A High Offset Distribution Tolerance High Resolution ISFET Array With Auto-Compensation for Long-Term Bacterial Metabolism Monitoring.

This paper presents a CMOS ion-sensitive-field-effect-transistor (ISFET) array with superior offset distribution tolerance, resolution and linearity for long-term bacterial metabolism monitoring. A floating gate ISFET is adopted as the sensing front end to maximize ion sensitivity and support ultra-long-term measurement. To solve the DC offset issue induced by trapped chargers and drifts in each ISFET sensor, a complementary readout scheme with column offset compensation is proposed. P-type and N-type source followers are combined to cover a wide range of input DC offsets while maintaining small area and high linearity. The DC offset is digitally compensated during signal readout to facilitate global amplification and quantization. Fabricated in 0.18 µm standard CMOS process, the ISFET array can tolerate an offset distribution beyond power supply with a linear pH-to-output response. Due to high ion sensitivity and low circuit noise, the whole system achieves a high resolution of 0.017 pH. The proposed ISFET system has successfully demonstrated an accurate pH monitoring of normal Escherichis coli growth for 11 hours and its response to antibiotics, showing long-term bacterial metabolism monitoring capability.

ODX: A Fitness Tracker-Based Device for Continuous Bacterial Growth Monitoring.

Continuous monitoring of bacterial growth in aqueous media is a crucial process in academic research as well as in the biotechnology industry. Bacterial growth is usually monitored by measuring the optical density of bacteria in liquid media, using benchtop spectrophotometers. Due to the large form factor of the existing spectrophotometers, they cannot be used for live monitoring of the bacteria inside bacterial incubation chambers. Additionally, the use of benchtop spectrometers for continuous monitoring requires multiple samplings and is labor intensive. To overcome these challenges, we have developed an optical density measuring device (ODX) by modifying a generic fitness tracker. The resulting ODX device is an ultraportable and low-cost device that can be used inside bacterial incubators for real-time monitoring even while shaking is in progress. We evaluated the performance of ODX with different bacterial types and growth conditions and compared it with a commercial benchtop spectrophotometer. In all cases, ODX showed comparable performance to that of the standard benchtop spectrophotometer. Finally, we demonstrate a simple and useful smartphone application whereby the user is notified when the bacterial concentration reaches the targeted value. Due to its potential for automation and mass production, we believe that the ODX has a wide range of applications in biotechnology research and industry.

[Mass spectrometry in bacteriology]. / Place de la spectrométrie de masse en bactériologie.

Recently, different bacteriological laboratory interventions that decrease reporting time have been developed. These promising new broad-based techniques have merit, based on their ability to identify rapidly many bacteria, organisms difficult to grow or newly emerging strains, as well as their capacity to track disease transmission. Maldi-TOF MS has been proven to be an accurate and reliable method for organism identification including bacteria, yeast, molds, and mycobacteria. It is rapid, with results often 24 hours earlier than traditional methods, and inexpensive. The range of applications of Maldi-TOF MS has been growing constantly, from rapid species identification to labor-intensive proteomic studies of bacterial physiology (bacterial resistance and virulence). The purpose of this review is to present the different solutions commercialized in France, summarize the place of this technology in microbiology lab and to analyze future perspectives in this field.

Effect of heat-assisted pulsed electric fields and bacteriophage on enterohemorrhagic Escherichia coli O157:H7.

Pulsed electric fields (PEF), heat-assisted PEF (H-PEF), and virulent bacteriophage (VP) are non-thermal techniques for pathogen inactivation in liquids that were investigated individually, and in combination (PEF/VP, H-PEF/VP) to control enterohemorrhagic Escherichia coli (EHEC) O157:H7 in Luria-Bertani broth (LBB) and Ringer's solution (RS). Treated cells were subsequently incubated at refrigeration (4°C) and temperature-abuse conditions (12°C) for 5 days. When EHEC cells grown in LBB were subjected to non-thermal processing and subsequently stored at 12°C for 5 days, reductions in count of between 0.1 and 0.6 log cycles were observed and following storage at 4°C the decrease in counts varied between 0.2 and 1.1 log10 . For bacteria cells suspended in RS values ranged from 0.1 to ≥3.9 log cycles at both storage temperatures. The most effective treatments were H-PEF and H-PEF/VP, both producing a >3.4 log cycle reduction of cells suspended in non-nutrient RS. Analysis of EHEC recovery on selective and non-selective media indicated no occurrence of sub-lethal damage for VP, PEF/VP, and H-PEF/VP-treated cells. The findings indicate that combining PEF and lytic phage may represent a suitable alternative to conventional fluid decontamination following further process optimization.

