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Shunt infections are a common complication when treating hydrocephalus by cerebrospinal fluid (CSF) shunt placement. The source of infecting pathogens is not well understood. One hypothesis, which we explored here, is that microorganisms persist chronically in the host long before a symptomatic infection occurs and may be detectable in surgical events preceding infection. A cohort of 13 patients was selected, for which CSF samples were available from an infection episode and from a previous surgery event, which was either an initial shunt placement or a revision. Microbiota were analyzed both directly from CSF and from isolates cultured from CSF on aerobic and anaerobic media. The detection and identification of bacteria was done with high throughput DNA sequencing methods and mass spectrometry. The presence of bacteria was confirmed in 4 infection samples, of which 2 were after initial placement and 2 after revision surgery. Taxonomic identification was consistent with clinical microbiology laboratory results. Bacteria were not detected in any of the CSF samples collected at the time of the previous surgical events. While our findings do not provide direct evidence for long-term persistence of pathogens, they suggest the need for consideration of additional source material, such as biofilm and environmental swabs, and/or the use of more sensitive and specific analytical methods. [ABSTRACT FROM AUTHOR]

Self-healing bacteria, when integrated with natural fiber-reinforced concrete, form a distinctive and sustainable building material with the inherent ability to enhance strength and facilitate crack healing. This paper reports on effective curing method that can reduce the excessive consumption of curing water for self-healing bacteria integrated natural fiber-reinforced concrete. A comprehensive analysis is conducted to evaluate parameters such as compressive strength (CS), compressive strength regain (CSR), and ultrasonic pulse velocity (UPV) under different curing systems, namely, pond curing (PC) and wet covering (WC). The investigation commences with the identification of bacteria from a suitable environment, followed by their direct addition to concrete, along with varying percentages of jute fibers (0.3, 0.5, and 0.7). The results obtained from the WC system reveal that, in comparison with Bacillus paramycoides, Bacillus tropicus exhibits increased values of CSR, UPV, and crack healing by 88%, 28%, and 92%, respectively. Numerical analysis is carried for evaluating crack pattern behavior of cubes under compression and compared with experimental data. Microstructural analysis explores the fact that the porous microstructure of the cement matrix is densified through the microbial-induced precipitation of various polymorphs of calcium carbonates. [ABSTRACT FROM AUTHOR]

Background: Bacteria are present on all surfaces, to which they were carried by many direct and indirect methods of transmission. A toilet is simply a receptacle into which both solid and liquid waste of human origin, in the form of urine and excreta are discharged. In public toilets, complete strangers mix and use the same sanitary facilities, with all the related risks of bodily fluid exchange, contamination and organism transmission. Unhygienic use of the toilet's facilities may cause urine and fecal residues after use to serve as a major reservoir or source of human pathogen, which may in turn bring about disease outbreak. Aim: This study aimed at Identification of Bacteria from Public Toilets of Modern Market (Goico) In Musanze Town, Rwanda Method: This cross-sectional study was conducted to identify bacteria from GOICO market toilets. About 40 samples; 20 from male and 20 from female toilets were collected and transported to INES-clinical microbiology laboratory for microbiological analysis. Laboratory techniques including culture, gram stain, biochemical tests and antibiogram were performed. Results: The most predominant bacteria isolated was S. aureus (31.43%), followed by S. typhi (20%), Streptococcus(15.71%), E. coli(12.86%), P. aeuriginosa(10%), P. mirabilis(7.14%), C. freundi(1.43%), S. epidermidis (1.43%). It was noted that female toilets were more contaminated (51.43%) than male toilets (48.57%). All gram positive and gram-negative bacteria were sensitive to Gentamicin. Almost all bacteria except P. mirabilis were sensitive to Norfloxacin, gram negative showed a resistance to Vancomycin and Novobiocin. Conclusion: These results should alert public toilets users that extreme caution must be executed while using these toilets, as they may be a source of pathogenic bacteria. The best way to keep a toilet and its seat free of bacteria is to clean it with bleach. Otherwise, keep the bacteria at bay by washing your hands, and if you just don't trust that toilet seat, wipe it down with a disinfectant or antibacterial wipe before you sit. [ABSTRACT FROM AUTHOR]

