ORF 8 genes of lipopolysaccharide (LPS) and sequence-based types of 616 L. pneumophila serogroup 1 strains isolated in Japan (206 clinical, 225 environmental) and China (13 clinical and 172 environmental). The lag-1 gene was harbored by significantly more of the clinical isolates compared with the environmental isolates (90.3 vs. 19.1% and 61.6 vs. 3.0%, respectively; both P < 0.001). ORF 7 genes were detected in 51.0% of Japanese clinical and 36.0% of Japanese environmental (P = 0.001) isolates, as well as 15.3% of Chinese clinical and 9.9% of Chinese environmental isolates (P = 0.544). ORF 8 genes were detected in 12.1% of Japanese clinical and 5.8% of Japanese environmental (P = 0.017) isolates, as well as 7.7% of Chinese clinical and 3.4% of Chinese environmental isolates (P = 0.388). The Japanese and Chinese isolates were assigned to 203 and 36 different sequence-types (ST), respectively. ST1 was predominant. Most isolates with the same ST also had the same lag-1, ORF 7, and ORF 8 gene subgroups. In conclusion, the lag-1 was present in most of the clinical isolates, but was absent from most of the environmental isolates from both China and Japan, regardless of the water source and SBT type. PCR-based serotyping and subgrouping methods can be used to define a hierarchy of virulence genotypes that require stringent surveillance to prevent human disease.

9.
J Clin Microbiol ; 57(9)2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31315959

RESUMO

Corynebacterium striatum is an emerging multidrug-resistant (MDR) pathogen that occurs primarily among immunocompromised and chronically ill patients. However, little is known about the genomic diversity of C. striatum, which contributes to its long-term persistence and transmission in hospitals. In this study, a total of 192 C. striatum isolates obtained from 14 September 2017 to 29 March 2018 in a hospital in Beijing, China, were analyzed by antimicrobial susceptibility testing and pulsed-field gel electrophoresis (PFGE). Whole-genome sequencing was conducted on 91 isolates. Nearly all isolates (96.3%, 183/190) were MDR. The highest resistance rate was observed for ciprofloxacin (99.0%, 190/192), followed by cefotaxime (90.6%, 174/192) and erythromycin (89.1%, 171/192). PFGE separated the 192 isolates into 79 pulsotypes, and differences in core genome single-nucleotide polymorphisms (SNPs) partitioned the 91 isolates sequenced into four clades. Isolates of the same pulsotype were identical or nearly identical at the genome level, with some exceptions. Two dominant subclones, clade 3a, and clade 4a, were responsible for the hospital-wide dissemination. Genomic analysis further revealed nine resistance genes mobilized by eight unique cassettes. PFGE and whole-genome sequencing revealed that the C. striatum isolates studied were the result mainly of predominant clones spreading in the hospital. C. striatum isolates in the hospital progressively acquired resistance to antimicrobial agents, demonstrating that isolates of C. striatum may adapt rapidly through the acquisition and accumulation of resistance genes and thus evolve into dominant and persistent clones. These insights will be useful for the prevention of C. striatum infection in hospitals.

10.
J Microbiol Methods ; 164: 105675, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31351107

RESUMO

Corynebacterium striatum is an emerging multidrug-resistant pathogen causing increasing numbers of infections and nosocomial outbreaks worldwide. Thus, a simple, rapid and accurate method for C. striatum is urgently required for improving diagnosis efficiency. In this study, a C. striatum-multiple cross displacement amplification (MCDA) with visual detection reagent (VR) assay (C. striatum-MCDA-VR), which was a novel isothermal amplification-based method, was established to detect the species-specific ftr1 gene of C. striatum. Amplification was performed at a constant temperature (68 °C) for only 40 min, and the reaction results could be easily elucidated by observation of reaction mixture color when employing the VR. The limit of detection of this method was 10 fg of pure C. striatum DNA. No cross-reaction was observed with non-C. striatum strains. In testing of clinical sputum samples, the C. striatum-MCDA-VR assay showed excellent sensitivity and specificity when compared with sputum smear tests and PCR. The C. striatum-MCDA-VR assay is a simple, rapid and cost-effective approach for identifying C. striatum in microbiological laboratories, especially in resource-limited settings.

