Integration of surface swab with optical microscopy for detection and quantification of bacterial cells from stainless-steel surfaces

Swab sampling is a common method for recovering microbes on various environmental surfaces. Its successful application for a specific target depends on the proper swab method and the following detection assay. Herein, we evaluated critical factors influencing surface swab sampling, aiming to achieve the optimal detection and quantification performance of optical detection for bacterial cells on stainless-steel surfaces. Our results showed the recovery rate of Salmonella enterica (SE1045) cells from the 10 × 10 cm2 stainless-steel surface reached up to 92.71 ± 2.19% when using ammonia bicarbonate-moistened polyurethane foam swabs for gentle collection, followed by ultrasound-assisted release in NH4HCO3 solution. Among the six different foam swabs, the Puritan™ Sterile Large Foam Swab contributed the lowest background noise and highest recovery efficiency when integrated with the optical detection assay. Notably, our method exhibited a strong linear relationship (r2 = 0.9983) between the detected cell numbers and the theoretical number of SE1045 cells seeded on surfaces in the range of 104-107 Colony Forming Units (CFU), with a limit of detection of 7.2 × 104 CFU 100 cm-2. This integration was completed within 2 h, exhibiting the applicable potential in various settings.

PMSOMA: optical microscope algorithm based on piecewise linear chaotic mapping and sparse adaptive exploration

The optical microscope algorithm (OMA) is a metaheuristic algorithm that draws inspiration from the magnifying functionality of optical microscopes. This study introduces an enhanced variant of OMA, termed PMSOMA, designed to mitigate the original version's limitations, notably its slow convergence rates and vulnerability to local optima. PMSOMA integrates a piecewise linear chaotic map to refine population initialization and augment diversity, alongside a sparse adaptive exploration mechanism to bolster search efficacy. The performance of PMSOMA was rigorously tested using a suite of 50 benchmark functions, the CEC2017 test suite, feature selection datasets, and three classical engineering challenges. The empirical findings confirm that PMSOMA surpasses both the original OMA and competing algorithms by delivering superior solutions, accelerating convergence, and demonstrating enhanced robustness in convergence.

Bacterial image analysis using multi-task deep learning approaches for clinical microscopy

Background

Bacterial image analysis plays a vital role in various fields, providing valuable information and insights for studying bacterial structural biology, diagnosing and treating infectious diseases caused by pathogenic bacteria, discovering and developing drugs that can combat bacterial infections, etc. As a result, it has prompted efforts to automate bacterial image analysis tasks. By automating analysis tasks and leveraging more advanced computational techniques, such as deep learning (DL) algorithms, bacterial image analysis can contribute to rapid, more accurate, efficient, reliable, and standardised analysis, leading to enhanced understanding, diagnosis, and control of bacterial-related phenomena.

Methods

Three object detection networks of DL algorithms, namely SSD-MobileNetV2, EfficientDet, and YOLOv4, were developed to automatically detect Escherichia coli (E. coli) bacteria from microscopic images. The multi-task DL framework is developed to classify the bacteria according to their respective growth stages, which include rod-shaped cells, dividing cells, and microcolonies. Data preprocessing steps were carried out before training the object detection models, including image augmentation, image annotation, and data splitting. The performance of the DL techniques is evaluated using the quantitative assessment method based on mean average precision (mAP), precision, recall, and F1-score. The performance metrics of the models were compared and analysed. The best DL model was then selected to perform multi-task object detections in identifying rod-shaped cells, dividing cells, and microcolonies.

Results

The output of the test images generated from the three proposed DL models displayed high detection accuracy, with YOLOv4 achieving the highest confidence score range of detection and being able to create different coloured bounding boxes for different growth stages of E. coli bacteria. In terms of statistical analysis, among the three proposed models, YOLOv4 demonstrates superior performance, achieving the highest mAP of 98% with the highest precision, recall, and F1-score of 86%, 97%, and 91%, respectively.

Conclusions

This study has demonstrated the effectiveness, potential, and applicability of DL approaches in multi-task bacterial image analysis, focusing on automating the detection and classification of bacteria from microscopic images. The proposed models can output images with bounding boxes surrounding each detected E. coli bacteria, labelled with their growth stage and confidence level of detection. All proposed object detection models have achieved promising results, with YOLOv4 outperforming the other models.

Biodegradation of paraquat by Pseudomonas putida and Bacillus subtilis immobilized on ceramic with supplemented wastewater sludge

This work aimed to study the performance of paraquat removal by cell-immobilized ceramics. Two strains of paraquat degrading bacteria, Pseudomonas putida and Bacillus subtilis, were separately immobilized on the ceramic with and without wastewater sludge addition. Results showed that the ceramic surface with sludge has more functional groups and a more highly negative charge on the surface than the original ceramic. The ceramic with sludge had 2-3-fold of the immobilized cells higher than that of the control (without sludge) and less leaching of the immobilized cells. The sludge addition at 20% (w/w) to the ceramic provided the highest cell adhesion for both P. putida and B. subtilis. The paraquat removal efficiencies were higher than 98%, while the control ceramic could remove only 77 ± 1.2%. The immobilized cells on ceramic with sludge provided a significant degree of dissolved organic nitrogen reduction (82%) during the paraquat removal. Most organic nitrogen in paraquat was biologically mineralized (ammonified). Findings from this work suggest the superiority of ceramic with sludge in mineralizing organic nitrogen associated with paraquat.