RESUMO
Outbreaks of Streptococcus pyogenes hypervirulent clones are constant public health threats. In western Switzerland, an increase of severe cases of S. pyogenes invasive infections was observed between December 2015 and March 2016. Our aim was (i) to investigate these cases by the use of Whole Genome Sequencing (WGS) and (ii) to determine the specific virulome and resistome of each isolate in order to undertake adequate public health measures. Eleven Streptococcus pyogenes strains isolated from 11 patients with severe invasive infections between December 13, 2015 and March 12, 2016 were included in our study. Practically, emm-typing, MLST and WGS were used to investigate the relatedness between the isolates. The presence of virulence and antibiotic resistance genes as well as mutations in transcriptional regulators of virulence and in genes encoding for antibiotic targets were assessed. Three and two groups of isolates shared the same emm-type and ST type, respectively. Single Nucleotide Polymorphism (SNP) analysis revealed 14 to 32 SNPs between the strains of the same emm-type group, ruling out the possibility of a clonal outbreak. Mutations found in covS and rocA could partially explain an increased virulence. As these reassuring results were obtained in less than 10 days, no specific hospital hygiene and no dedicated public health measures had to be undertaken. WGS is a powerful technique to discriminate between closely related strains, excluding an outbreak in less than 10 days. Moreover, WGS provided extensive data on the virulome and resistome of all these strains.
Assuntos
Técnicas Bacteriológicas/métodos , Surtos de Doenças , Técnicas de Diagnóstico Molecular/métodos , Infecções Estreptocócicas/diagnóstico , Infecções Estreptocócicas/epidemiologia , Streptococcus pyogenes/isolamento & purificação , Sequenciamento Completo do Genoma/métodos , Adolescente , Idoso , Criança , Pré-Escolar , Farmacorresistência Bacteriana , Feminino , Genótipo , Humanos , Lactente , Masculino , Pessoa de Meia-Idade , Tipagem Molecular/métodos , Suíça/epidemiologia , Fatores de Virulência/genéticaRESUMO
Despite the development of novel typing methods based on whole genome sequencing, most laboratories still rely on classical molecular methods for outbreak investigation or surveillance. Reference methods for Clostridium difficile include ribotyping and pulsed-field gel electrophoresis, which are band-comparing methods often difficult to establish and which require reference strain collections. Here, we present the double locus sequence typing (DLST) scheme as a tool to analyse C. difficile isolates. Using a collection of clinical C. difficile isolates recovered during a 1-year period, we evaluated the performance of DLST and compared the results to multilocus sequence typing (MLST), a sequence-based method that has been used to study the structure of bacterial populations and highlight major clones. DLST had a higher discriminatory power compared to MLST (Simpson's index of diversity of 0.979 versus 0.965) and successfully identified all isolates of the study (100 % typeability). Previous studies showed that the discriminatory power of ribotyping was comparable to that of MLST; thus, DLST might be more discriminatory than ribotyping. DLST is easy to establish and provides several advantages, including absence of DNA extraction [polymerase chain reaction (PCR) is performed on colonies], no specific instrumentation, low cost and unambiguous definition of types. Moreover, the implementation of a DLST typing scheme on an Internet database, such as that previously done for Staphylococcus aureus and Pseudomonas aeruginosa ( http://www.dlst.org ), will allow users to easily obtain the DLST type by submitting directly sequencing files and will avoid problems associated with multiple databases.
Assuntos
Clostridioides difficile/classificação , Clostridioides difficile/isolamento & purificação , Infecções por Clostridium/diagnóstico , Tipagem de Sequências Multilocus/métodos , Sequência de Bases , Clostridioides difficile/genética , Infecções por Clostridium/epidemiologia , Infecções por Clostridium/microbiologia , Infecção Hospitalar/microbiologia , DNA Bacteriano/genética , Humanos , Epidemiologia Molecular , Análise de Sequência de DNA , Suíça/epidemiologiaRESUMO
We report the case of a lung transplant recipient in whom the diagnosis of visceral leishmaniasis (VL) was made by detection of parasites in a peripheral blood smear when the parasite load already reached 8.9 × 103 parasites/mL. We demonstrated that the VL diagnosis could have been done months before the development of symptoms by the use of Leishmania-specific real-time polymerase chain reaction (PCR), suggesting the role of preemptive PCR-based diagnosis in transplant recipients at risk for VL.