Antibodies against rickettsiae from spotted fever groups in horses from two mesoregions in the state of Santa Catarina, Brazil / Anticorpos contra rickettsias do grupo da febre maculosa em equinos de duas mesorregiões de Santa Catarina, Brasil

Bacteria of the Rickettsia genus are agents of Brazilian Spotted Fever (BSF), a zoonotic disease which is difficult to diagnose, evolves quickly and can result in death. Antibodies against Rickettsia spp. in horses were studied, by means of Indirect Immunofluorescence Assay (IFAT ≥64), in 150 blood samples taken from animals in two Santa Catarina mesoregions (Planalto Serrano and Vale do Itajaí). The overall occurrence of Rickettsia spp. antibodies in horses was 18.66%, with cross-reactivity occurring in all positive samples for at least two of the species tested. Separately, according to the species, 25 (16.66%) samples were positive for R. rickettsii, 15 (10%) for R. parkeri, 22 (14.66%) for R. amblyommii, 23 (15.33%) for R. rhipicephali, 16 (10.66%) for R. bellii and 19 (12.66%) for R. felis. Only two animals resulted in a conclusive serodiagnosis, one for R. bellii and the other for R. rickettsii, at maximum dilutions of 1:4096 and 1:512, respectively. The occurrence of antibodies against Rickettsia spp. in horses from two mesoregions in the state of Santa Catarina indicates the movement of BSF agents in these sentinel animals and confirms the importance of studying spotted fever in the state of Santa Catarina.

Bactérias do gênero Rickettsia são agentes da Febre Maculosa Brasileira (FMB), uma doença zoonótica, de difícil diagnóstico, rápida evolução e que pode levar o indivíduo à morte. Anticorpos contra Rickettsia spp. em equinos foram pesquisados, por meio da Reação de Imunofluorescência Indireta (RIFI≥64), em 150 amostras de sangue colhidas de animais em duas mesorregiões de Santa Catarina (Planalto Serrano e Vale do Itajaí). A ocorrência de anticorpos contra Rickettsia spp. observada em equinos de duas mesorregiões de Santa Catarina foi de 18,66%, ocorrendo reações cruzadas em todas as amostras positivas para, no mínimo, duas das espécies testadas. Isoladamente, de acordo com as espécies, 25 (16,66%) amostras foram positivas para R. rickettsii, 15 (10%) para R. parkeri, 22 (14,66%) para R. amblyommii, 23 (15,33%) para R. rhipicephali, 16 (10,66%) para R. bellii e 19 (12,66%) para R. felis. Somente dois animais resultaram em um sorodiagnóstico conclusivo, um para Rickettsia bellii e outro para R. rickettsii, nas diluições máximas de 1:4096 e 1:512, respectivamente. A ocorrência de anticorpos contra Rickettsia spp. em equinos de duas mesorregiões de Santa Catarina indica a circulação de agentes da FMB nestes animais sentinela e ratificam a importância do estudo da febre maculosa no estado de Santa Catarina.

Depth-dependent differences in community structure of the human colonic microbiota in health.

OBJECTIVE: The aims of this study were to develop techniques for spatial microbial assessment in humans and to establish colonic luminal and mucosal spatial ecology, encompassing longitudinal and cross-sectional axes. DESIGN: A microbiological protected specimen brush was used in conjunction with a biopsy forceps to sample the colon in nine healthy volunteers undergoing colonoscopy. Terminal Restriction Fragment Length Polymorphism analysis was used to determine the major variables in the spatial organization of the colonic microbiota. RESULTS: Protected Specimen Brush sampling retrieved region-specific, uncontaminated samples that were enriched for bacterial DNA and depleted in human DNA when compared to biopsy samples. Terminal Restriction Fragment Length Polymorphism analysis revealed a segmentation of bacterial communities between the luminal brush and biopsy-associated ecological niches with little variability across the longitudinal axis of the colon and reduced diversity in brush samples. CONCLUSION: These results support the concept of a microbiota with little longitudinal variability but with some degree of segregation between luminal and mucosal communities.

[Bergey's Manual of Systematic Bacteriology (second edition) Volume 5 and the study of Actinomycetes systematic in China].

