Gram Staining: a Comparison of Two Automated Systems and Manual Staining

Saccharopolyspora mangrovi sp. nov., a novel mangrove soil actinobacterium with distinct metabolic potential revealed by comparative genomic analysis

A novel mangrove soil-derived actinomycete, strain S2-29T, was found to be most closely related to Saccharopolyspora karakumensis 5K548T based on 16 S rRNA sequence (99.24% similarity) and genomic phylogenetic analyses. However, significant divergence in digital DNA-DNA hybridization, average nucleotide identity, and unique biosynthetic gene cluster possession distinguished S2-29T as a distinct Saccharopolyspora species. Pan genome evaluation revealed exceptional genomic flexibility in genus Saccharopolyspora, with > 95% accessory genome content. Strain S2-29T harbored 718 unique genes, largely implicated in energetic metabolisms, indicating different metabolic capacities from its close relatives. Several uncharacterized biosynthetic gene clusters in strain S2-29T highlighted the strain's untapped capacity to produce novel functional compounds with potential biotechnological applications. Designation as novel species Saccharopolyspora mangrovi sp. nov. (type strain S2-29T = JCM 34,548T = CGMCC 4.7716T) was warranted, expanding the known Saccharopolyspora diversity and ecology. The discovery of this mangrove-adapted strain advances understanding of the genus while highlighting an untapped source of chemical diversity.

Improvement of gram staining effect by ethanol pretreatment and quantization of staining image by unsupervised machine learning

In this study, we propose an Ethanol Pretreatment Gram staining method that significantly enhances the color contrast of the stain, thereby improving the accuracy of judgement, and demonstrated the effectiveness of the modification by eliminating unaided-eye observational errors with unsupervised machine learning image analysis. By comparing the traditional Gram staining method with the improved method on various bacterial samples, results showed that the improved method offers distinct color contrast. Using multimodal assessment strategies, including unaided-eye observation, manual image segmentation, and advanced unsupervised machine learning automatic image segmentation, the practicality of ethanol pretreatment on Gram staining was comprehensively validated. In our quantitative analysis, the application of the CIEDE2000, and CMC color difference standards confirmed the significant effect of the method in enhancing the discrimination of Gram staining.This study not only improved the efficacy of Gram staining, but also provided a more accurate and standardized strategy for analyzing Gram staining results, which might provide an useful analytical tool in microbiological diagnostics.

Pathogenetic characterization of a Micrococcus luteus strain isolated from an infant

Purpose

To explore the clinical characteristics of Micrococcus luteus bloodstream infection in an infant and characterize the phenotype and genotype of the isolated strains, as well as seek suitable infection models for assessing virulence.

Methods

Clinical data was collected from an infant patient diagnosed with M. luteus bloodstream infection. Metagenomic sequencing was performed on the isolated blood sample. The strain was isolated and underwent mass spectrometry, biochemical tests, antibiotic susceptibility assays, and whole-genome sequencing. The Galleria mellonella infection model was used to assess M. luteus virulence.

Results

Patient responded poorly to cephalosporins, but recovered after Linezolid treatment. Metagenomic sequencing identified M. luteus as the predominant species in the sample, confirming infection. They were identified as M. luteus with a high confidence level of 98.99% using mass spectrometry. The strain showed positive results for Catalase, Oxidase, and Urea tests, and negative results for Mannose, Xylose, Lactose, Mannitol, Arginine, and Galactose tests, consistent with the biochemical profile of M. luteus reference standards. M. luteus susceptibility to 15 antibiotics was demonstrated and no resistance genes were detected. Predicted virulence genes, including clpB, were associated with metabolic pathways and the type VI secretion system. The infection model demonstrated dose-dependent survival rates.

Conclusion

The infant likely developed a bloodstream infection with M. luteus due to compromised immunity. Although the isolated strain is sensitive to cephalosporin antibiotics and has low pathogenicity in infection models, clinical treatment with cephalosporins was ineffective. Linezolid proved to be effective, providing valuable guidance for future clinical management of such rare infections.