The Acidaminococcus genus is a part of the normal flora in gastrointestinal tract. It is a strictly anaerob Gram-negative coccus that is rarely pathogenic. We report the case of a 58-year-old man, who presented to surgery department A of the Charles Nicolle hospital, complaining of a wide inflammatory lesion in the anterior abdominal wall evolving for two weeks. Patient's anamnestic data included smoking, hypertension, and diabetes mellitus with poor compliance. The patient underwent flattening with excision of necrotic tissues and surgical drainage using a DELBET blade. Empirical antibiotic therapy with imipenem 1gx3/d, teicoplanin 400 mg 1 inj x2/d and gentamicin 400 mg 1 inj/d was administered pending bacteriological results. The bacteriological examination of a sample of necrotic tissue, after 72 h of incubation at 37 °C in anaerobic atmosphere, was able to detect a Gram-negative coccus, that the VITEK2 ANC system identified as Actinomyces canis with an accuracy of 80%. Whole genome sequencing was subsequently performed, that identified Acidaminococcus sp. AM33-14BH and demonstrated the following resistance genes: cfxa, tet(X) and tet(Q). An antibiogram for anaerobes was performed showing that the strain was resistant to amoxicillin but sensitive to amoxicillin-clavulanic acid, piperacillin-tazobactam, ertapenem, imipenem, meropenem and rifampin. Patient's condition improved after treatment with imipenem for 2 weeks, followed by oral amoxicillin-clavulanic acid for 16 days. This work highlights the role of molecular biology in the diagnosis of infections caused by anaerobes. Although the Vitek 2 ANC card provides rapid and acceptable identification of the most common anaerobic bacteria, improvements are needed for the identification of bacteria in the genera Acidaminococcus and Actinomyces. [ABSTRACT FROM AUTHOR]

Background: Commonly used approaches for genomic investigation of bacterial outbreaks, including SNP and gene-by-gene approaches, are limited by the requirement for background genomes and curated allele schemes, respectively. As a result, they only work on a select subset of known organisms, and fail on novel or less studied pathogens. We introduce refMLST, a gene-by-gene approach using the reference genome of a bacterium to form a scalable, reproducible and robust method to perform outbreak investigation. Results: When applied to multiple outbreak causing bacteria including 1263 Salmonella enterica, 331 Yersinia enterocolitica and 6526 Campylobacter jejuni genomes, refMLST enabled consistent clustering, improved resolution, and faster processing in comparison to commonly used tools like chewieSnake. Conclusions: refMLST is a novel multilocus sequence typing approach that is applicable to any bacterial species with a public reference genome, does not require a curated scheme, and automatically accounts for genetic recombination. Availability and implementation: refMLST is freely available for academic use at https://bugseq.com/academic. [ABSTRACT FROM AUTHOR]

We evaluated the performance of Zybio EXS2600 matrix‐assisted laser desorption ionization time‐of‐flight mass spectrometry (MALDI‐TOF MS) (Zybio Inc., Chongqing, China) for the identification of bacteria from positive blood culture (BC) bottles using Blood Culture Positive Sample Pretreatment Kit (Zybio Inc., Chongqing, China) in comparison to an in‐house saponin method. Following a positive signal by the BACTEC™ FX system, confirmation of identification was achieved using subcultured growing biomass used for MALDI‐TOF MS analysis. A total of 94 positive BC bottles with 97 bacterial isolates were analyzed. The overall identification rates at the genus and species levels for the saponin method were 89.7% (87/97) and 74.2% (72/97), respectively. With the Zybio Kit, 88.7% (86/97) and 80.4% (78/97) of microorganisms were correctly identified to the genus and species levels, respectively. The saponin method identified 65.3% (32/49) of Gram‐positive bacteria at the species level, whereas the Zybio Kit achieved a higher species‐level identification rate of 79.6% (39/49) (p = 0.1153). The saponin method with additional on‐plate formic acid extraction showed a significantly higher overall identification rate in comparison to the saponin method without that step for both genus (87.6% [85/97] vs. 70.1% [68/97], p = 0.0029) and species level (70.1% [68/97] vs. 46.4% [45/97], p = 0.0008). Identification rates of Gram‐negative bacteria showed a higher identification rate, however, not statistically significant with additional Zybio Kit protocol step on both genus (85.4% [41/48] vs. 81.3% [39/48], p = 0.5858) and species level (77.1% [37/48] vs. 75% [36/48], p = 0.8120). Zybio Kit could offer an advantage in species‐level identification, particularly for Gram‐positive bacteria. The inclusion of on‐plate formic acid extraction in the saponin method notably enhanced identification at both genus and species levels for Gram‐positive bacteria. The extended protocol provided by the Zybio Kit could potentially offer an advantage in the identification of Gram‐negative bacteria at both genus and species levels. Enhancements to the Zybio EXS2600 MALDI‐TOF instrument software database are necessary. [ABSTRACT FROM AUTHOR]

