Microbial ex situ preservation supporting science and bioeconomy in Brazil / Preservação de microrganismos ex situ como suporte para a ciência e a bioeconomia no Brasil

Abstract One of the texts in the "Biodiversity in the State of São Paulo" series, within the FAPESP-Biota Program, was dedicated to the Infrastructure for Biodiversity Conservation, with a focus on Biological Collections and Conservation Units. From the early 1960s, when FAPESP was established, to the present day, financial resources have been invested in the preservation of the biodiversity of the national genetic heritage, besides other fields. History of years of advances in scientific knowledge was built, which can be portrayed through the projects that resulted in high-quality data of national and international impact. Microbiological collections are centers that generate technology and specialized human resources, and act (among other things) as living repositories preserving reference material and as witnesses to the history of microbial biodiversity because they preserve what may no longer exist. They have enormous potential to promote the global bioeconomy and address problems that have resulted from the misuse of natural resources. This reading brings everyone the history, advances, and future perspectives of culture collections, within the efforts of 60-year scientific activities in Brazil.

Resumo Um dos textos da série "Biodiversidade do Estado de São Paulo", dentro do Programa FAPESP-Biota, foi dedicado à Infraestrutura para Conservação da Biodiversidade, com foco nas coleções biológicas e nas unidades de conservação. Do início dos anos 60, quando a FAPESP foi criada, até os dias atuais muito foi investido em pesquisa nas mais diversas áreas, incluindo a preservação da biodiversidade do patrimônio genético nacional. Uma história de longos anos de avanços no conhecimento científico foi construída, a qual pode ser retratada através dos projetos que resultaram em dados de alta qualidade com impacto nacional e internacional. As coleções microbiológicas são centros geradores de tecnologia e recursos humanos especializados, que atuam (dentre outros) como repositórios vivos, preservando material de referência, e como testemunho da história da biodiversidade microbiana, preservando o que pode não mais existir. Possuem enorme potencial para alavancar a bioeconomia global e tratar de problemas que resultaram do mau uso dos recursos naturais. Essa leitura traz a todos o histórico, os avanços e as perspectivas futuras das coleções de microrganismos, dentro dos esforços de 60 anos de atividades científicas no Brasil.

Establishment and preliminary application of a joint detection method for transplantation-associated infection pathogens / 中国输血杂志

【Objective】 To investigate the effectiveness of multilink real-time fluorescence quantitative PCR (qPCR) in the detection of common pathogens in transplantation. 【Methods】 The primers of the qPCR detection system were designed for 24 common infectious pathogens after clinical transplantation, and the standard plasmids of each pathogen were used to verify the qPCR reaction.After the primer probe effect and concentration of each pathogen reaction system in this experiment was optimized, the sensitivity, correlation coefficient (R2) and amplification efficiency (E) of qPCR method were analyzed and confirmed.Twenty-two samples from patients, who underwent liver and kidney transplantation in transplant ICU of Sichuan Provincial People′s Hospital, were used to verify the application of the detection system.The total nucleic acid of 100 μL was extracted from each individual and divided into two aliquots, which were detected by multi-link qPCR reaction system and analyzed by high-throughput sequencing method (NGS). At the same time, samples (2 mL each) were taken from the transplanted patients for microbial culture.The results of the three detection methods were compared, and the NGS method was taken as the gold standard to analyze the positive detection rate of the multi-link qPCR method and its difference with the culture method and NGS. 【Results】 The lower limit of qPCR detection for 24 pathogens in the established qPCR detection system was 101cp/μL(R2>0.99), with the positive rate of pathogens at 59.1% (13/22), showing significant difference versus microbial culture (18.2%, 4/22)(P<0.05), but not versus NGS (63.6%, 14/22)(P>0.05). Percentage of pathogens detected was as follows: human herpetic virus type 6 (HHV-6) 30.8% (4/13), cytomegalovirus (HCMV) 23.1% (3/13), Epstein-Barr virus (EBV) 23.1% (3/13), human parvovirus B19 15.4% (2/13), Haemophilus influenzae (Hin) 15.4% (2/13), Enterococcus faecium (EFM) 15.4% (2/13), Clostridium difficile 15.4% (2/13), Escherichia coli 7.7% (1/13), Stenotrophomonas maltophilia (Sma) 7.7% (1/13), Klebsiella pneumoniae (Kpn) 7.7% (1/13), Enterococcus faecalis (Efa) 7.7% (1/13) and Streptococcus pneumoniae (Spn) 7.7% (1/13). The consistency rate of pathogens detected by the three methods was 32% (7/22), among which the consistency rate of multi-link qPCR with NGS method was 59% (13/22), and multi-link qPCR with microbial culture was 41% (9/22). 【Conclusion】 Compared with the microbial culture, the multi-link qPCR method demonstrated high sensitivity, accurate quantification, short time and low cost for the detection of common pathogens in clinical transplantation.Multi-link qPCR combined with NGS and microbial culture is helpful to quickly predict the pathogen infection status of patients after transplantation.