Antibiotic Delivery System for Treating Bacteria-Induced Anterior Blepharitis

The eyelid-related disease of blepharitis remains a tricky ocular disorder and affects patient compliance. However, there is no available and effective treatment, making it extremely challenging. Herein, an antibacterial system based on antibiotic delivery was developed and applied in a blepharitis model induced by bacteria. The antibacterial tests against Staphylococcus aureus both in vitro and in vivo demonstrated that the system shows a favorable bactericidal effect. Then, histological evaluation indicated that the system shows both antibacterial and anti-inflammatory effects. This facile design provided an effective ocular infection management, which displays a promising prospect while addressing other complex ocular disorders.

Automation of slide staining for large tissue sections

Staining is a critical step in tissue analysis as it enhances the visibility and contrast of tissue structures for microscopic examination. Large tissue sections such as the human brain, heart, and liver are becoming increasingly important in studying complex tissue structures, providing critical information about the tissue's normal or abnormal development, function, and disease processes. Manual staining methods are still widely used and are prone to inconsistencies and inaccuracies, leading to unreliable results. Commercially available automated staining systems offer a more efficient alternative, but currently, these systems are only available for smaller 1" x 3" slides which are ill-suited for examining larger tissue sections. To address this challenge, we present a custom-designed Large format Automated Slide Stainer that can handle various glass slides, from the standard 1" x 3" slides to the custom-sized 2" x 3", 5" x 7", and 6" x 8" glass slides. The system uses a Cartesian robotic arm to stain the slides and has a user-friendly and intuitive interface for creating and modifying custom staining protocols. Safety features include chemical isolation, a ventilation system, an emergency shutdown, and a protective shield to minimize hazards from handling chemicals and biological materials. The automated stainer showed little variability in positioning with a mean offset error of 1.65 ± 0.65 mm and 1.73 ± 0.76 mm in the X and Y axes, respectively. In addition, the automated staining process showed better uniformity than manual staining. A pairwise distance was used to evaluate how well image histograms matched within a batch. The automated staining had a mean pairwise distance of 0.0070 ± 0.0017 (Nissl) and 0.0060 ± 0.0003 (Hematoxylin and Eosin(H&E)), which were far superior to the manual staining distances (Nissl: 0.0173 ± 0.0107 and H&E: 0.0185 ± 0.0067). This system represents a substantial advancement in tissue staining and has the potential to improve the reliability of tissue analysis significantly.Clinical relevance - Automated system for providing accurate, reproducible, and high-throughput staining of large tissue sections for use in histopathology and research.

Vaginal Carriage of Group B Streptococcus (GBS) in Pregnant Women, Antibiotic Sensitivity and Associated Risk Factors in Dakar, Senegal

The eradication of neonatal Group B Streptococcus (GBS) infections, considered as a major public health priority, necessarily requires a mastery of the data on vaginal carriage in pregnant women. The aims of this study were to determine the prevalence of vaginal carriage of GBS in pregnant women, antibiotic susceptibility, and associated risk factors. This was a cross-sectional, descriptive study conducted over a period of 9 months (July 2020 to March 2021) in pregnant women between 34 and 38 weeks of gestation (WG) followed at the Nabil Choucair health center in Dakar. Identification and antibiotic susceptibility of GBS isolates were performed on the Vitek 2 from vaginal swabs cultured on Granada medium. Demographic and obstetric interview data were collected and analyzed on SPSS (version 25). The level of significance for all statistical tests was set at P < .05. The search of GBS vaginal carriage had involved 279 women aged 16 to 46 years, with a median pregnancy age of 34 (34-37) weeks' gestation. GBS was found in 43 women, for a vaginal carriage rate of 15.4%. In 27.9% (12/43) of volunteers screened, this carriage was monomicrobial, while in 72.1% (31/43) of women, GBS was associated with other pathogens such as Candida spp. (60.5%), Trichomonas vaginalis (2.3%), Gardnerella vaginalis (34.9%) and/or Mobiluncus spp. (11.6%). The level of resistance was 27.9% (12/43) for penicillin G, 53.5% (23/43) for erythromycin, 25.6% (11/43) for clindamycin and 100% for tetracycline. However, the strains had retained fully susceptible to vancomycin and teicoplanin. The main risk factor associated with maternal GBS carriage were ectocervical inflammation associated with contact bleeding (OR = 3.55; P = .005). The high rate of maternal vaginal GBS carriage and the levels of resistance to the various antibiotics tested confirm the importance of continuous GBS surveillance in our resource-limited countries.