Whole-genome sequencing (WGS) is revolutionizing clinical bacteriology. However, bacterial typing remains investigated by reference techniques with inherent limitations. This stresses the need for alternative methods providing robust and accurate sequence type (ST) classification. This study optimized and evaluated a GridION nanopore sequencing protocol, adapted for the PromethION platform. Forty-eight Escherichia coli clinical isolates with diverse STs were sequenced to assess two alternative typing methods and resistance profiling applications. Multi-locus sequence typing (MLST) was used as the reference typing method. Genomic relatedness was assessed using Average Nucleotide Identity (ANI) and digital DNA-DNA Hybridization (DDH), and cut-offs for discriminative strain resolution were evaluated. WGS-based antibiotic resistance prediction was compared to reference Minimum Inhibitory Concentration (MIC) assays. We found ANI and DDH cut-offs of 99.3% and 94.1%, respectively, which correlated well with MLST classifications and demonstrated potentially higher discriminative resolution than MLST. WGS-based antibiotic resistance prediction showed categorical agreements of ≥ 93% with MIC assays for amoxicillin, ceftazidime, amikacin, tobramycin, and trimethoprim-sulfamethoxazole. Performance was suboptimal (68.8–81.3%) for amoxicillin-clavulanic acid, cefepime, aztreonam, and ciprofloxacin. A minimal sequencing coverage of 12× was required to maintain essential genomic features and typing accuracy. Our protocol allows the integration of PromethION technology in clinical laboratories, with ANI and DDH proving to be accurate and robust alternative typing methods, potentially offering superior resolution. WGS-based antibiotic resistance prediction holds promise for specific antibiotic classes. [ABSTRACT FROM AUTHOR]

Exploring plant growth-promoting (PGP) bacterial activity of microbial components aggregated by wastewater treatment can reduce dependence on fossil fuel-derived fertilisers. This study describes the isolation and identification of bacteria from microalgae-bacteria flocs (MaB-flocs) generated in high-rate algal oxidation ponds (HRAOP) of an integrated algal pond system (IAPS) remediating municipal wastewater. Amplified 16S rRNA gene sequence analysis determined the molecular identity of the individual strains. Genetic relatedness to known PGP rhizobacteria in the NCBI GenBank database was by metagenomics. Isolated strains were screened for the production of indoles (measured as indole-3-acetic acid; IAA) and an ability to mineralise ${\rm NH}_4^ +$ NH 4 + , ${\rm PO}_4^{3-}$ PO 4 3 − , and K +. Of the twelve bacterial strains isolated from HRAOP MaB-flocs, four produced indoles, nine mineralised ${\rm NH}_4^ +$ NH 4 + , seven solubilised P, and one K. Potential of isolated strains for PGP activity according to one-way ANOVA on ranks was: ECCN 7b > ECCN 4b > ECCN 6b > ECCN 3b = ECCN 10b > ECCN 1b = ECCN 5b > ECCN 8b > ECCN 2b > ECCN 12b > ECCN 9b = ECCN 11b. Further study revealed that cell-free filtrate from indole-producing cultures of Aeromonas strain ECCN 4b, Enterobacter strain ECCN 7b, and Arthrobacter strain ECCN 6b promoted mung bean adventitious root formation suggestive of the presence of auxin-like biological activity. [ABSTRACT FROM AUTHOR]