Technology development and instrumentation of a high-throughput and automated microbial microdroplet culture system for microbial evolution and screening / 生物工程学报

Since microdroplets are able to be generated rapidly in large amount and each droplet can be well controlled as an independent micro-cultivator, droplet microfluidic technology can be potentially used in the culture of microorganisms, and provide the microbial culture with high throughput manner. But its application mostly stays in the laboratory-level building and using for scientific research, and the wide use of droplet microfluidics in microbial technology has been limited by the key problems that the operation for microdroplets needs high technical requirements with wide affecting factors and the difficulties in integration of automatic microdroplet instrumentation. In this study, by realizing and integrating the complicated operations of droplet generation, cultivation, detection, splitting, fusion and sorting, we design a miniaturized, fully automated and high-throughput microbial microdroplet culture system (MMC). The MMC can be widely used in microbial growth curve test, laboratory adaptive evolution, single factor and multi-level analysis of microbial culture, metabolite detection and so on, and provide a powerful instrument platform for customized microbial evolution and screening aiming at efficient strain engineering.

Infectious keratitis in southern Brazil: a comparison culture negative and culture positive patients / Ceratite infecciosa no sul do Brasil: comparação entre pacientes com cultura negativa e positiva

Abstract Purpose: To compare clinical-epidemiological profile and treatment outcome between culture negative and culture positive keratitis patients. Methods: Patients with suspected infectious keratitis seen at two ophthalmic hospitals in Curitiba, Brazil, between June 2014 and April 2016, were prospectively studied. Ophthalmological exam with corneal scraping and microbiological tests were performed. Data regarding follow up, surgical interventions and treatment outcome were collected after 12 weeks of the first visit trough medical chart review. From the results of the culture, two groups were formed: culture negative keratitis (CNK) and culture positive keratitis (CPK). Results: According to inclusion criteria 21 patients were classified as culture negative keratitis and 20 patients as culture positive keratitis. The number of patients on antibiotic drops at the first visit was greater in CNK group (90.5% versus 60%; p=0.032). Surgical procedures were necessary in 3 patients (15%) in CNK group and in 7 patients (36,8%) in CPK group (p=0.155). Treatment success was achieved by 85% (17/20) of the patients in CNK group and by 61% (11/18) of the patients in CPK group (p=0.144). There was no significant difference between groups regarding age, gender, place of residence, presence of comorbidities, risk factors for infectious keratitis, duration of symptoms and characteristics of corneal ulcer. Conclusions: Previous treatment with antibiotics correlates with negative culture results. There was no significant difference in treatment outcome between culture negative and culture positive keratitis patients.

Resumo Objetivo: Comparar os perfis clinico-epidemiológicos e os desfechos entre pacientes com ceratite com cultura positiva e pacientes com ceratite com cultura negativa. Métodos: Pacientes com ceratite infecciosa, atendidos em dois hospitais oftalmológicos em Curitiba, Brasil, entre junho de 2014 e abril de 2016, foram estudados prospectivamente. Exame oftalmológico, raspado de córnea e exames microbiológicos foram realizados no primeiro atendimento. Os dados quanto a seguimento e desfecho foram coletados após 12 semanas do primeiro atendimento através de revisão de prontuário. A partir dos resultados das culturas, dois grupos foram formados: ceratite com cultura negativa e ceratite com cultura positiva. Resultados: Vinte e um pacientes foram classificados como ceratite com cultura negativa e 20 como ceratite com cultura positiva. O número de pacientes em uso de colírio antibiótico no primeiro atendimento foi maior no grupo de cultura negativa (90,5% versus 60%; p=0,032). Sete pacientes (37%) no grupo cultura positiva precisaram de procedimentos cirúrgicos no manejo da ceratite, versus 3 pacientes (15%) do grupo cultura negativa (p=0,155). Oitenta e cinco por cento (17/20) dos pacientes do grupo cultura negativa alcançaram sucesso no tratamento, contra 61% (11/18) dos pacientes no grupo cultura positiva (p=0,144). Não houve diferença entre os grupos quanto a idade, gênero, local de procedência, presença de comorbidades, fatores de risco, duração dos sintomas e características da úlcera de córnea. Conclusão: Tratamento prévio com colírio de antibiótico correlaciona-se com resultados negativos de cultura. Não houve diferença no desfecho após tratamento entre os pacientes com cultura negativa e cultura positiva.