Streptomonospora mangrovi sp. nov., isolated from mangrove soil showing similar metabolic capabilities, but distinct secondary metabolites profiles

A novel actinomycete, designated strain S1-112 ^T, was isolated from a mangrove soil sample from Hainan, China, and characterized using a polyphasic approach. Strain S1-112 ^T showed the highest similarity of the 16S rRNA gene to Streptomonospora nanhaiensis 12A09^T (99.24%). Their close relationship was further supported by phylogenetic analyses, which placed these two strains within a stable clade. The highest values of digital DNA-DNA hybridization (dDDH, 41.4%) and average nucleotide identity (ANI, 90.55%) were detected between strain S1-112 ^T and Streptomonospora halotolerans NEAU-Jh2-17 ^T. Genotypic and phenotypic characteristics demonstrated that strain S1-112 ^T could be distinguished from its closely related relatives. We also profiled the pan-genome and metabolic features of genomic assemblies of strains belonging to the genus Streptomonospora, indicating similar functional capacities and metabolic activities. However, all of these strains showed promising potential for producing diverse types of secondary metabolites. In conclusion, strain S1-112 ^T represents a novel species of the genus Streptomonospora, for which the name Streptomonospora mangrovi sp. nov. was proposed. The type strain is S1-112 ^T (= JCM 34292 ^T).

Identification, characteristics and rice growth promotion of a highly efficient cellulolytic bacterial strain, Cellulomonas iranensis ZJW-6, isolated from paddy soil in central China

The microbial degradation of lignocellulose is the best way to treat straw, which has a broad application prospect. It is consistent with the idea of agricultural sustainable development and has an important impact on the utilization of biomass resources. To explore and utilize the microbial resources of lignocellulose degradation, 27 lignocellulose degrading strains were screened from 13 regions in China. ZJW-6 was selected because of its 49.6% lignocellulose weight loss rate. According to the theoretical analysis of the experimental results, the following straw degradation conditions were obtained by ZJW-6: nitrogen source input of 8.45 g/L, a pH of 8.57, and a temperature of 31.63°C, the maximum weight loss rate of rice straw could reach 54.8%. It was concluded that ZJW-6 belonged to Cellulomonas iranensis according to 16S rRNA-encoding gene sequence comparison and identification. ZJW-6 is a Gram-positive bacterium that grows slowly and has a small yellowish green colony. To explain the degradation mechanism of lignocellulose, the experiment of enzymatic properties of the strain was prepared and carried out. It was discovered that ZJW-6 has an excellent ability to degrade cellulose, hemicellulose, and lignin, with cellulose and hemicellulose loss rates reaching almost 50% in 4 days and lignin loss rates reaching nearly 30%. Furthermore, ZJW-6 demonstrated lignocellulose degradation under aerobic and anaerobic conditions, indicating the strain's broad application potential. ZJW-6 was found to be more effective than ordinary humic acid in improving rice soil (available phosphorus, available nitrogen, organic matter) and promoting rice growth in a rice pot experiment (increasing root-shoot ratio, root activity, chlorophyll content and net photosynthetic rate). ZJW-6 plays an important role in promoting the development and utilization of straw resources. It has important significance for the advancement of green agriculture.