Staphylococcal cassette chromosome mec (SCC mec) typing is crucial for investigating methicillin-resistant Staphylococcus aureus (MRSA), relying primarily on the combination of ccr and mec gene complexes. To date, 19 ccr genes and 10 ccr gene complexes have been identified, forming 15 SCC mec types. With the vast release of bacterial genome sequences, mining the database for novel ccr gene complexes and SCC/SCC mec elements could enhance MRSA epidemiological studies. In this study, we identified 12 novel ccr genes (6 ccrA , 3 ccrB, and 3 ccrC) through mining of the National Center for Biotechnology Information (NCBI) database, forming 12 novel ccr gene complexes and 10 novel SCC elements. Overexpression of 5 groups of novel Ccr recombinases (CcrA9B3, CcrA10B1, CcrC3, CcrC4, and CcrC5) in a mutant MRSA strain lacking the ccr gene and extrachromosomal circular intermediate (ciSCC) production significantly promoted ciSCC production, demonstrating their biological activity. This discovery provides an opportunity to advance MRSA epidemiological research and develop database-based bacterial typing methods. [ABSTRACT FROM AUTHOR]

The proliferation and dissemination of antimicrobial-resistant bacteria is an increasingly global challenge and is attributed mainly to the excessive or improper use of antibiotics. Currently, the gold-standard phenotypic methodology for detecting resistant strains is agar plating, which is a time-consuming process that involves multiple subculturing steps. Genotypic analysis techniques are fast, but they require pure starting samples and cannot differentiate between viable and non-viable organisms. Thus, there is a need to develop a better method to identify and prevent the spread of antimicrobial resistance. This work presents a novel method for detecting and identifying antibiotic-resistant strains by combining a cell sorter for bacterial detection and an elastic-light-scattering method for bacterial classification. The cell sorter was equipped with safety mechanisms for handling pathogenic organisms and enabled precise placement of individual bacteria onto an agar plate. The patterning was performed on an antibiotic-gradient plate, where the growth of colonies in sections with high antibiotic concentrations confirmed the presence of a resistant strain. The antibiotic-gradient plate was also tested with an elastic-light-scattering device where each colony's unique colony scatter pattern was recorded and classified using machine learning for rapid identification of bacteria. Sorting and patterning bacteria on an antibiotic-gradient plate using a cell sorter reduced the number of subculturing steps and allowed direct qualitative binary detection of resistant strains. Elastic-light-scattering technology is a rapid, label-free, and non-destructive method that permits instantaneous classification of pathogenic strains based on the unique bacterial colony scatter pattern. Key points: • Individual bacteria cells are placed on gradient agar plates by a cell sorter • Laser-light scatter patterns are used to recognize antibiotic-resistant organisms • Scatter patterns formed by colonies correspond to AMR-associated phenotypes [ABSTRACT FROM AUTHOR]

Red swamp crayfish (Procambarus clarkii) like to eat aquatic plants. The intestinal microorganism plays an important role in cellulose degradation and utilization. Isolating bacteria which can degrade cellulose from the intestines of P. clarkii can provide a theoretical basis for the development of probiotics in forage for P. clarkii. Three selective media including carboxymethyl-cellulose, microcrystalline cellulose, and cellobiose were used in plate cultures for 48h and then dyed with Congo red. It was found that 5 strains produced hydrolytic rings on 3 culture media at 48h. Based on the results of 16S rRNA molecular analysis, strains C, E, G, H, and M were identified as Citrobacter sp., Staphylococcus sp., Acinetobacter johnsonii, Shewanella sp., and Aeromonas caviae, respectively. Specifically, Staphylococcus sp. exhibited the strongest capacity for the degradation of cellulose. Shewanella sp. showed the strongest degradation capacity for cellobiose. Acinetobacter johnsonii and Shewanella sp. can degrade cellulose and are expected to be used as probiotic feed for P. clarkii. This study can provide a theoretical basis for the healthy culture of P. clarkii. [ABSTRACT FROM AUTHOR]