Bacterial Investigation and Antibiogram in Corneal Ulcers in Dogs

Corneal ulcers in dogs usually have a traumatic origin. They cause a break in the continuity of underlying corneal stroma and become rapidly contaminated with bacteria. Twenty eight clinical samples were obtained from corneal ulcer affected dogs for bacterial isolation and anti-microbial susceptibility. Bacterial growth was observed in 100% of the samples (n=28) and Staphylococcus spp. was isolated and characterized by culture, gram staining and various biochemical tests. Antibiogram pattern revealed that gatifloxacin and moxifloxacin antibiotics were found to be highly effective in the treatment of corneal ulcers in dogs. Corneal culture and sensitivity testing provided useful information for the diagnosis, determination of appropriate treatment and antimicrobial therapy for corneal diseases in dogs

Two kinds of test methods of Mycoplasma pneumoniae infection in children / 中国生化药物杂志

Objective To investigate two methods for the detection of Mycoplasma pneumoniae infection in children. Methods The choice of the January 2015-2017 year in January in our hospital 60 cases of Mycoplasma pneumoniae infection in children as the research object, underwent rapid serological tests (control group), rapid detection of microbial culture (observation group), the detailed records of the two group with the experimental data,and the data for comparative analysis and discuss the diagnostic value of two test methods of Mycoplasma pneumoniae infection in children. Results The positive rate of the observation group was higher than that of the control group, and the positive rate of the children in the age group of 4-8 was higher than that of other age groups, the difference was statistically significant (P<0.05). Conclusion Children with Mycoplasma pneumoniae infection have a higher positive rate of rapid detection of microorganisms, especially in children of 4-8 years of age.It is worthy of wide clinical application.

Interpretation and Countermeasure of the Microbiological Examination for Nonsterile Products：Tests for Specified Microorganisms in Chinese Pharmacopoeia (2015 Edition) / 中国药师

Objective:To interpret the main revision of the microbiological examination for nonsterile products:tests for specified microorganisms in Chinese Pharmacopoeia (2015 edition). Methods:The microbiological examination for nonsterile products:tests for specified microorganisms in Chinese Pharmacopoeia (2015 edition) was compared with the relevant content in the 2010 edition, and then the differences were investigated. Results:Microbiological examination for nonsterile products:tests for specified microorganisms in Chinese Pharmacopoeia (2015 edition) had been revised at a comparatively large scale in the inspection items, test method, micro-bial culture system, the quality control concept and so on. Conclusion:Microbial inspection system in Chinese Pharmacopoeia (2015 edition) is gradually improved to become a high standard check system in line with the international standards.

Clinical presentation and microorganisms sensitivity profile for diabetic foot ulcers: a pilot study

SUMMARY Introduction: Patients suffering from diabetes mellitus (DM) frequently present with infected diabetic foot ulcers (DFU). This study was done to record the anatomical site and the grade of ulcers according to Wagner’s classification and to culture the microorganisms from the ulcers and determine their antibiotic sensitivity. Materials and methods: Prospective study was conducted on 77 diabetic patients who were admitted with DFU from June until December 2011. Patients with end stage renal failure, those who had previous vascular surgery on the involved limb, or hyperbaric oxygen or maggot therapy for the ulcers, or had unrelated skin diseases around the involved foot were excluded from the study. Specimens for culture were obtained by a sterile swab stick or tissue sample was taken from the wound with sterile surgical instruments. Results: Wagner’s grade III and IV ulcers were most common. Majority of the ulcers involved toes (48%). Gram negative microorganisms were predominantly isolated (71.1%). Gram positive microorganisms were less frequently cultured (27.7%). Fungus was cultured from one sample (1.2%). Gram negative microorganisms were sensitive to aminoglycosides, cephalosporins or β-lactamase inhibitors. More than 40% were resistant to ampicillin. Gram positive microorganisms were sensitive to cloxacillin. MRSA were sensitive to vancomycin. Conclusion: Empirical use of antibiotics should be curtailed to prevent development of drug resistant strains of microorganisms and MRSA. We suggest use of antiseptic solutions to clean the ulcers until antibiotic sensitivity report is available. Results of our altered treatment regimen we plan to publish in a later study.