Assuntos
Anfotericina B/uso terapêutico , Antiprotozoários/uso terapêutico , DNA de Protozoário/isolamento & purificação , Fibrose Pulmonar Idiopática/cirurgia , Leishmania/isolamento & purificação , Leishmaniose Visceral/diagnóstico , Transplante de Pulmão/efeitos adversos , Anfotericina B/administração & dosagem , Antiprotozoários/administração & dosagem , Diagnóstico Precoce , Humanos , Leishmaniose Visceral/sangue , Leishmaniose Visceral/tratamento farmacológico , Leishmaniose Visceral/parasitologia , Masculino , Pessoa de Meia-Idade , Carga Parasitária , Reação em Cadeia da Polimerase em Tempo Real , Sensibilidade e Especificidade , TransplantadosRESUMO
The impact of round-the-clock cerebrospinal fluid (CSF) Gram stain on overnight empirical therapy for suspected central nervous system (CNS) infections was investigated. All consecutive overnight CSF Gram stains between 2006 and 2011 were included. The impact of a positive or a negative test on empirical therapy was evaluated and compared to other clinical and biological indications based on institutional guidelines. Bacterial CNS infection was documented in 51/241 suspected cases. Overnight CSF Gram stain was positive in 24/51. Upon validation, there were two false-positive and one false-negative results. The sensitivity and specificity were 41 and 99 %, respectively. All patients but one had other indications for empirical therapy than Gram stain alone. Upon obtaining the Gram result, empirical therapy was modified in 7/24, including the addition of an appropriate agent (1), addition of unnecessary agents (3) and simplification of unnecessary combination therapy (3/11). Among 74 cases with a negative CSF Gram stain and without formal indication for empirical therapy, antibiotics were withheld in only 29. Round-the-clock CSF Gram stain had a low impact on overnight empirical therapy for suspected CNS infections and was associated with several misinterpretation errors. Clinicians showed little confidence in CSF direct examination for simplifying or withholding therapy before definite microbiological results.
Assuntos
Líquido Cefalorraquidiano/microbiologia , Infecções Comunitárias Adquiridas/diagnóstico , Infecção Hospitalar/diagnóstico , Violeta Genciana , Meningites Bacterianas/diagnóstico , Fenazinas , Adolescente , Adulto , Idoso , Idoso de 80 Anos ou mais , Antibacterianos/uso terapêutico , Criança , Pré-Escolar , Infecções Comunitárias Adquiridas/microbiologia , Infecção Hospitalar/microbiologia , Feminino , Humanos , Lactente , Recém-Nascido , Masculino , Meningites Bacterianas/tratamento farmacológico , Meningites Bacterianas/microbiologia , Pessoa de Meia-Idade , Reação em Cadeia da Polimerase , Estudos Retrospectivos , Sensibilidade e Especificidade , Coloração e Rotulagem/métodos , Centros de Atenção Terciária , Adulto JovemRESUMO
Uncomplicated urinary tract infections are commonly encountered in primary care and frequently lead to empirical antibiotic prescriptions. The development of antibiotic resistance in the community explains treatment failures observed with commonly-prescribed drugs such as quinolones and co-trimoxazole. This article describes the epidemiology of antibiotic resistance among pathogens causing uncomplicated urinary tract infections and the consequences in terms of recommendations for empirical antibiotic therapy.
