ScanGrow: Deep Learning-Based Live Tracking of Bacterial Growth in Broth

Monitoring the growth of bacterial cultures is one of the most common techniques in microbiology. This is usually achieved by using expensive and bulky spectrophotometric plate readers which periodically measure the optical density of bacterial cultures during the incubation period. In this study, we present a completely novel way of obtaining bacterial growth curves based on the classification of scanned images of cultures rather than using spectrophotometric measurements. We trained a deep learning model with images of bacterial broths contained in microplates, and we integrated it into a custom-made software application that triggers a flatbed scanner to timely capture images, automatically processes the images, and represents all growth curves. The developed tool, ScanGrow, is presented as a low-cost and high-throughput alternative to plate readers, and it only requires a computer connected to a flatbed scanner and equipped with our open-source ScanGrow application. In addition, this application also assists in the pre-processing of data to create and evaluate new models, having the potential to facilitate many routine microbiological techniques.

Imitation of β-lactam binding enables broad-spectrum metallo-β-lactamase inhibitors

Carbapenems are vital antibiotics, but their efficacy is increasingly compromised by metallo-β-lactamases (MBLs). Here we report the discovery and optimization of potent broad-spectrum MBL inhibitors. A high-throughput screen for NDM-1 inhibitors identified indole-2-carboxylates (InCs) as potential β-lactamase stable β-lactam mimics. Subsequent structure-activity relationship studies revealed InCs as a new class of potent MBL inhibitor, active against all MBL classes of major clinical relevance. Crystallographic studies revealed a binding mode of the InCs to MBLs that, in some regards, mimics that predicted for intact carbapenems, including with respect to maintenance of the Zn(II)-bound hydroxyl, and in other regards mimics binding observed in MBL-carbapenem product complexes. InCs restore carbapenem activity against multiple drug-resistant Gram-negative bacteria and have a low frequency of resistance. InCs also have a good in vivo safety profile, and when combined with meropenem show a strong in vivo efficacy in peritonitis and thigh mouse infection models.

An approach to increase the success rate of cultivation of soil bacteria based on fluorescence-activated cell sorting

Soil microbiota are considered a source of undiscovered bioactive compounds, yet cultivation of most bacteria within a sample remains generally unsuccessful. Two main reasons behind the unculturability of bacteria are the presence of cells in a viable but not culturable state (such as dormant cells) and the failure to provide the necessary growth requirements in vitro (leading to the classification of some bacterial taxa as yet-to-be-cultured). The present work focuses on the development of a single procedure that helps distinguish between both phenomena of unculturability based on viability staining coupled with flow cytometry and fluorescence-activated cell sorting. In the selected soil sample, the success rate of cultured bacteria was doubled by selecting viable and metabolically active bacteria. It was determined that most of the uncultured fraction was not dormant or dead but likely required different growth conditions. It was also determined that the staining process introduced changes in the taxonomic composition of the outgrown bacterial biomass, which should be considered for further developments. This research shows the potential of flow cytometry and fluorescence-activated cell sorting applied to soil samples to improve the success rate of bacterial cultivation by estimating the proportion of dormant and yet-to-be-cultured bacteria and by directly excluding dormant cells from being inoculated into growth media.

Antimicrobial activity of suspensions and nanoemulsions of citral in combination with heat or pulsed electric fields

The application of essential oils in form of nanoemulsions has been proposed as a method to improve their solubility in aqueous solutions, and hence their antimicrobial activity. The objective of this study was to evaluate the antimicrobial activity of citral, applied directly or in combined treatments with heat or pulsed electric fields (PEF), as a function of the inoculation procedure assayed: (i) a simple, vigorous shaking method by vortex agitation (suspension of citral; s-citral) or (ii) the previous preparation of nanoemulsions by the emulsion phase inversion (EPI) method (nanoemulsion of citral; n-citral). n-Citral was more effective in either inhibiting or inactivating Escherichia coli O157:H7 Sakai than s-citral. However, when combined with heat, a greater synergistic effect was observed with s-citral rather than with n-citral, either in lab media (pH 7·0 and 4·0) or apple juice. For instance, while almost 5 log₁₀ cell cycles were inactivated in apple juice after 15 min at 53°C in the presence of 0·1 μl ml^-1 of s-citral, the use of n-citral required 30 min. The use of nanoemulsions did not modify the slight synergism observed when citral and mild PEF were combined (150 μs, 30 kV cm^-1 ).

SIGNIFICANCE AND IMPACT OF THE STUDY

The exploration of different delivery systems of antimicrobial compounds such as citral in aqueous food products aids in the establishment of successful combined treatments for food preservation. While at room temperature, citral in form of a nanoemulsion shows a higher antimicrobial activity; its combination with heat would imply a partial loss of the outstanding synergistic lethal effect achieved when added in suspension form. Therefore, the most suitable procedure to magnify the synergism between heat and citral when processing juices would merely require an intense homogenization step prior to the combined treatment.