Occultella gossypii sp. nov., an alkali-resistant isolate from soil sampled in a cotton field

A non-spore-forming, motile and alkali-resistant actinobacterium, designated N2-46T, was isolated from an alkaline soil sample collected from a cotton field in the Xinjiang region of PR China. Strain N2-46T formed creamy colonies on tryptone soy agar and managed to survive in extreme alkaline conditions at a pH value of 11. Strain N2-46T displayed the highest 16S rRNA gene similarity of 99.65 % to Haloactinobacterium kanbiaonis HY164T, followed by Occultella aeris F300T (99.61%) and Occultella glacieicola T3246-1T (98.54 %). 16S rRNA-directed phylogenetic analysis showed that strain N2-46T was embedded in a subclade with O. aeris F300T with a bootstrap value of 71.8 %. The phylogenetic tree based on core genes of genome sequences showed that strain N2-46T formed a unique subclade next to H. kanbiaonis HY164T and O. aeris F300T with a bootstrap value of 100 %. Digital DNA–DNA hybridization and the average nucleotide identity analyses showed that strain N2-46T displayed the highest values of 67.1 % (63.2–70.7 %) and 91.82 % with H. kanbiaonis HY164T, respectively. Comparative genomic analysis indicated that strain N2-46T and its three closest neighbours exhibited comparable distribution patterns in heavy metal resistance genes and biosynthetic gene clusters, while displaying distinctions probably related to ecological adaptation. MK-8(H4) was identified as the predominant isoprenoid quinone. The main fatty acids were identified as iso-C14 : 0 and anteiso-C15 : 0. Polar lipids are composed of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, mono and diacylated phosphatidylinositol dimannosides, as well as several uncharacterized polar lipid, glycolipid, and phospholipids. Genotypic and physiological analyses support the view that strain N2-46T (=JCM 34413T=CGMCC 1.18819T) should be classified as a novel species of the genus Occultella , for which the name Occultella gossypii sp. nov. is proposed.

Comparison of an automated DNA extraction and 16S rDNA real time PCR/sequencing diagnostic method using optimized reagents with culture during a 15-month study using specimens from sterile body sites

Background

16S rDNA-PCR for the identification of a bacterial species is an established method. However, the DNA extraction reagents as well as the PCR reagents may contain residual bacterial DNA, which consequently generates false-positive PCR results. Additionally, previously used methods are frequently time-consuming. Here, we describe the results obtained with a new technology that uses DNA-free reagents for automated DNA extraction and subsequent real time PCR using sterile clinical specimens.

Results

In total, we compared 803 clinical specimens using real time PCR and culturing. The clinical specimens were mainly of orthopedic origin received at our diagnostic laboratory. In 595 (74.1%) samples, the results were concordant negative, and in 102 (12.7%) the results were concordant positive. A total of 170 (21.2%) clinical specimens were PCR-positive, of which 62 (36.5% from PCR positive, 7.7% in total) gave an additional benefit to the patient since only the PCR result was positive. Many of these 62 positive specimens were strongly positive based on crossingpoint values (54% < Cp 30), and these 62 positive clinical specimens were diagnosed as medically relevant as well. Thirty-eight (4.2%) clinical specimens were culture-positive (25 of them were only enrichment culture positive) but PCR-negative, mainly for S. epidermidis, S. aureus and C. acnes. The turnaround times for negative specimens were 4 hours (automated DNA extraction and real time PCR) and 1 working day for positive specimens (including Sanger sequencing). Melting-curve analysis of SYBR Green-PCR enables the differentiation of specific and unspecific PCR products. Using Ripseq, even mixed infections of 2 bacterial species could be resolved.

Conclusions

For endocarditis cases, the added benefit of PCR is obvious. The crucial innovations of the technology enable timely reporting of explicit reliable results for adequate treatment of patients. Clinical specimens with truly PCR-positive but culture-negative results represent an additional benefit for patients. Very few results at the detection limit still have to be critically examined.