11.
Emerg Infect Dis ; 25(6): 1218-1219, 2019 06.
Artigo em Inglês | MEDLINE | ID: mdl-31107214

RESUMO

We report national surveillance of Legionnaires' disease in China. Urine samples from 11 (3.85%) of 286 patients with severe pneumonia of unknown cause were positive for the Legionella pneumophila serogroup 1 antigen. We isolated Legionella strains from 7 patients. Improved diagnostic testing is needed for this underestimated disease in China.


Assuntos
Legionella pneumophila , Doença dos Legionários/epidemiologia , Doença dos Legionários/microbiologia , Adulto , Idoso , Antígenos de Bactérias/imunologia , China/epidemiologia , Feminino , Humanos , Legionella pneumophila/classificação , Legionella pneumophila/efeitos dos fármacos , Legionella pneumophila/genética , Legionella pneumophila/imunologia , Doença dos Legionários/diagnóstico , Masculino , Testes de Sensibilidade Microbiana , Pessoa de Meia-Idade , Tipagem Molecular , Vigilância em Saúde Pública , Sorogrupo , Adulto Jovem
12.
EBioMedicine ; 42: 133-144, 2019 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-30905850

RESUMO

BACKGROUND: Colistin resistance mediated by mcr-1-harbouring plasmids is an emerging threat in Enterobacteriaceae, like Salmonella. Based on its major contribution to the diarrhoea burden, the epidemic state and threat of mcr-1-harbouring Salmonella in community-acquired infections should be estimated. METHODS: This retrospective study analysed the mcr-1 gene incidence in Salmonella strains collected from a surveillance on diarrhoeal outpatients in Shanghai Municipality, China, 2006-2016. Molecular characteristics of the mcr-1-positive strains and their plasmids were determined by genome sequencing. The transfer abilities of these plasmids were measured with various conjugation strains, species, and serotypes. FINDINGS: Among the 12,053 Salmonella isolates, 37 mcr-1-harbouring strains, in which 35 were serovar Typhimurium, were detected first in 2012 and with increasing frequency after 2015. Most patients infected with mcr-1-harbouring strains were aged <5 years. All strains, including fluoroquinolone-resistant and/or extended-spectrum ß-lactamase-producing strains, were multi-drug resistant. S. Typhimurium had higher mcr-1 plasmid acquisition ability compared with other common serovars. Phylogeny based on the genomes combined with complete plasmid sequences revealed some clusters, suggesting the presence of mcr-1-harbouring Salmonella outbreaks in the community. Most mcr-1-positive strains were clustered together with the pork strains, strongly suggesting pork consumption as a main infection source. INTERPRETATION: The mcr-1-harbouring Salmonella prevalence in community-acquired diarrhoea displays a rapid increase trend, and the ESBL-mcr-1-harbouring Salmonella poses a threat for children. These findings highlight the necessary and significance of prohibiting colistin use in animals and continuous monitoring of mcr-1-harbouring Salmonella.


Assuntos
Diarreia/epidemiologia , Diarreia/microbiologia , Genes Bacterianos , Genoma Bacteriano , Pacientes Ambulatoriais , Infecções por Salmonella/epidemiologia , Infecções por Salmonella/microbiologia , Salmonella/genética , Antibacterianos/farmacologia , Criança , Pré-Escolar , China/epidemiologia , Diarreia/história , Feminino , Genômica/métodos , História do Século XXI , Humanos , Lactente , Masculino , Testes de Sensibilidade Microbiana , Tipagem Molecular , Filogenia , Plasmídeos/genética , Vigilância em Saúde Pública , Salmonella/classificação , Salmonella/efeitos dos fármacos , Infecções por Salmonella/história , Sorogrupo
13.
Front Microbiol ; 10: 54, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-30804895