Detection of Thermal Sublethal Injury in Escherichia coli via the Selective Medium Plating Technique: Mechanisms and Improvements

In food preservation, the synergistic combination of different technologies aims to maximize the total lethality of the process and minimize the intensity of each hurdle. This is especially the case when at least one of the treatments can cause sublethal (reparable) injury in a great proportion of the population, so that sublethally injured cells can end up being entirely inactivated by the other hurdle(s). The selective medium plating technique (SMPT) is extensively used to enumerate bacterial sublethal injury after inimical treatments, being sodium chloride added to the recovery medium to detect damaged bacterial envelopes. However, little work has been done to explain the reasons for the inability of sublethally injured cells to outgrow in selective agar media, whereas they are able to grow in non-selective agar. In the present paper, the performance of SMPT on Escherichia coli cells after heat treatments is explored by applying different selective agents in the recovery media, using mutants lacking factors involved in osmoregulation, and also by examining the integrity of the cytoplasmic membrane. In view of the results, the possibility of a specific toxic effect of Na⁺ as the main mechanism under SMPT was discarded, since the same level of sublethal injury was detected using KCl instead of NaCl. The synthesis of the osmoprotectant trehalose determined the maximum osmotolerance of intact cells to the selective agents, but was not crucial in the quantification of sublethal injury. Moreover, for the first time, the extent of sublethal injury detected via SMPT was directly correlated with the physical loss of integrity of the cell membrane in 99.999% of the initial population. This was achieved through statistical analysis of flow cytometry data using propidium iodide-exclusion technique when that dye was added before thermal treatments. The present work confirms the adequacy of SMPT as a tool for detecting the occurrence and quantity of sublethally injured cells after thermal treatments and thus, for efficiently designing the combination of heat with other preservation techniques. We also propose the study of statistical analysis from flow cytometry data for a more rapid quantification of bacterial sublethal injury in a broad detection range.

Combination of pulsed electric fields, mild heat and essential oils as an alternative to the ultrapasteurization of liquid whole egg

The production of microbiologically safe liquid whole egg (LWE) by industrial ultrapasteurization is restricted by the high thermal sensitivity of LWE components. This research proposes an alternative treatment based on the application of pulsed electric fields (PEF) and mild heat, in the presence of natural essential oils (EOs) or their individual components (ICs). The obtained results indicate that the successive application of PEF (25kV/ and 100kJ/kg) followed by heat (60°C during 3.5') to LWE added with 200μL/L of lemon EO would reach 4log10cycles of inactivation of Salmonella Senftenberg 775W and Listeria monocytogenes, when any of these barriers acting alone inactivated less than 1.5log10cycles of either bacteria. Therefore, the synergism between lemon EO and the successive application of PEF and heat would provide a safety level similar to that of ultrapasteurization treatment for Salmonella Senftenberg 775W and L. monocytogenes, but at a lower temperature. To a lesser extent, synergism with the successive application of PEF and heat was also observed in the presence of 200μL/L of carvacrol, citral, (+)-limonene, or mandarin EO, reaching about 3.5log10cycles of inactivation in Salmonella Senftenberg and 3.0log10cycles in L. monocytogenes, respectively. A sensory test on LWE containing 200μL/L of each additive in the form of omelets and sponge cakes revealed that this concentration of mandarin EO, lemon EO, or (+)-limonene did not decrease the sensory acceptability of the LWE-containing products, and lemon EO and mandarin EO even increased the hedonic acceptability of sponge cakes. In conclusion, this process could be applied in the food industry to obtain microbiologically safe LWE, which could be used to produce egg-based products without decreasing (and even increasing) their sensory appeal.

Chemical composition and antioxidant properties of Laurus nobilis L. and Myrtus communis L. essential oils from Morocco and evaluation of their antimicrobial activity acting alone or in combined processes for food preservation

BACKGROUND

This study describes the antioxidant and antimicrobial activity of Laurus nobilis L. and Myrtus communis L. essential oils (EOs). This is the first report of the synergistic antimicrobial effect of these EOs in combination with physical food preservation treatments.

RESULTS

EOs obtained by steam distillation from aerial parts of Laurus nobilis and Myrtus communis were analysed by using gas chromatography-mass spectrometry. The main compounds were 1,8-cineole and 2-carene (L. nobilis EO); and myrtenyl acetate, 1,8-cineole and α-pinene (M. communis EO). L. nobilis EO showed higher antioxidant activity than M. communis EO in three complementary antioxidant tests. Although antimicrobial activity tests demonstrated the effectiveness of L. nobilis EO and the lack of bactericidal effect of M. communis EO, synergistic lethal effects were observed when combining each EO (0.2 µL mL(-1)) with mild heat (54°C for 10 min) or high hydrostatic pressure (175-400 MPa for 20 min). In contrast, combination of EOs with pulsed electric fields (30 kV cm(-1) for 25 pulses) showed no additional effects.