At a particular aquaculture facility in Zhangjiajie in China, the Chinese giant salamander (Andrias davidianus) exhibited analogous clinical manifestations, culminating in sequential mortalities. This study used rigorous aseptic sampling methods to isolate bacteria from the affected liver of salamanders to determine the causative agent behind the decline in amphibians. A bacterial pathogen was isolated from diseased A. davidianus, and the strain was named DN-3. This isolate was subjected to bacterial identification, antibiotic susceptibility assays, reinfection experiments, and biochemical profiling. The isolated bacterial strain was definitively identified as Acinetobacter schindleri using 16S rRNA sequence analysis and biochemical identification. Antibiotic susceptibility testing revealed that this isolate was susceptible to neomycin, macrolides, doxycycline, piperacillin, nitrofurantoin, and carbenicillin. Subsequent reinfection assays, in which varying concentrations of the bacterial inoculum were administered to healthy salamanders, confirmed that the pathogen elicited varying degrees of morbidity or mortality within an eight-day observation period. The median lethal dose (LD50) of A. schindleri DN-3 for A. davidianus was calculated to be 6.25×104 CFU/mL. This result supports the significant pathogenicity of the strain for A. davidianus. The findings of this study provide empirical insights into the clinical management and epidemiological control of diseases affecting A. davidianus. [ABSTRACT FROM AUTHOR]

Morganella morganii is a psychrotolerant organism recognized as a histamine-producing bacteria by decarboxylation of histidine amino acid, it has been involved in cases of histamine fish poisoning reported in different seafood products. In this study, we collected a total of 125 random samples of frozen Mackerel fish stored at -18°C from different fish markets in New Valley Governorate, Egypt. Through isolation from the tissue of fish samples on Chromogenic agar plates, bacteria forming light brown colonies were identified. Confirmatory identification of bacteria was conducted using 16S rRNA as a species-specific gene, revealing the presence of 14 M. morganii strains from samples, representing an incidence of 11.2% of all samples. Morganella morganii is a prominent adaptive nosocomial bacterium that can cause urinary tract infections and bacteremia. [ABSTRACT FROM AUTHOR]

Ecosystems on the planet have myriads of microbes having unique features and characteristics to survive the habitat. In present investigation bacteria were isolated from the soils exposed to electronic waste processing. From these soils bacterial strains were isolated by serial diluting the soil suspension at room temperature using phosphate buffer saline. Per gram soil average population of bacteria in investigated soils ranged between 1.3-5.4 × 107. The bacteria were identified based on the colony morphology, colour, shape, Gram's staining and biochemical test such as catalase, glucose fermentation, oxidase activity, litmus milk coagulation, peptonized reduced, gelatine hydrolysis etc. A total of 19 bacteria were isolated and 14 were identified based on biochemical and morphological features. The bacteria belonged to Micrococcus, Streptococcus, Escherichia, Alcaligen, Pseudomonas, Bacillus and Lactobacillus. [ABSTRACT FROM AUTHOR]

The dinoflagellate Alexandrium catenella is a well-known paralytic shellfish toxin producer that forms harmful algal blooms, repeatedly causing damage to Chilean coastal waters. The causes and behavior of algal blooms are complex and vary across different regions. As bacterial interactions with algal species are increasingly recognized as a key factor driving algal blooms, the present study identifies several bacterial candidates potentially associated with Chilean Alexandrium catenella. This research narrowed down the selection of bacteria from the Chilean A. catenella culture using antibiotic treatment and 16S rRNA metabarcoding analysis. Subsequently, seawater from two Chilean coastal stations, Isla Julia and Isla San Pedro, was monitored for two years to detect Alexandrium species and the selected bacteria, utilizing 16S and 18S rRNA gene metabarcoding analyses. The results suggested a potential association between Alexandrium species and Spongiibacteraceae at both stations. The proposed candidate bacteria within the Spongiibacteraceae family, potentially engaging in mutualistic relationships with Alexandrium species, included the genus of BD1-7 clade, Spongiibbacter, and Zhongshania. [ABSTRACT FROM AUTHOR]