Assuntos
Biota , Resistência Microbiana a Medicamentos/fisiologia , Medicina Interna/tendências , Infecções Urinárias/terapia , Antibacterianos/uso terapêutico , Humanos , Medicina Interna/métodos , Metagenoma/fisiologia , Guias de Prática Clínica como Assunto , Padrões de Prática Médica/estatística & dados numéricos , Padrões de Prática Médica/tendências , Pielonefrite/etiologia , Pielonefrite/microbiologia , Pielonefrite/terapia , Infecções Urinárias/epidemiologia , Infecções Urinárias/microbiologiaRESUMO
Conventional methods are sometimes insufficient to identify human bacterial pathogens, and alternative techniques, often molecular, are required. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) identified with a valid score 45.9% of 410 clinical isolates from 207 different difficult-to-identify species having required 16S rRNA gene sequencing. MALDI-TOF MS might represent an alternative to 16S rRNA gene sequencing.
Assuntos
Bactérias/química , Bactérias/classificação , Infecções Bacterianas/diagnóstico , Infecções Bacterianas/microbiologia , Técnicas Bacteriológicas/métodos , Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz/métodos , Bactérias/isolamento & purificação , DNA Bacteriano/química , DNA Bacteriano/genética , DNA Ribossômico/química , DNA Ribossômico/genética , Humanos , RNA Ribossômico 16S/genética , Análise de Sequência de DNAAssuntos
Antibacterianos/farmacologia , Bacteriemia/microbiologia , Técnicas Bacteriológicas/métodos , Colistina/farmacologia , Farmacorresistência Bacteriana , Infecções por Enterobacteriaceae/microbiologia , Enterobacteriaceae/efeitos dos fármacos , Enterobacteriaceae/genética , Enterobacteriaceae/isolamento & purificação , Humanos , Programas de Rastreamento/métodos , Plasmídeos/análiseRESUMO
Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has recently been introduced in diagnostic microbiology laboratories for the identification of bacterial and yeast strains isolated from clinical samples. In the present study, we prospectively compared MALDI-TOF MS to the conventional phenotypic method for the identification of routine isolates. Colonies were analyzed by MALDI-TOF MS either by direct deposition on the target plate or after a formic acid-acetonitrile extraction step if no valid result was initially obtained. Among 1,371 isolates identified by conventional methods, 1,278 (93.2%) were putatively identified to the species level by MALDI-TOF MS and 73 (5.3%) were identified to the genus level, but no reliable identification was obtained for 20 (1.5%). Among the 1,278 isolates identified to the species level by MALDI-TOF MS, 63 (4.9%) discordant results were initially identified. Most discordant results (42/63) were due to systematic database-related taxonomical differences, 14 were explained by poor discrimination of the MALDI-TOF MS spectra obtained, and 7 were due to errors in the initial conventional identification. An extraction step was required to obtain a valid MALDI-TOF MS identification for 25.6% of the 1,278 valid isolates. In conclusion, our results show that MALDI-TOF MS is a fast and reliable technique which has the potential to replace conventional phenotypic identification for most bacterial strains routinely isolated in clinical microbiology laboratories.
Assuntos
Bactérias/isolamento & purificação , Infecções Bacterianas/diagnóstico , Técnicas Bacteriológicas/métodos , Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz/métodos , Bactérias/química , Infecções Bacterianas/microbiologia , Humanos , Sensibilidade e Especificidade , Fatores de TempoRESUMO
The frequent lack of microbiological documentation of infection by blood cultures (BC) has a major impact on clinical management of febrile neutropenic patients, especially in cases of unexplained persistent fever. We assessed the diagnostic utility of the LightCycler SeptiFast test (SF), a multiplex blood PCR, in febrile neutropenia. Blood for BC and SF was drawn at the onset of fever and every 3 days of persistent fever. SF results were compared with those of BC, clinical documentation of infection, and standard clinical, radiological, and microbiological criteria for invasive fungal infections (IFI). A total of 141 febrile neutropenic episodes in 86 hematological patients were studied: 44 (31%) microbiologically and 49 (35%) clinically documented infections and 48 (34%) unexplained fevers. At the onset of fever, BC detected 44 microorganisms in 35/141 (25%) episodes. Together, BC and SF identified 78 microorganisms in 61/141 (43%) episodes (P = 0.002 versus BC or SF alone): 12 were detected by BC and SF, 32 by BC only, and 34 by SF only. In 19/52 (37%) episodes of persistent fever, SF detected 28 new microorganisms (7 Gram-positive bacterial species, 15 Gram-negative bacterial species, and 6 fungal species [89% with a clinically documented site of infection]) whereas BC detected only 4 pathogens (8%) (P = 0.001). While BC did not detect fungi, SF identified 5 Candida spp. and 1 Aspergillus sp. in 5/7 probable or possible cases of IFI. Using SeptiFast PCR combined with blood cultures improves microbiological documentation in febrile neutropenia, especially when fever persists and invasive fungal infection is suspected. Technical adjustments may enhance the efficiency of this new molecular tool in this specific setting.