CONCLUSION

This study shows the great potential of these EOs in combined treatments with mild heat and high hydrostatic pressure to obtain a higher inactivation of foodborne pathogens, which might help in the design of safe processes applied at low intensity.

Mechanism of bacterial inactivation by (+)-limonene and its potential use in food preservation combined processes

This work explores the bactericidal effect of (+)-limonene, the major constituent of citrus fruits' essential oils, against E. coli. The degree of E. coli BJ4 inactivation achieved by (+)-limonene was influenced by the pH of the treatment medium, being more bactericidal at pH 4.0 than at pH 7.0. Deletion of rpoS and exposure to a sub-lethal heat or an acid shock did not modify E. coli BJ4 resistance to (+)-limonene. However, exposure to a sub-lethal cold shock decreased its resistance to (+)-limonene. Although no sub-lethal injury was detected in the cell envelopes after exposure to (+)-limonene by the selective-plating technique, the uptake of propidium iodide by inactivated E. coli BJ4 cells pointed out these structures as important targets in the mechanism of action. Attenuated Total Reflectance Infrared Microspectroscopy (ATR-IRMS) allowed identification of altered E. coli BJ4 structures after (+)-limonene treatments as a function of the treatment pH: β-sheet proteins at pH 4.0 and phosphodiester bonds at pH 7.0. The increased sensitivity to (+)-limonene observed at pH 4.0 in an E. coli MC4100 lptD4213 mutant with an increased outer membrane permeability along with the identification of altered β-sheet proteins by ATR-IRMS indicated the importance of this structure in the mechanism of action of (+)-limonene. The study of mechanism of inactivation by (+)-limonene led to the design of a synergistic combined process with heat for the inactivation of the pathogen E. coli O157:H7 in fruit juices. These results show the potential of (+)-limonene in food preservation, either acting alone or in combination with lethal heat treatments.

Synergistic combinations of high hydrostatic pressure and essential oils or their constituents and their use in preservation of fruit juices

This work addresses the inactivation achieved with Escherichia coli O157:H7 and Listeria monocytogenes EGD-e by combined processes of high hydrostatic pressure (HHP) and essential oils (EOs) or their chemical constituents (CCs). HHP treatments (175-400 MPa for 20 min) were combined with 200 μL/L of each EO (Citrus sinensis L., Citrus lemon L., Citrus reticulata L., Thymus algeriensis L., Eucalyptus globulus L., Rosmarinus officinalis L., Mentha pulegium L., Juniperus phoenicea L., and Cyperus longus L.) or each CC ((+)-limonene, α-pinene, β-pinene, p-cymene, thymol, carvacrol, borneol, linalool, terpinen-4-ol, 1,8-cineole, α-terpinyl acetate, camphor, and (+)-pulegone) in buffer of pH 4.0 or 7.0. The tested combinations achieved different degrees of inactivation, the most effective being (+)-limonene, carvacrol, C. reticulata L. EO, T. algeriensis L. EO and C. sinensis L. EO which were capable of inactivating about 4-5 log(10) cycles of the initial cell populations in combination with HHP, and therefore showed outstanding synergistic effects. (+)-Limonene was also capable of inactivating 5 log(10) cycles of the initial E. coli O157:H7 population in combination with HHP (300 MPa for 20 min) in orange and apple juices, and a direct relationship was established between the inactivation degree caused by the combined process with (+)-limonene and the occurrence of sublethal injury after the HHP treatment. This work shows the potential of EOs and CCs in the inactivation of foodborne pathogens in combined treatments with HHP, and proposes their possible use in liquid food such as fruit juices.

New insights in mechanisms of bacterial inactivation by carvacrol

AIMS

To study the mechanism of bacterial inactivation by carvacrol and the influence of genetic and environmental factors in its antimicrobial activity.

METHODS AND RESULTS

In general, bacterial inactivation by carvacrol was higher in the Gram-positive Listeria monocytogenes than in the Gram-negative Escherichia coli and at acidic pH. At pH 4.0, 25 μl l(-1) of carvacrol for 5 h inactivated 1 and more than 5 log(10) cycles of E. coli and L. monocytogenes populations, respectively. Genetic and environmental factors also influenced cell resistance to carvacrol: rpoS and sigB deletion decreased carvacrol resistance in E. coli and L. monocytogenes, respectively; a heat shock induced a phenomenon of cross-protection to carvacrol treatments. Repair of sublethal injuries in cell envelopes suggested that carvacrol targets lipid fractions and proteins of these structures. This result was corroborated by attenuated total reflectance infrared microspectroscopy analysis.