RESUMO

Previous studies showed that high concentration of particulate matter (PM) 2.5 and PM10 carried a large number of bacterial and archaeal species, including pathogens and opportunistic pathogens. In this study, pharyngeal swabs from 83 subjects working in an open air farmer's market were sampled before and after exposure to smog with PM2.5 and PM10 levels up to 200 and 300 µg/m3, respectively. Their microbiota were investigated using high-throughput sequencing targeting the V3-V4 regions of the 16S rRNA gene. The genus level phylotypes was increased from 649 to 767 in the post-smog pharyngeal microbiota, of which 142 were new and detected only in the post-smog microbiota. The 142 new genera were traced to sources such as soil, marine, feces, sewage sludge, freshwater, hot springs, and saline lakes. The abundance of the genera Streptococcus, Haemophilus, Moraxella, and Staphylococcus increased in the post-smog pharyngeal microbiota. All six alpha diversity indices and principal component analysis showed that the taxonomic composition of the post-smog pharyngeal microbiota was significantly different to that of the pre-smog pharyngeal microbiota. Redundancy analysis showed that the influences of PM2.5/PM10 exposure and smoking on the taxonomic composition of the pharyngeal microbiota were statistically significant (p < 0.001). Two days of exposure to high concentrations of PM2.5/PM10 changed the pharyngeal microbiota profiles, which may lead to an increase in respiratory diseases. Wearing masks could reduce the effect of high-level PM2.5/PM10 exposure on the pharyngeal microbiota.

14.
Infect Drug Resist ; 11: 1783-1793, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-30349335

RESUMO

Background: We recently reported the complete sequence of a blaKPC-2- and rmtB-carrying IncFII-family plasmid p675920-1 with the pKPC-LK30/pHN7A8 hybrid structure. Comparative genomics of additional sequenced plasmids with similar hybrid structures and their prevalence in bla KPC-carrying Klebsiella pneumoniae strains from China were investigated in this follow-up study. Methods: A total of 51 bla KPC-carrying K. pneumoniae strains were isolated from 2012 to 2016 from five Chinese hospitals and genotyped by multilocus sequence typing. The bla KPC-carrying plasmids from four representative strains were sequenced and compared with p675920-1 and pCT-KPC. Plasmid transfer, carbapenemase activity determination, and bacterial antimicrobial susceptibility test were performed to characterize resistance phenotypes mediated by these plasmids. The prevalence of pCT-KPC-like plasmids in these bla KPC-carrying K. pneumoniae strains was screened by PCR. Result: The six KPC-encoding plasmids p1068-KPC, p20049-KPC, p12139-KPC and p64917-KPC (sequenced in this study) and p675920-1 and pCT-KPC slightly differed from one another due to deletion and acquisition of various backbone and accessory regions. Two major accessory resistance regions, which included the blaKPC-2 region harboring blaKPC-2 (carbapenem resistance) and blaSHV-12 (ß-lactam resistance), and the MDR region carrying rmtB (aminoglycoside resistance), fosA3 (fosfomycin resistance), bla TEM-1B (ß-lactam resistance) and bla CTX-M-65 (ß-lactam resistance), were found in each of these six plasmids and exhibited several parallel evolution routes. The pCT-KPC-like plasmids were present in all the 51 K. pneumoniae isolates, all of which belonged to CG258. Conclusion: There was clonal dissemination of K. pneumoniae CG258 strains, harboring bla KPC-2- and rmtB-carrying IncFII-family pKPC-LK30/pHN7A8 hybrid plasmids, among multiple Chinese hospitals.