Bergey's Manual of Systematic Bacteriology (hereinafter referred to as "Bergey's Manual") is the collection of academic views accepted by taxonomists in many countries. It has scientificity, unitarity and practicality. "Bergey's Manual" (special issue of Actinomycetes) divided into two parts (part A and part B) was published in May, 2012. Under the guidance and the organization of Michael Goodfellow et al., the great work has been completed successfully in May 2012. "Bergey's Manual" made a great modification on the systematic of Actinomycetes and formally set up the phylum of Actinobacteria, which encompasses 6 classes, 23 orders (include one order incertae sides), 53 families, 222 genera and about 3000 species. The taxonomic catalogue is Bacteria, phylum of Actinobacteria, under the phylum there are class, order, family, genera and species. "Bergey's Manual" collected a great deal of new taxa, which were published in IJSEM (International Journal of Systematic and Evolutionary Microbiology) by Chinese scientists. We need to indicate that due to its too rigorous, conservative writing purpose and long publication periods, "Bergey's Manual" fails to collect new research results using the molecular approaches of multilocus sequence analysis "MLSA", gene chip technology and genome technologies, which however will profoundly change the taxonomy of prokaryotes in the near future.

[Who saw them the first?]. / ¿Quién las vio primero?

From the theory of Girolamo Fracastoro in 1530, suggesting the participation of invisible seeds in the contagion of some diseases, to the universal genius Athanasius Kircher, who saw little worms in the blood of patients suffering from plague in 1659 and the final discovery of Anthony Van Leeuwenhoek in 1674, the existence of bacteria was surely in the mind of a few investigators. Kirchner, who seems to be the winner of this race, did not give any special meaning to his observations. Leeuwenhoek, instead, was deeply concerned about the importance of his discovery in the field of biology, but was unable to establish a link between these animalcula and human epidemic diseases.

Detecção de Helicobacter spp. em amostras de mucosa gástrica de cães assintomáticos e alterações histológicas associadas / Identification of Helicobacter spp. in gastric mucosa samples asymptomatic dogs and associate histological alterations

O presente estudo teve por objetivo correlacionar o número de bactérias espiraladas e as alterações histológicas da mucosa gástrica em cães de vida livre. Foram analisadas biopsias gástricas endoscópicas de 28 cães assintomáticos. Para análise histológica, foi realizada avaliação qualitativa, onde foram atribuídos escores de 0 a 3, considerando a densidade de bactérias espiraladas por campo (400x), a presença de células inflamatórias, o número de agregados linfoides e a existência de alteração degenerativa glandular. A prevalência de Helicobacter spp, identificado pela histologia (Carbol-Fucscina) e positividade no teste da urease, foi de 100%. Dos 28 cães, 18 (64,3%) receberam escore 3 e 10 (35,7%) o escore 2 para a densidade de bactérias. O infiltrado inflamatório predominantemente linfoplasmocitário foi de grau leve (escore 1) em 17 (60,7%) cães e moderado em 6 (21,4%) cães. Dos 28 cães, 14 (50%) receberam escore 1 para degeneração glandular e 9 (32,1%), o escore 0. As regiões do corpo e antro apresentaram maior número de resultados positivos à histopatologia. Apesar do número elevado de bactérias encontrado nas amostras analisadas, as alterações histológicas foram classificadas como de grau leve na maioria dos animais. A presença do Helicobacter spp. não parece estar relacionado com sintomatologia de gastrite.

The objective of the present study was to establish a relationship between the number of spiral bacteria and gastric mucosa histological alterations in mongrel dogs. Endoscopic biopsies of 28 asymptomatic dogs were analyzed. Qualitative evaluation was performed for histological analysis, in which scores from 0 to 3 were attributed, considering the density of spiral bacteria per field (400x), presence of inflammatory cells, number of lymphoid aggregates and existence of gland degenerative alteration. The prevalence of Helicobacter spp., identified by hystological technique (Carbol – fuchsine) and positive urease test, was100%. Eighteen (64.3%) of the 28 dogs presented score 3, and 10 (35.7%0), score 2 for the density of bacteria. The inflammatory infiltrate, predominantly lymphocytic, was slight (score 1) in 17dogs (60.7%) and moderate in 6 (21.4%). From the 28 dogs, 14 (50%) scored 1 for glandular degeneration and 9 (32.1%) scored 0. The body and antrum regions presented the highest positive result to histopathology. Despite the high number of bacteria found in the analyzed samples, the histological alterations have been classified as slight in most of the animals. The presence of Helicobacter spp. apparently does not produces gastritis symptoms.

Automation in clinical bacteriology: what system to choose?