Engineering Shewanella carassii, a newly isolated exoelectrogen from activated sludge, to enhance methyl orange degradation and bioelectricity harvest

Electroactive microorganisms (EAMs) play important roles in biogeochemical redox processes and have been of great interest in the fields of energy recovery, waste treatment, and environmental remediation. However, the currently identified EAMs are difficult to be widely used in complex and diverse environments, due to the existence of poor electron transfer capability, weak environmental adaptability, and difficulty with engineering modifications, etc. Therefore, rapid and efficient screening of high performance EAMs from environments is an effective strategy to facilitate applications of microbial fuel cells (MFCs). In this study, to achieve efficient degradation of methyl orange (MO) by MFC and electricity harvest, a more efficient exoelectrogen Shewanella carassii-D₅ that belongs to Shewanella spp. was first isolated from activated sludge by WO₃ nanocluster probe technique. Physiological properties experiments confirmed that S. carassii-D₅ is a Gram-negative strain with rounded colonies and smooth, slightly reddish surface, which could survive in media containing lactate at 30 °C. Moreover, we found that S. carassii-D₅ exhibited remarkable MO degradation ability, which could degrade 66% of MO within 72 h, 1.7 times higher than that of Shewanella oneidensis MR-1. Electrochemical measurements showed that MFCs inoculated with S. carassii-D₅ could generate a maximum power density of 704.6 mW/m², which was 5.6 times higher than that of S. oneidensis MR-1. Further investigation of the extracellular electron transfer (EET) mechanism found that S. carassii-D₅ strain had high level of c-type cytochromes and strong biofilm formation ability compared with S. oneidensis MR-1, thus facilitating direct EET. Therefore, to enhance indirect electron transfer and MO degradation capacity, a synthetic gene cluster ribADEHC encoding riboflavin synthesis pathway from Bacillus subtilis was heterologously expressed in S. carassii-D₅, increasing riboflavin yield from 1.9 to 9.0 mg/g DCW with 1286.3 mW/m² power density output in lactate fed-MFCs. Furthermore, results showed that the high EET rate endowed a faster degradation efficient of MO from 66% to 86% with a maximum power density of 192.3 mW/m², which was 1.3 and 1.6 times higher than that of S. carassii-D₅, respectively. Our research suggests that screening and engineering high-efficient EAMs from sludge is a feasible strategy in treating organic pollutants.

Rapid Detection of Pathogenic Bacteria by the Naked Eye

Escherichia coli O157:H7 and Staphylococcus aureus are common pathogens. Gram-negative bacteria, such as E. coli, contain high concentrations of endogenous peroxidases, whereas Gram-positive bacteria, such as S. aureus, possess abundant endogenous catalases. Colorless 3,5,3',5'-tetramethyl benzidine (TMB) changes to blue oxidized TMB in the presence of E. coli and a low concentration of H2O2 (e.g., ~11 mM) at pH of 3. Moreover, visible air bubbles containing oxygen are generated after S. aureus reacts with H2O2 at a high concentration (e.g., 180 mM) at pH of 3. A novel method for rapidly detecting the presence of bacteria on the surfaces of samples, on the basis of these two endogenous enzymatic reactions, was explored. Briefly, a cotton swab was used for collecting bacteria from the surfaces of samples, such as tomatoes and door handles, then two-step endogenous enzymatic reactions were carried out. In the first step, a cotton swab containing bacteria was immersed in a reagent comprising H2O2 (11.2 mM) and TMB for 25 min. In the second step, the swab was dipped further in H2O2 (180 mM) at pH 3 for 5 min. Results showed that the presence of Gram-negative bacteria, such as E. coli with a cell number of ≥ ~105, and Gram-positive bacteria, such as S. aureus with a cell number of ≥ ~106, can be visually confirmed according to the appearance of the blue color in the swab and the formation of air bubbles in the reagent solution, respectively, within ~30 min. To improve visual sensitivity, we dipped the swab carrying the bacteria in a vial containing a growth broth, incubated it for ~4 h, and carried out the two-stage reaction steps. Results showed that bluish swabs resulting from the presence of E. coli O157: H7 with initial cell numbers of ≥ ~34 were obtained, whereas air bubbles were visible in the samples containing S. aureus with initial cell numbers of ≥ ~8.5 × 103.