15.
Artigo em Inglês | MEDLINE | ID: mdl-29881543

RESUMO

Background: Carbapenem-resistant Klebsiella pneumoniae (CRKP) is a major cause of nosocomial infections worldwide. The transmission route of CRKP isolates within an outbreak is rarely described. This study aimed to reveal the molecular characteristics and transmission route of CRKP isolates within an outbreak of nosocomial infection. Methods: Collecting case information, active screening and targeted environmental monitoring were carried out. The antibiotic susceptibility, drug-resistant genes, molecular subtype and whole genome sequence of CRKP strains were analyzed. Results: Between October and December 2011, 26 CRKP isolates were collected from eight patients in a surgical intensive care unit and subsequent transfer wards of Beijing Tongren hospital, China. All 26 isolates harbored blaKPC-2, blaSHV-1, and blaCTX-M-15 genes, had the same or similar pulsed-field gel electrophoresis patterns, and belonged to the sequence type 11 (ST11) clone. By comprehensive consideration of genomic and epidemiological information, a putative transmission map was constructed, including identifying one case as an independent event distinct from the other seven cases, and revealing two transmissions starting from the same case. Conclusions: This study provided the first report confirming an outbreak caused by K. pneumoniae ST11 clone co-harboring the blaKPC-2, blaCTX-M-15, and blaSHV-1 genes, and suggested that comprehensive consideration of genomic and epidemiological data can yield a fine transmission map of an outbreak and facilitate the control of nosocomial transmission.


Assuntos
Proteínas de Bactérias/genética , Enterobacteriáceas Resistentes a Carbapenêmicos/isolamento & purificação , Infecção Hospitalar/epidemiologia , Infecção Hospitalar/transmissão , Surtos de Doenças/estatística & dados numéricos , Infecções por Klebsiella/epidemiologia , Infecções por Klebsiella/transmissão , Klebsiella pneumoniae/genética , beta-Lactamases/genética , Antibacterianos/farmacologia , Carbapenêmicos/farmacologia , China/epidemiologia , Cuidados Críticos/estatística & dados numéricos , Infecção Hospitalar/microbiologia , Farmacorresistência Bacteriana Múltipla , Eletroforese em Gel de Campo Pulsado , Genoma Bacteriano/genética , Humanos , Klebsiella pneumoniae/isolamento & purificação , Testes de Sensibilidade Microbiana , Tipagem de Sequências Multilocus , Estudos Retrospectivos , Sequenciamento Completo do Genoma
16.
Front Med ; 12(1): 23-33, 2018 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-29318441

RESUMO

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.


Assuntos
Bactérias/genética , Infecções Bacterianas/epidemiologia , Surtos de Doenças/prevenção & controle , Genoma Bacteriano , Vigilância da População , Infecções Bacterianas/microbiologia , Infecções Bacterianas/transmissão , Técnicas de Tipagem Bacteriana , Genótipo , Humanos , Sequenciamento Completo do Genoma
17.
Infect Genet Evol ; 56: 117-124, 2017 12.
Artigo em Inglês | MEDLINE | ID: mdl-29155241

RESUMO

This work revealed the drug resistance and population structure of Moraxella catarrhalis strains isolated from children less than three years old with pneumonia. Forty-four independent M. catarrhalis strains were analyzed using broth dilution antimicrobial susceptibility testing and multilocus sequence typing (MLST). The highest non-susceptibility rate was observed for amoxicillin (AMX), which reached 95.5%, followed by clindamycin (CLI) (n=33; 75.0%), azithromycin (AZM) (61.4%), cefaclor (CEC) (25.0%), trimethoprim-sulfamethoxazole (SXT) (15.9%), cefuroxime (CXM) (4.5%), tetracycline (TE) (2.3%), and doxycycline (DOX) (2.3%). There was no strain showing non-susceptibility to other six antimicrobials. Using MLST, the 44 M. catarrhalis strains were divided into 33 sequence types (STs). Based on their allelic profiles, the 33 STs were divided into one CC (CC363) and 28 singletons. CC363 contained five STs and ST363 was the founder ST. CC363 contained 63.6%, 33.3%, and 40.7% of CEC non-susceptible, CLI non-susceptible and AZM non-susceptible strains, respectively. The proportions of CEC non-susceptible, CLI non-susceptible and AZM non-susceptible strains in CC363 were higher than that of singletons; these differences were significant for CEC (p=0.002) and AZM (p=0.011). Furthermore, CC363 contained more AMX-CLI-AZM co-non-susceptible and AMX-CEC-CLI-AZM co-non-susceptible strains than the singletons (p=0.007 and p<0.001, respectively). CC363 is a drug-resistant clone of clinical M. catarrhalis strains in China. Expansion of this clone under selective pressure of antibiotics should be noted and long-term monitoring should be established.