Background: Bacteria are present on all surfaces, to which they were carried by many direct and indirect methods of transmission. A toilet is simply a receptacle into which both solid and liquid waste of human origin, in the form of urine and excreta are discharged. In public toilets, complete strangers mix and use the same sanitary facilities, with all the related risks of bodily fluid exchange, contamination and organism transmission. Unhygienic use of the toilet's facilities may cause urine and fecal residues after use to serve as a major reservoir or source of human pathogen, which may in turn bring about disease outbreak. Aim: This study aimed at Identification of Bacteria from Public Toilets of Modern Market (Goico) In Musanze Town, Rwanda Method: This cross-sectional study was conducted to identify bacteria from GOICO market toilets. About 40 samples; 20 from male and 20 from female toilets were collected and transported to INES-clinical microbiology laboratory for microbiological analysis. Laboratory techniques including culture, gram stain, biochemical tests and antibiogram were performed. Results: The most predominant bacteria isolated was S. aureus (31.43%), followed by S. typhi (20%), Streptococcus(15.71%), E. coli(12.86%), P. aeuriginosa(10%), P. mirabilis(7.14%), C. freundi(1.43%), S. epidermidis (1.43%). It was noted that female toilets were more contaminated (51.43%) than male toilets (48.57%). All gram positive and gram-negative bacteria were sensitive to Gentamicin. Almost all bacteria except P. mirabilis were sensitive to Norfloxacin, gram negative showed a resistance to Vancomycin and Novobiocin. Conclusion: These results should alert public toilets users that extreme caution must be executed while using these toilets, as they may be a source of pathogenic bacteria. The best way to keep a toilet and its seat free of bacteria is to clean it with bleach. Otherwise, keep the bacteria at bay by washing your hands, and if you just don't trust that toilet seat, wipe it down with a disinfectant or antibacterial wipe before you sit. [ABSTRACT FROM AUTHOR]

Background: Electronic devices have become one of the most essential accessories being used in daily lives including schools. Those devices increase the communication and using them makes learning much easier. Microbial contamination of electronic devices and inanimate surface of electronic equipment at INES-Ruhengeri can have a significant role for transmission of pathogenic bacteria. Aim: The aim of this study was to isolate and identify bacteria from electronic devices used by students and staffs at INES-Ruhengeri University. Methodology: This cross-sectional study was done on 40 electronic devices such as computers, microscopes, global positioning system (GPS) and total stations A random sampling method was applied from sterile swab soaked in peptone water solution by the technique of bearing on the surface of the entire devices and then placed in a transport medium. Collected samples were then taken in INES-Ruhengeri Microbiology laboratory for further experiments. Results: All 40 electronic devices were contaminated with bacteria. The most predominant bacteria isolated from electronic devices was S.aureus (25.9%) followed by Bacillus spp(24.1%), K.pneumonia(12.9%), S.epidermis(12.9%), Micrococcus spp(7.4%), P.aeruginosa(5.5%), E.coli(3.3%), Salmonella spp(3.3%) and Shigella spp(3.3%). Antimicrobial susceptibility pattern of selected antibiotics was performed. Norfloxin was the most sensitive antibiotic on all isolated bacteria. Chloramphenicol antibiotic shown no activity over any of the isolated bacteria, to imply that all bacteria had resistance on it. Conclusion: This study shown that there is bacterial contamination to all devices and antibiotic susceptibility test shown that some antibiotics were sensitive and resistant to the isolated bacteria. [ABSTRACT FROM AUTHOR]