CONCLUSIONS

This study shows critical genetic and environmental factors, such as rpoS or sigB and heat shocks, and reveals new microbial structures involved in the mechanism of bacterial inactivation by carvacrol.

SIGNIFICANCE AND IMPACT OF THE STUDY

A better understanding of the mechanisms of microbial inactivation is of great relevance to design more appropriate carvacrol treatments with high antimicrobial effects.

Effect of citral on the thermal inactivation of Escherichia coli O157:H7 in citrate phosphate buffer and apple juice

Inactivation and sublethal injury of Escherichia coli O157:H7 cells induced by heat in citrate phosphate buffer and apple juice (both at pH 3.8) were studied, and the effect of a combined preservation treatment using citral and heat treatments was determined. Heat resistance of E. coli O157:H7 was similar in both treatment media; after 27 min at 54°C, 3 log units of the initial cell population was inactivated in both treatment media. However, under less harsh conditions a protective effect of apple juice was found. Whereas inactivation followed linear kinetics in the citrate phosphate buffer, when cells were treated in apple juice the survival curves were concave downward. Heat treatment caused a great degree of sublethal injury; 4 min at 54°C inactivated less than 0.5 log CFU/ml but sublethally injured more than 3 log CFU/ml. The addition of 18 and 200 ppm of citral to the treatment medium acted synergistically with heat at 54°C to inactivate 3 × 10(4) and 3 × 10(7) CFU/ml, respectively. Addition of citral thus reduced the time needed to inactivate 1 log unit of the initial E. coli O157:H7 population from 8.9 to 1.7 min. These results indicate that a combined process of heat and citral can inactivate E. coli O157:H7 cells and reduce their potential negative effects.

Clinical and epidemiologic studies of cleft lip and palate in the Philippines

Clinical and epidemiologic studies of defined geographic populations can serve as a means of establishing data important for genetic counseling and as a first step in identifying strategies best suited for identification of causes. Under the sponsorship of Operation Smile International, clinical, genetic, and epidemiologic studies were carried out at six sites within the Philippines between 1989 and 1996. Patients who were being evaluated for surgical repair of craniofacial anomalies (primarily clefts of the lip and palate) were briefly examined for the presence of associated anomalies, and a family history was obtained to look for the frequency of cleft lip and palate in siblings. Birth records of 47,969 newborns over an 8-year period at one hospital in Bacolod City in the province of Negros Occidental were reviewed. Medical records of infants born with clefts of the lip and/or palate and other major anomalies were reviewed and birth prevalence rates calculated. Findings include a birth prevalence of 1.94 per 1000 live births for cleft lip with/without palate in the Philippines. Recurrence rates in siblings for nonsyndromic clefts of the lip and palate were 23 per 1000 for cleft lip with or without cleft palate, and 14 per 1000 for cleft palate only. The percentage of clefts associated with multiple anomalies was 21% at birth and 6% for individuals examined during the screening process, providing evidence for a high postnatal death rate. These data provide groundwork for additional etiologic studies including segregation analysis and molecular genetic studies involving linkage or association, as well as for studies of environmental contributions to clefting such as vitamin deficiencies. Preliminary molecular analysis using an association approach is reported in a companion paper. The findings suggest a high incidence of cleft lip and palate in native-born Filipinos.

Short- and long-term effect of oral salbutamol on growth hormone secretion in prepubertal asthmatic children

Salbutamol, a beta 2-adrenergic agonist, is being extensively used in Venezuela as a brochodilator in the treatment of asthma in children. Previous reports have shown oral salbutamol either to inhibit or not to affect growth hormone (GH) secretion. We evaluated the effect of oral salbutamol (0.1 mg/kg every 6 hours for 3 months) on GH secretion in eight prepubertal short children with mild asthma. Levels of GH during sleep (samples taken every 30 minutes from 9 PM to 6 AM) and after GH-releasing hormone ([GHRH] 1 microgram/kg intravenously [IV]) were measured before, at 24 hours, and at 3 months of salbutamol treatment. Overnight integrated concentrations of GH and peak GH levels following GHRH diminished significantly after 24 hours of salbutamol therapy (from 4.5 +/- 1.3 to 3.4 +/- 0.8 micrograms/L and from 46.6 +/- 47.3 to 16.2 +/- 7.9 micrograms/L, respectively, P < .05). However, GH levels after 3 months of salbutamol were not different from basal levels (4.5 +/- 1.3 v 5.1 +/- 5.1 +/- 2.9 micrograms/L during the overnight studies and 46.6 +/- 47.3 v 37.8 +/- 30.4 micrograms/L after GHRH). Our data suggest an inhibition of both spontaneous and stimulated GH secretion following short-term oral salbutamol ingestion, but this suppressive effect is not maintained with its long-term use.