Assuntos
Bactérias/isolamento & purificação , Infecções Bacterianas/diagnóstico , Sangue/microbiologia , Febre de Causa Desconhecida/complicações , Fungos/isolamento & purificação , Micoses/diagnóstico , Reação em Cadeia da Polimerase/métodos , Adolescente , Adulto , Idoso , Bactérias/genética , Bactérias/crescimento & desenvolvimento , Feminino , Fungos/genética , Fungos/crescimento & desenvolvimento , Humanos , Hospedeiro Imunocomprometido , Masculino , Técnicas Microbiológicas/métodos , Pessoa de Meia-Idade , Neutropenia/complicações , Adulto JovemRESUMO
BACKGROUND: Empirical antibacterial therapy in hospitals is usually guided by local epidemiologic features reflected by institutional cumulative antibiograms. We investigated additional information inferred by aggregating cumulative antibiograms by type of unit or according to the place of acquisition (i.e. community vs. hospital) of the bacteria. MATERIALS AND METHODS: Antimicrobial susceptibility rates of selected pathogens were collected over a 4-year period in an university-affiliated hospital. Hospital-wide antibiograms were compared with those selected by type of unit and sampling time (<48 or >48 h after hospital admission). RESULTS: Strains isolated >48 h after admission were less susceptible than those presumably arising from the community (<48 h). The comparison of units revealed significant differences among strains isolated >48 h after admission. When compared to hospital-wide antibiograms, susceptibility rates were lower in the ICU and surgical units for Escherichia coli to amoxicillin-clavulanate, enterococci to penicillin, and Pseudomonas aeruginosa to anti-pseudomonal beta-lactams, and in medical units for Staphylococcus aureus to oxacillin. In contrast, few differences were observed among strains isolated within 48 h of admission. CONCLUSIONS: Hospital-wide antibiograms reflect the susceptibility pattern for a specific unit with respect to community-acquired, but not to hospital-acquired strains. Antibiograms adjusted to these parameters may be useful in guiding the choice of empirical antibacterial therapy.
Assuntos
Antibacterianos/farmacologia , Bactérias/efeitos dos fármacos , Infecções Bacterianas/microbiologia , Infecções Comunitárias Adquiridas/microbiologia , Infecção Hospitalar/microbiologia , Infecções Bacterianas/tratamento farmacológico , Infecções Bacterianas/epidemiologia , Infecções Comunitárias Adquiridas/tratamento farmacológico , Infecções Comunitárias Adquiridas/epidemiologia , Infecção Hospitalar/tratamento farmacológico , Infecção Hospitalar/epidemiologia , Farmacorresistência Bacteriana , Estudos Epidemiológicos , Escherichia coli/efeitos dos fármacos , Humanos , Testes de Sensibilidade Microbiana , Staphylococcus aureus/efeitos dos fármacos , Suíça/epidemiologiaRESUMO
OBJECTIVES: Becton-Dickinson recently developed the Phoenix™ CPO (carbapenemase-producing organism) Detect Test, a growth-based test embedded in Gram-negative (GN) panels for the detection and confirmation of bacteria producing class A, B and D carbapenemases. This study aimed to (a) determine the performance of the CPO test, and (b) assess its added value in routine diagnostic workflows. METHODS: The performance of the BD Phoenix CPO test was analysed retrospectively on a collection of 185 molecularly characterized strains, including 92 CPOs, and prospectively on 135 and 160 routine isolates with and without CPO suspicion, respectively. RESULTS: In the retrospective study the CPO test exhibited 92.4% accuracy (95%CI 87.6-95.8), 97.8% sensitivity (95%CI 92.4-99.7) and 87.1% specificity (95%CI 78.6-93.2) for carbapenemase detection. The CPO test provided a classification to class A, B, and D for 81.3% of detected carbapenemases with 94.6% accuracy (95%CI 86.7-98.5). In the prospective study the CPO test detection performance showed 77.8% accuracy (95%CI 68.8-84.5), 100% sensitivity (95%CI 91.2-100) and 67.8% specificity (95%CI 