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The VITEK MS PRIME (bioMérieux, Marcy-l'Étoile, France), a newly developed matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) system, alongside the VITEK PICKME pen (PICKME), offers easy sample preparation for bacteria and yeasts. The VITEK MS PRIME also offers two software platforms for filamentous fungi: the IVD database and the RUO database. Our study evaluated its identification agreement on 320 clinical isolates of bacteria and yeasts, comparing PICKME and traditional wooden toothpick sampling techniques against MicroIDSys Elite (ASTA) results. Additionally, we assessed the IVD (v3.2) and SARAMIS (v4.16) RUO databases on 289 filamentous fungi against molecular sequencing. The concordance rates for species-level identification of bacteria and yeasts were about 89.4% (286/320) between the PICKME and wooden toothpick, and about 83.4–85.3% between the VITEK MS PRIME and ASTA MicroIDSys Elite. Retesting with PICKME improved concordance to 91.9%. For filamentous fungi, species-level identification reached 71.3% with the IVD database and 85.8% with RUO, which significantly enhanced basidiomycetes' identification from 35.3% to 100%. Some strains in the IVD database, like Aspergillus versicolor, Exophiala xenobiotica, and Nannizzia gypsea, failed to be identified. The VITEK MS PRIME with PICKME offers reliable and efficient microorganism identification. For filamentous fungi, combined use of the RUO database can be beneficial, especially for basidiomycetes. [ABSTRACT FROM AUTHOR]

The majority of cases of undifferentiated acute febrile illness (AFI) in the tropics have an undefined etiology. In Thailand, AFI accounts for two-thirds of illnesses reported to the Ministry of Public Health. To characterize the bacterial and viral causes of these AFIs, we conducted molecular pathogen screening and serological analyses in patients who sought treatment in Chum Phae Hospital, Khon Kaen province, during the period from 2015 to 2016. Through integrated approaches, we successfully identified the etiology in 25.5% of cases, with dengue virus infection being the most common cause, noted in 17% of the study population, followed by scrub typhus in 3.8% and rickettsioses in 6.8%. Further investigations targeting viruses in patients revealed the presence of Guadeloupe mosquito virus (GMV) in four patients without other pathogen co-infections. The characterization of four complete genome sequences of GMV amplified from AFI patients showed a 93–97% nucleotide sequence identity with GMV previously reported in mosquitoes. Nucleotide substitutions resulted in amino acid differences between GMV amplified from AFI patients and mosquitoes, observed in 37 positions. However, these changes had undergone purifying selection pressure and potentially had a minimal impact on protein function. Our study suggests that the GMV strains identified in the AFI patients are relatively similar to those previously reported in mosquitoes, highlighting their potential role associated with febrile illness. [ABSTRACT FROM AUTHOR]

Fourier-transform infrared (FTIR) spectroscopy has the potential to be used for bacterial typing and outbreak characterization. We evaluated FTIR for the characterization of an outbreak caused by Elizabethkingia miricola. During the 2020–2021 period, 26 isolates (23 clinical and 3 environmental) were collected and analyzed by FTIR (IR Biotyper) and core-genome MLST (cgMLST), in addition to antimicrobial susceptibility testing. FTIR spectroscopy and cgMLST showed that 22 of the isolates were related to the outbreak, including the environmental samples, with only one discordance between both methods. Then, FTIR is useful for E. miricola typing and can be easily implemented in the laboratory. [ABSTRACT FROM AUTHOR]