Condiciones microbiológicas para el cultivo de Helicobacter pylori / Microbiological conditions for culturing Helicobacter Pylori

El diagnóstico oportuno y de cultivo de Helicobacter pylori es de gran importancia para estudiar las características de su crecimiento, así como para contribuir al conocimiento de la epidemiología clásica y molecular,la diversidad genética y la susceptibilidad frente a los antibióticos. La ubicuidad e importancia como patógenode este microorganismo a nivel mundial nos obliga a considerar y a proponer alternativas efectivas paraaislarlo e identificarlo de rutina en los laboratorios de microbiología. La presente revisión estuvo orientadaa describir la literatura referente a las condiciones requeridas para el cultivo de este microorganismo en ellaboratorio

Early diagnosis and culturing of Helicobacter pylori are of great importance for the study of the growth characteristicsof these bacteria which can contribute to knowledge of classical and molecular epidemiology, geneticdiversity and susceptibility to antibiotics. The ubiquity and importance of this pathogen throughout the worldhas forced us to consider and propose effective routine alternatives for isolating and identifying these bacteriain microbiology laboratories. This review was conducted to describe the literature concerning the conditionsfor cultivation of this organism in the laboratory

Kinetic comparison of microbial assemblages for the anaerobic treatment of wastewater with high sulfate and heavy metal contents.

Mixed-microbial assemblages enriched from a septic tank, coastal sediment samples, the digester sludge of a brewery wastewater treatment plant and acidic sulfate soil samples were compared on the basis of growth rate, waste and sulfate reduction rate under sulfate reducing conditions at 30oC. The specific growth rate of various cultures was in the range 0.0013-0.0022 hr-1. Estimates of waste and sulfate reduction rate were obtained by fitting substrate depletion and sulfate reduction data with the Michaelis-Menten equation. The waste reduction rates were in the range 4x10-8-1x10-7 l mg-1hr-1 and generally increased in the presence of copper, likely by copper sulfide precipitation that reduced sulfide and copper toxicity and thus protected the anaerobic microbes. Anaerobic microorganisms from a brewery digester sludge were found to be the most appropriate culture for the treatment of wastewater with high sulfate and heavy metal content due to their growth rate, and waste and sulfate reduction rate.

Investigation of the Information about Microbial Samples Collecting for Nurses / 中华医院感染学杂志

OBJECTIVE To understand the nurses′ awareness of specimen collection and explore the impact of acquisition-related factors and provide the basis for standardized training.METHODS A questionnaire was designed for specimen collection survey about microorganisms in level-3 hospital.RESULTS 90.38 percent of nurses consulted the laboratory,80.77 percent communicated with other nurses to solve the problom about microbiology specimen collection and 94.2% thought it necessary about continuing education.The ward nurses′ knowledge about microbiology specimen collection was better than these from surgical department.CONCLUSIONS It is urgent that stundard training of specimen collection should be implement in medintely due to lacking the awareness.

Comparison of Rhizosphere Microorganisms Between Fusarium Wilt Resistant and Susceptible Watermelon / 微生物学通报

In this paper, the number of rhizosphere and non-rhizosphere microbial organisms of fusarium wilt resistant and susceptible watermelon under soil culture and soilless substrate culture was studied by traditional culture methods. The results showed that, the number of rhizoshpere microorganisms was significantly higher than non-rhizosphere, and the number was changed with the stage of watermelon grow, the number was the lowest in seedling stage and increased with the watermelon grow, and achieved highest at the flowering and fruiting stage, decreased with the watermelon ageing. The fusarium wilt resistant of watermelon was correspondence with number of rhizosphere bacteria; the number of rhizosphere bacteria of resistant watermelon was higher than that of susceptible watermelon in each stage under soil culture and soilless culture. The fusarium wilt resistant of watermelon is no correspondence with number of rhizosphere fungi and actinomycete. The number of non-rhizosphere microbial organisms was changed in a small range in the whole growing stage. The non-rhizosphere bacteria have no significant change in the whole stage under soil culture and increased quickly under soilless substrate culture and decreased at the later stage. The non-rhizosphere fungi and actinomycete reached highest at the later stage under soil culture or soilless sub-strate culture.

Preventing Catheter-associated Urinary Tract Infection by Smearing Catheter Surface with Chloramphenicol:A Clinical Research / 中华医院感染学杂志

OBJECTIVE To explore the effect of smearing catheter surface with chloramphenicol for preventing catheter -associated urinary tract infections. METHODS Totally 100 cases of preoperative patients needed for indwelling urethral catheters were randomly grouped, 50 of 100 cases as test group, and the others 50 cases as the control group. Catheters after smearing surface with chloramphenicol were inserted using aseptic technique in the test group, urinary catheters without using chloramphenicol were inserted in the control group according to routine aseptic technique protocol, and then regularly taken out urinary specimen from two groups respectively for microbial culture. RESULTS The observation showed bacterial growth positive rate was 30%, and 66.7%, respectively in the control group, but positive rate was 6.7%, and 30%, respectively in the test group after the seventh day and the tenth day. There was a statistic significant difference (P