57.3-77.1) with 135 CPO-suspicious isolates and 98.8% accuracy and specificity (95%CI 95.6-99.9) with 160 non-CPO-suspicious isolates. Compared to routine testing, the implementation of the CPO test allowed a mean reduction of 21.3 h (95%CI 17.6-25) in turnaround time, 16.8 min (95%CI 13.4-20.2) in hands-on time, and 20.6 CHF (95%CI 16.5-24.8) in costs. CONCLUSIONS: The CPO test is reliable for the detection of CPO with a high sensitivity. However, the relatively low detection specificity required the use of additional confirmatory methods. The carbapenemase classification accuracy is robust in providing preliminary results before molecular characterization. Finally, the implementation of the test in routine workflows allowed a significant reduction in turnaround time, hands-on time and cost compared to the conventional approach.
Assuntos
Proteínas de Bactérias/metabolismo , Técnicas Bacteriológicas/métodos , Bactérias Gram-Negativas/enzimologia , Testes de Sensibilidade Microbiana/métodos , beta-Lactamases/metabolismo , Proteínas de Bactérias/classificação , Testes Diagnósticos de Rotina , Bactérias Gram-Negativas/isolamento & purificação , Humanos , Estudos Prospectivos , Estudos Retrospectivos , Sensibilidade e Especificidade , Fatores de Tempo , beta-Lactamases/classificaçãoRESUMO
POCT have a great potential in ambulatory infectious diseases diagnosis, due to their impact on antibiotic administration and on communicable diseases prevention. Some are in use for long (S. pyogenes antigen, HIV antibodies) or short time (S. pneumoniae antigen, P. falciparum). The additional major indications will be community-acquired lower respiratory tract infections, infectious diarrhoea in children (rotavirus, enterotoxigenic E. coli), and hopefully sexually transmitted infections. Easy to use, these tests based on antigen-antibody reaction allow a rapid diagnosis in less than one hour; the new generation of POCT relying on nucleic acid detection are just introduced in practice (detection of GBS in pregnant women, carriage of MRSA), and will be extended to many pathogens.
Assuntos
Doenças Transmissíveis/diagnóstico , Sistemas Automatizados de Assistência Junto ao Leito , Infecções Comunitárias Adquiridas/diagnóstico , Humanos , Infecções Sexualmente Transmissíveis/diagnósticoRESUMO
Bacillus cereus bacteraemia can be severe, especially among patients with haematologic malignancy. We retrospectively reviewed first episodes of true B. cereus bacteraemia (more than one positive bottle plus signs of infection) at our institution between 1997 and 2013 with the aim to compare haematologic versus nonhaematologic patients and analyse episodes with complicated outcome. Among 56 episodes of positive-blood cultures for B. cereus, 21 were considered significant. Median age was 54 years (range 23-82 years). Ten patients (48%) had a haematologic malignancy; all were neutropenic at the time of B. cereus bacteraemia. Nonhaematologic patients were either intravenous drug users (n = 3, 14%), polytraumatized (n = 3, 14%) or had multiple chronic comorbidities (n = 5, 24%). Most episodes were hospital acquired (15, 71%). Sources of bacteraemia were intravascular catheter (n = 11, 52%), digestive tract (n = 6, 29%), drug injection (n = 3, 14%) and wound (n = 1, 5%). Adequate antibiotic therapy was provided to 18 patients (86%) during a median of 17 days (range 2-253 days). The intravascular catheter was removed in eight cases (42%). Three haematologic patients had a complicated course with neurologic complications (meningoencephalitis and cerebral abscesses). Complications appeared to be associated with catheter infection (100% of complicated cases vs. 29% of noncomplicated cases). In conclusion, B. cereus bacteraemia can have a complicated course in a subset of patients, mainly those with haematologic malignancy. Catheter infection may be associated with a worse outcome with frequent neurologic complications.