With increased activity and reduced financial and human resources, there is a need for automation in clinical bacteriology. Initial processing of clinical samples includes repetitive and fastidious steps. These tasks are suitable for automation, and several instruments are now available on the market, including the WASP (Copan), Previ-Isola (BioMerieux), Innova (Becton-Dickinson) and Inoqula (KIESTRA) systems. These new instruments allow efficient and accurate inoculation of samples, including four main steps: (i) selecting the appropriate Petri dish; (ii) inoculating the sample; (iii) spreading the inoculum on agar plates to obtain, upon incubation, well-separated bacterial colonies; and (iv) accurate labelling and sorting of each inoculated media. The challenge for clinical bacteriologists is to determine what is the ideal automated system for their own laboratory. Indeed, different solutions will be preferred, according to the number and variety of samples, and to the types of sample that will be processed with the automated system. The final choice is troublesome, because audits proposed by industrials risk being biased towards the solution proposed by their company, and because these automated systems may not be easily tested on site prior to the final decision, owing to the complexity of computer connections between the laboratory information system and the instrument. This article thus summarizes the main parameters that need to be taken into account for choosing the optimal system, and provides some clues to help clinical bacteriologists to make their choice.

Seguimiento durante 8-12 años de pacientes de lepra muy bacilíferos tratados con multiterapia OMS / No disponible

Objetivos: El seguimiento de pacientes de lepra muy bacilíferos durante un largo período después del alta de su tratamiento (RFT) y la detección de posibles recidivas. Resultados: Se siguió a 600 pacientes con un índice bacteriológico de positividad 4+, 5+ o 6+ y que habían completado la multiterapia OMS y dados de alta. Se controló la regularidad de su tratamiento mediante visitas domiciliarias. Después de la RFT fueron revisados dos veces, una entre los 4-9 años y otra a los 7-12 años. Se examinaron 516 pacientes en la segunda revisión. Por criterios de la OMS, 5 pacientes habían recidivado, con un índice de recidivas del 0.103 por 100 personas/año. Esta baja recidiva podría atribuirse a la elevada adherencia al tratamiento. Conclusión: Se puede conseguir mediante un MDT supervisado y buena adherencia al tratamiento un bajo índice de recidivas (AU)

Objective. To follow up highly bacillated leprosy patients for a long period after release from treatment (RFT) and to look out for possibility of relapses. Results. 660 patients with an initial bacterial positivity of 4 +, 5 + or 6 + who had undergone WHO multi-drug therapy and released from treatment, were followed up. The regularity of their treatment was kept high by close monitoring with home visits. They were reviewed twice, once 4 to 9 years after RFT and again 7 to 12 years after RFT. 516 patients were available in the second review. As per WHO definition, 5 patients were found to have relapsed, giving a relapse rate of 0.103 per 100 person years. This low relapse rate could be due to high regularity of treatment. Conclusion. With well supervised MDT and high regularity of treatment and proper consumption of drugs, relapse rate is very low (AU)

Effect of blood and mucus on tympanostomy tube biofilm formation.

OBJECTIVES/HYPOTHESIS: Tympanostomy tube (TT) biofilm formation may lead to refractory otorrhea and occlusion. The aim of this study was to determine whether TT biofilm formation may be promoted by mucus or blood exposure. STUDY DESIGN: In vitro, controlled. METHODS: Fluoroplastic TTs were exposed to blood, mucoid effusion, or saline. Half were allowed to dry. TTs were cultured with Pseudomonas aeruginosa. After 4 days, gentamicin was added to kill planktonic bacteria. Biofilm formation was assessed by quantitative bacterial counts and scanning electron microscopy. RESULTS: Mucus pretreatment (dry and wet) did not increase biofilm formation. Both dry and wet blood exposure increased biofilm formation by bacterial counts (P < .0001). Biofilm formation was demonstrated by electron microscopy in all groups. CONCLUSIONS: P. aeruginosa biofilm formation on fluoroplastic TTs is enhanced by blood exposure. Care should be taken to minimize bleeding with TT placement to reduce the risk of biofilm formation.

System for real-time monitoring of mutation-in-progress.

AIMS: There has been an increasing number of pathogens becoming resistant to multiple classes of antibiotics. The study on how mutation emerges is therefore crucial to promote further understanding in this area. Conventional methods for such studies involve the monitoring of growth by standard plate count and biomolecular sequencing. This is however tedious and not cost effective. The aim of this paper is thus to introduce a novel system that enables real-time monitoring of bacterial 'mutation-in-progress'. METHODS AND RESULTS: This system provides real-time data, thus enabling confirmatory and further work to be performed at the important points when mutation is initiated. The system integrates spectroscopic techniques as the detection system and various supporting systems, such as a nutrient replenishing system, a pH control system and a waste system to allow for extended monitoring. In this paper, the feasibility of monitoring the emergence of ciprofloxacin resistance in Staphylococcus aureus was demonstrated as an initial example. The integrated system was found to require significantly less material resource and manpower compared with conventional techniques. CONCLUSIONS: The novel system to monitor bacterial mutation-in-progress is presented. The work reported herein demonstrates such a system to be effective and efficient in performing real-time monitoring of mutation-in-progress, especially in extended time frames for mutation into the weeks and months. SIGNIFICANCE AND IMPACT OF THE STUDY: With the successful optimization of this system, researchers can learn about the dynamics of antibiotic resistance and further understand how the mutation of bacteria occurs.