Assuntos
Antibacterianos/farmacologia , Farmacorresistência Bacteriana , /genética , Tipagem de Sequências Multilocus , Pneumonia Bacteriana/microbiologia , Criança , Humanos , Testes de Sensibilidade Microbiana , Filogenia , Pneumonia Bacteriana/tratamento farmacológico , Pneumonia Bacteriana/epidemiologia
18.
Infect Genet Evol ; 55: 104-111, 2017 11.
Artigo em Inglês | MEDLINE | ID: mdl-28867594

RESUMO

Streptococcus pneumoniae is an important human pathogen causing various diseases. In this study, S. pneumoniae from invasive (IPD) and noninvasive pneumococcal disease (NIPD) were studied by serotype and multilocus sequence typing (MLST) for population structure characteristics. A total of 169 clinical S. pneumoniae, containing 63 IPD and 106 NIPD strains, were analyzed. 19F, 19A, 6A, 6B, 1, 14 and 23F were the dominant serotypes in both IPD and NIPD strains. By MLST, 169 strains were divided into 85 sequence types (STs) with an index of discrimination (IOD) value of 0.9606. The seven predominant STs were ST271, ST320, ST876, ST3173, ST236, ST81 and ST342, which were mainly associated with serotypes 19F, 19A, 14, 6A, 19F, 1, and 1/23F, respectively. The 63 IPD strains were divided into 20 serotypes (IOD=0.9135) and 44 STs (IOD=0.9795); the 106 NIPD strains were divided into 16 serotypes (IOD=0.8334) and 49 STs (IOD=0.9430). In conclusion, the serotypes and ST distribution of IPD and NIPD strains analyzed in this study are similar to the profiles observed in other cities of China, suggesting that the clinical S. pneumoniae isolates were derived from clones generally circulating in China. The strains showed a variety of serotypes and STs, and the IPD strains showed higher serotype and genetic diversity than NIPD strains.


Assuntos
Tipagem de Sequências Multilocus , Infecções Pneumocócicas/microbiologia , Sorogrupo , Streptococcus pneumoniae/classificação , Streptococcus pneumoniae/genética , Antibacterianos/farmacologia , Criança , Pré-Escolar , Feminino , Variação Genética , Humanos , Lactente , Masculino , Testes de Sensibilidade Microbiana , Filogenia , Infecções Pneumocócicas/diagnóstico , Sorotipagem , Streptococcus pneumoniae/efeitos dos fármacos
19.
Gut Pathog ; 9: 39, 2017.
Artigo em Inglês | MEDLINE | ID: mdl-28670346