RESUMO
OBJECTIVES: The management of bloodstream infection, a life-threatening disease, largely relies on early detection of infecting microorganisms and accurate determination of their antibiotic susceptibility to reduce both mortality and morbidity. Recently we developed a new technique based on atomic force microscopy capable of detecting movements of biologic samples at the nanoscale. Such sensor is able to monitor the response of bacteria to antibiotic's pressure, allowing a fast and versatile susceptibility test. Furthermore, rapid preparation of a bacterial pellet from a positive blood culture can improve downstream characterization of the recovered pathogen as a result of the increased bacterial concentration obtained. METHODS: Using artificially inoculated blood cultures, we combined these two innovative procedures and validated them in double-blind experiments to determine the susceptibility and resistance of Escherichia coli strains (ATCC 25933 as susceptible and a characterized clinical isolate as resistant strain) towards a selection of antibiotics commonly used in clinical settings. RESULTS: On the basis of the variance of the sensor movements, we were able to positively discriminate the resistant from the susceptible E. coli strains in 16 of 17 blindly investigated cases. Furthermore, we defined a variance change threshold of 60% that discriminates susceptible from resistant strains. CONCLUSIONS: By combining the nanomotion sensor with the rapid preparation method of blood culture pellets, we obtained an innovative, rapid and relatively accurate method for antibiotic susceptibility test directly from positive blood culture bottles, without the need for bacterial subculture.
Assuntos
Antibacterianos/farmacologia , Bacteriemia/microbiologia , Infecções por Escherichia coli/microbiologia , Escherichia coli/efeitos dos fármacos , Ampicilina/farmacologia , Ampicilina/uso terapêutico , Antibacterianos/uso terapêutico , Bacteriemia/tratamento farmacológico , Hemocultura , Ceftriaxona/farmacologia , Ceftriaxona/uso terapêutico , Ciprofloxacina/farmacologia , Ciprofloxacina/uso terapêutico , Método Duplo-Cego , Farmacorresistência Bacteriana , Escherichia coli/classificação , Infecções por Escherichia coli/tratamento farmacológico , Humanos , Testes de Sensibilidade Microbiana , Microscopia de Força Atômica , NanotecnologiaRESUMO
Automation was introduced many years ago in several diagnostic disciplines such as chemistry, haematology and molecular biology. The first laboratory automation system for clinical bacteriology was released in 2006, and it rapidly proved its value by increasing productivity, allowing a continuous increase in sample volumes despite limited budgets and personnel shortages. Today, two major manufacturers, BD Kiestra and Copan, are commercializing partial or complete laboratory automation systems for bacteriology. The laboratory automation systems are rapidly evolving to provide improved hardware and software solutions to optimize laboratory efficiency. However, the complex parameters of the laboratory and automation systems must be considered to determine the best system for each given laboratory. We address several topics on laboratory automation that may help clinical bacteriologists to understand the particularities and operative modalities of the different systems. We present (a) a comparison of the engineering and technical features of the various elements composing the two different automated systems currently available, (b) the system workflows of partial and complete laboratory automation, which define the basis for laboratory reorganization required to optimize system efficiency, (c) the concept of digital imaging and telebacteriology, (d) the connectivity of laboratory automation to the laboratory information system, (e) the general advantages and disadvantages as well as the expected impacts provided by laboratory automation and (f) the laboratory data required to conduct a workflow assessment to determine the best configuration of an automated system for the laboratory activities and specificities.