Stenotrophomonas maltophilia, bacilo gram negativo no fermentador aislados de muestras clínicas de pacientes pediátricos / Stenotrophomas maltophilia gram negativ rod isloted ferment with nosocomial of patients infants

Stenotrophomonas maltophilia (SMA) es un bacilo gram negativo no fermentador que causa infecciones en pacientes con defensas disminuidas y/o instrumentados. Se realizó un análisis retrospectivo de los aislamientos obtenidos en el año 2003 en el laboratorio de Bacteriología del Hospital de Niños Sor María Ludovica. Se obtuvieron 64 aislamientos de los cuales 36 fueron de origen respiratorio y 24 de hemocultivos. Tanto su resistencia a carbapenemes como su sensibilidad a TMS son orientadores para su diagnóstico microbiológico. Este perfil asociado a resistencia a otros antibióticos suele plantear problemas terapéuticos severos

Direct identification of Mycobacterium avium complex and Mycobacterium gordonae from MB/BacT bottles using AccuProbe.

We evaluated the ability of the AccuProbe (Gen-Probe, San Diego, Calif.) to detect Mycobacterium gordonae and Mycobacterium avium complex directly in liquid medium flagged positive by the MB/BacT (Organon Teknika Corp., Durham, N.C.). Seventy-one bottles from clinical specimens containing M. gordonae and 34 containing M. avium, confirmed by culture, were tested by direct AccuProbe assay for both organisms after additional incubation for > or = 48 h and centrifugation at 4,500 x g for 15 min. Relative light unit (RLU) values were analyzed using the manufacturer's recommended cutoff of 30,000 RLU and a lower cutoff of 10,000 RLU. Using the 30,000 RLU cutoff, 55 of 71 (77.5%) specimens containing M. gordonae yielded positive results, whereas 28 of 34 (82.3%) M. avium complex specimens were correctly identified by direct probe. No specimens shown by culture to contain either M. gordonae or M. avium complex tested positive with the probe for the opposite organism (100% specificity). When the cutoff was lowered to 10,000 RLU, 67 of 71 M. gordonae (94.4%) and 32 of 34 M. avium complex (94.1%) specimens were correctly identified. This difference was significant for M. gordonae (P = 0.004) but not for M. avium complex (P = 0.26) compared to detection using the recommended RLU cutoff. Specificity was 100% for specimens containing M. gordonae that were tested with the M. avium complex probe using the 10,000 RLU cutoff, whereas specificity for specimens containing M. avium complex tested with the M. gordonae probe was 97%. Using a lower RLU cutoff for determining a positive result using the M. gordonae or M. avium complex probes when testing instrument-positive MB/BacT bottles directly will improve sensitivity without substantially compromising specificity.

Un método sencillo para generar anaerobiosis en tubos de cultivo / A simple method to achieve anaerobiosis in culture media tubes

Introducción. El cultivo de bacterias anaerobias requiere una atmósfera libre de oxígeno, por lo cual, a pesar de la gran importancia clínica de los anaerobios, el diagnóstico usualmente es sólo microscópico. En este estudio se propone y evalúa un método para preparar tubos de medio de cultivo libres de oxígeno, sencillo, económico y al alcance de cualquier laboratorio. Material y métodos. La atmósfera anaerobia se logra durante el proceso de autoclavado y descompresión rápida de los tubos a los que se le ha incorporado un tapón de hule, tapa de rosca y una aguja a través de la cual se elimina la atmósfera aerobia. Para evaluar la efectividad de estos medios se crecieron 45 especies de clostridium y 12 especies de los géneros Bifidobacterium, acteroides, Lactobacillus, Propionibacterium y Actinomyces, (hasta completar 80 cepas), en tubos anaeróbios prerreducidos antes de esterilizar (PRAS) y en tubos preparados de acuerdo con el método propuesto. Resultados. Las 80 cepas de bacterias anaerobias crecieron en los tubos prerreducidos y sin prerreducir, no hubo diferencias en los grados de turbiedad. Discusión. El método propuesto para generar anaerobiosis en los tubos de cultivo es una posibilidad al alcance a cualquier laboratorio de bacteriología, para mejorar el diagnóstico, mediante cultivo, de infecciones por bacterias anaerobias