RESUMO

BACKGROUND: Klebsiella pneumoniae (K. pneumoniae) is an opportunistic pathogen associated with community-acquired infections and nosocomial infections. From 2010 to 2015, K. pneumoniae testing was included into the exiting diarrhea-syndrome surveillance with objective to estimate the prevalence of K. pneumoniae in diarrhea-syndrome patients, test antibiotics susceptibility and investigate molecular characteristics. METHODS: Stool specimens from diarrhea-syndrome outpatients were cultured and identified the pathogens by the Vitek2 Compact instrument. The isolated K. pneumoniae strains were tested for antibiotics susceptibility by minimal inhibitory concentration (MIC) method, and subtyped by pulsed field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). RESULTS: 22 K. pneumoniae strains were identified from 4340 stool specimens of outpatients who visited sentinel hospitals in Beijing during 2010-2015. All strains were sensitive to gentamicin, nalidixic acid, ciprofloxacin, ceftriaxone, cefotaxime, cefepime, imipenem. The highest resistance rate of K. pneumoniae strains was 100% to amoxicillin-clavulanate, followed by 72.7% to ampicillin. These 22 K. pneumoniae strains were characterized into 21 different PFGE types and 20 MLST types with less similarity. CONCLUSIONS: The detection rate of K. pneumoniae in stool specimens from outpatients with diarrhea syndromes was about 0.5% in Beijing. Less similarity of the isolated strains indicated the unlikely long-term circulating of K. pneumoniae in the community. ST23 was the most common genotype. Drug resistance of the community-acquired K. pneumoniae was not a serious problem in comparing with hospital-acquired infections. High vigilance in the community-acquired K. pneumoniae strains and investigation of pathogens' microbiological characteristics are valuable for signals detection for drug resistance in population and strains variation.

20.
Artigo em Inglês | MEDLINE | ID: mdl-28241513

RESUMO

Early diagnosis and treatment are crucial to the outcome of lower respiratory tract infections (LRTIs). In this study, we developed an assay combining multiplex PCR and Luminex technology (MPLT) for the detection of nine important respiratory bacterial pathogens, which frequently cause LRTIs. These were Streptococcus pneumoniae, Moraxella catarrhalis, Staphylococcus aureus, Streptococcus pyogenes, Haemophilus influenzae, Mycoplasma pneumoniae, Legionella spp., Pseudomonas aeruginosa, and Klebsiella pneumoniae. Through the hybridization reaction between two new synthesized multiplex PCR products and MagPlex-TAG Microspheres, we demonstrate that the detection limits for these nine pathogens were as low as 10²-10³ CFU/mL. Furthermore, 86 clinical bronchoalveolar lavage fluid specimens were used to evaluate this method. Compared with the results of nine simplex real-time PCR reactions targeting these nine pathogens, this MPLT assay demonstrated a high diagnostic accuracy for Streptococcus pneumoniae (sensitivity, 87.5% and specificity, 100%). Furthermore, sensitivity and specificity for the other eight pathogens all attained 100% diagnostic accuracy. In addition, the consistency between MPLT and the nine real-time PCR reactions exceeded 98.8%. In conclusion, MPLT is a high-throughput, labor-saving and reliable method with high sensitivity and specificity for identifying nine respiratory pathogens responsible for LRTIs. Indeed, this assay may be a promising supplement to conventional methods used to diagnose LRTIs.


Assuntos
Líquido da Lavagem Broncoalveolar/microbiologia , Reação em Cadeia da Polimerase Multiplex , Reação em Cadeia da Polimerase em Tempo Real , Infecções Respiratórias/diagnóstico , Infecções Respiratórias/microbiologia , China , Haemophilus influenzae/genética , Haemophilus influenzae/isolamento & purificação , Humanos , Klebsiella pneumoniae/genética , Klebsiella pneumoniae/isolamento & purificação , Legionella/genética , Legionella/isolamento & purificação , /isolamento & purificação , Mycoplasma pneumoniae/genética , Mycoplasma pneumoniae/isolamento & purificação , Pseudomonas aeruginosa/genética , Pseudomonas aeruginosa/isolamento & purificação , Sensibilidade e Especificidade , Staphylococcus aureus/genética , Staphylococcus aureus/isolamento & purificação , Streptococcus pneumoniae/genética , Streptococcus pneumoniae/isolamento & purificação , Streptococcus pyogenes/genética , Streptococcus pyogenes/isolamento & purificação
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