Assuntos
Automação Laboratorial , Técnicas Bacteriológicas , Bacteriologia , Laboratórios , Automação Laboratorial/instrumentação , Automação Laboratorial/métodos , Automação Laboratorial/normas , Técnicas Bacteriológicas/instrumentação , Técnicas Bacteriológicas/métodos , Técnicas Bacteriológicas/normas , Bacteriologia/normas , Humanos , Laboratórios/normasRESUMO
Airborne precautions are required at hospital admission for patients with suspected pulmonary tuberculosis. The isolation is maintained until 3 serially collected sputum smears are acid-fast bacilli negative, a time- and labor-intensive method with limited sensitivity and specificity, which has a great impact on patient flow management. We evaluated the possibility of replacing the result of microscopy by the semiquantitative result of the molecular point-of-care test Xpert MTB/RIF to assess patients' transmission risk to quickly guide airborne isolation decisions in low-endemic countries. The performance of the Xpert MTB/RIF, used as a first-line test, was compared to the results of microscopy for specimens (n=242) collected from May 2010 to December 2014 in Lausanne, Switzerland. The sensitivity and specificity of Xpert MTB/RIF were 91.5% (65/71) and 99.6% (170/171), respectively, vs. 64.8% (46/71) and 94.2% (161/171) for microscopy. Samples with negative Xpert MTB/RIF were all smear negative for Mycobacterium tuberculosis (negative predictive value, 100%). The semiquantitative results of Xpert MTB/RIF-high, medium, low or very low-were found to correlate with acid-fast bacilli detection: positive predictive value of 100% (6/6), 96.5% (27/28), 52.2% (12/23) and 11.1% (1/9) respectively. Finally, when including clinical criteria, we identified 11 smear-negative but Xpert MTB/RIF-positive patients with a significant transmission potential. In conclusion, our data support the introduction of an Xpert MTB/RIF-based strategy as a replacement of smear microscopy for a faster and more accurate management of tuberculosis patients' transmission risk in a low-prevalence country.
Assuntos
Microscopia/métodos , Técnicas de Diagnóstico Molecular/métodos , Mycobacterium tuberculosis/isolamento & purificação , Escarro/microbiologia , Tuberculose Pulmonar/diagnóstico , Adulto , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Mycobacterium tuberculosis/citologia , Mycobacterium tuberculosis/genética , Sistemas Automatizados de Assistência Junto ao Leito , Valor Preditivo dos Testes , Sensibilidade e Especificidade , Suíça , Adulto JovemRESUMO
BACKGROUND: During an environmental investigation of Pseudomonas aeruginosa in intensive care units, the liquid hand soap was found to be highly contaminated (up to 8 × 10(5)cfu/g) with this pathogen. It had been used over the previous five months and was probably contaminated during manufacturing. AIM: To evaluate the burden of this contamination on patients by conducting an epidemiological investigation using molecular typing combined with whole genome sequencing (WGS). METHODS: P. aeruginosa isolates from clinical specimens were analysed by double locus sequence typing (DLST) and compared with isolates recovered from the soap. Medical charts of patients infected with a genotype identical to those found in the soap were reviewed. WGS was performed on soap and patient isolates sharing the same genotype. FINDINGS: P. aeruginosa isolates (N = 776) were available in 358/382 patients (93.7%). Only three patients (0.8%) were infected with a genotype found in the soap. Epidemiological investigations showed that the first patient was not exposed to the soap, the second could have been exposed, and the third was indeed exposed. WGS showed a high number of core single nucleotide polymorphism differences between patients and soap isolates. No close genetic association was observed between soap and patient isolates, ruling out the hypothesis of transmission. CONCLUSION: Despite a highly contaminated soap, the combined investigation with DLST and WGS ruled out any impact on patients. Hand hygiene performed with alcohol-based solution for >15 years was probably the main reason. However, such contamination represents a putative reservoir of pathogens that should be avoided in the hospital setting.
Assuntos
Microbiologia Ambiental , Infecções por Pseudomonas/epidemiologia , Pseudomonas aeruginosa/isolamento & purificação , Sabões , Genoma Bacteriano , Genótipo , Humanos , Tipagem Molecular , Infecções por Pseudomonas/microbiologia , Pseudomonas aeruginosa/classificação , Pseudomonas aeruginosa/genética , Análise de Sequência de DNA , Centros de Atenção TerciáriaRESUMO
Since late 2014, multiple cases of abscesses and boils due to methicillin-susceptible Staphylococcus aureus (MSSA) expressing the Panton-Valentine leucocidin (PVL) were observed in Eritrean asylum seekers in Lausanne, Switzerland. Strains isolated from infected Eritrean and non-Eritrean patients were compared by whole genome sequencing to determine whether these numerous cases result from an outbreak. The genome of S. aureus PVL-producing strains were sequenced and compared. Clinical and epidemiological characteristics of patients infected by PVL-producing strains were investigated. This work reports 15 cases of infections due to PVL-producing strains affecting mostly asylum seekers (n = 10), people working with refugees and/or exposed to Africans (n = 3). Most infections were due to closely related strains of CC152 (n = 8) and CC15 (n = 3), two distantly related (>34 000 core single nucleotide polymorphisms) clonal complexes. An epidemiological link between the 15 cases could be ruled out by whole genome sequencing (33 to 172 core single nucleotide polymorphisms between the different strains of a given complex). Altogether, these results reflect the probable high incidence of CC15 and CC152 PVL-producing strains in eastern Africa. Clinicians facing unusual skin infections in African refugees (or in any person returning from this region of high endemicity) should consider S. aureus PVL-producer before suspecting rare infections such as leishmaniasis or rickettsiosis. Clinicians should also remember that PVL are frequently expressed by MSSA in some regions of the world and that antibiotics that are efficient on toxin expression, such as clindamycin, represent the best therapeutic option.
Assuntos
Toxinas Bacterianas/genética , Exotoxinas/genética , Leucocidinas/genética , Refugiados , Infecções Cutâneas Estafilocócicas/microbiologia , Staphylococcus aureus/genética , Adolescente , Adulto , Toxinas Bacterianas/biossíntese , Criança , Pré-Escolar , Surtos de Doenças , Eritreia/epidemiologia , Exotoxinas/biossíntese , Feminino , Genoma Bacteriano , Genômica , Humanos , Leucocidinas/biossíntese , Masculino , Pessoa de Meia-Idade , Filogenia , Polimorfismo de Nucleotídeo Único , Infecções Cutâneas Estafilocócicas/epidemiologia , Staphylococcus aureus/classificação , Adulto JovemRESUMO
Blood culture remains the best approach to identify the incriminating microorganisms when a bloodstream infection is suspected, and to guarantee that the antimicrobial treatment is adequate. Major improvements have been made in the last years to increase the sensitivity and specificity and to reduce the time to identification of microorganisms recovered from blood cultures. Among other factors, the introduction in clinical microbiology laboratories of the matrix-assisted laser desorption ionization time-of-flight mass spectrometry technology revolutionized the identification of microorganisms whereas the introduction of nucleic-acid-based methods, such as DNA hybridization or rapid PCR-based test, significantly reduce the time to results. Together with traditional antimicrobial susceptibility testing, new rapid methods for the detection of resistance mechanisms respond to major epidemiological concerns such as methicillin-resistant Staphylococcus aureus, extended-spectrum ß-lactamase or carbapenemases. This review presents and discusses the recent developments in microbial diagnosis of bloodstream infections based on blood cultures.
Assuntos
Bacteriemia/diagnóstico , Bactérias/isolamento & purificação , Técnicas Bacteriológicas/métodos , Sangue/microbiologia , Bactérias/crescimento & desenvolvimento , Humanos , Técnicas de Diagnóstico Molecular/métodos , Sensibilidade e Especificidade , Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz/métodos , Fatores de TempoRESUMO
Detection of cryptococcal antigen in serum or cerebrospinal fluid allows cryptococcal meningitis diagnosis within few hours with >90% sensitivity. In an HIV-positive patient with Cryptococcus neoformans meningitis, initial antigen detection by immunoagglutination was negative. We thus evaluated a new immunochromatographic detection assay that exhibited a higher sensitivity.