Introduction: The emergence of multi-drug resistant (MDR) pathogens linked to healthcare-associated infections (HCAIs) is an increasing concern in modern veterinary practice. Thus, rapid bacterial typing for real-time tracking of MDR hospital dissemination is still much needed to inform best infection control practices in a clinically relevant timeframe. To this end, the IR Biotyper using Fourier-Transform InfraRed (FTIR) spectroscopy has the potential to provide fast cluster analysis of potentially related organisms with substantial cost and turnaround time benefits. Materials and methods: A collection of MDR bacterial isolates (n = 199, comprising 92 Klebsiella pneumoniae and 107 Pseudomonas aeruginosa) obtained from companion animal (i.e., dogs, cats and horses) clinical investigations, faecal and environmental screening from four veterinary facilities between 2012 and 2019 was analysed retrospectively by FTIR spectroscopy. Its performance was compared against MLST extracted from whole genomes of a subset of clustering isolates (proportionally to cluster size) for investigation of potential nosocomial transmission between patients and the surrounding hospital environments. Results: Concordance between the FTIR and MLST types was overall high for K. pneumoniae (Adjusted Rand Index [ARI] of 0.958) and poor for P. aeruginosa (ARI of 0.313). FTIR K. pneumoniae clusters (n = 7) accurately segregated into their respective veterinary facility with evidence of intra-hospital spread of K. pneumoniae between patients and environmental surfaces. Notably, K. pneumoniae ST147 intensely circulated at one Small Animal Hospital ICU. Conversely, Pseudomonas aeruginosa FTIR clusters (n = 18) commonly contained isolates of diversified hospital source and heterogeneous genetic background (as also genetically related isolates spread across different clusters); nonetheless, dissemination of some clones, such as P. aeruginosa ST2644 in the equine hospital, was apparent. Importantly, FTIR clustering of clinical, colonisation and/or environmental isolates sharing genomically similar backgrounds was seen for both MDR organisms, highlighting likely cross-contamination events that led to clonal dissemination within settings. Conclusion: FTIR spectroscopy has high discriminatory power for hospital epidemiological surveillance of veterinary K. pneumoniae and could provide sufficient information to support early detection of clonal dissemination, facilitating implementation of appropriate infection control measures. Further work and careful optimisation need to be carried out to improve its performance for typing of P. aeruginosa veterinary isolates. [ABSTRACT FROM AUTHOR]

Introduction: Soil microorganisms play crucial roles in determining the fate of litter in desert steppes because their activities constitute a major component of the global carbon (C) cycle. Human activities lead to increased ecosystem nitrogen (N) deposition, which has unpredictable impacts on soil microorganism diversity and functions. Nowadays, it is necessary to further study the succession of these microorganisms in the process of litter decomposition in desert steppe, and explore the effect of N deposition on this process. This issue is particularly important to resolve because it contributes to the broader understanding of nutrient cycling processes in desert steppes. Methods: In this study, DNA stable isotope probing (DNA-SIP) was used to study changes in soil bacterial and fungal community composition and function during 8 weeks of culture of 13C-labeled litter in desert steppes. Results: The results were as follows: (1) Actinomycetota, Pseudomonadota, and Ascomycota are the main microorganisms involved in litter decomposition in desert steppes; (2) N deposition (50kgha-1 year-1) significantly increased the relative abundance of some microorganisms involved in the decomposition process; and (3) N deposition likely promotes litter decomposition in desert steppes by increasing the abundances of N cycles bacteria (usually carrying GH family functional genes). Discussion: These findings contribute to a deeper understanding of the C assimilation mechanisms associated with litter residue production, emphasizing the importance of extensive C utilization. [ABSTRACT FROM AUTHOR]

Raman spectroscopy is an emerging method for the identification of bacteria. Nevertheless, a lot of different parameters need to be considered to establish a reliable database capable of identifying real-world samples such as medical or environmental probes. In this review, the establishment of such reliable databases with the proper design in microbiological Raman studies is demonstrated, shining a light into all the parts that require attention. Aspects such as the strain selection, sample preparation and isolation requirements, the phenotypic influence, measurement strategies, as well as the statistical approaches for discrimination of bacteria, are presented. Furthermore, the influence of these aspects on spectra quality, result accuracy, and read-out are discussed. The aim of this review is to serve as a guide for the design of microbiological Raman studies that can support the establishment of this method in different fields. [ABSTRACT FROM AUTHOR]

Soil bacteria have an effective role in dissolving soil potassium. Bacillus mucilaginosus plays an effective role in dissolving potassium in the soil so that the plant may absorb it easily. The present study aimed to test the efficiency of bacteria in dissolving potassium present in the soil surrounding the roots of crops. B. mucilaginosus was isolated and diagnosed from the rhizosphere soil of Celery, Wheat, Basil and Alfalfa plants. The diagnosis included studying the isolates' culture, microscopic and biochemical characteristics. The laboratory study also included testing the efficiency of these bacterial isolates in dissolving potassium compounds in Modified Aleksandrov agar medium and estimating the dissolution coefficient. The results of isolation and identification of bacteria isolated from 19 out of 50 soil samples planted with different crops (Celery, Wheat, Basil and Alfalfa) showed that 8 isolates could dissolve potassium. The results of the microscopic examination of these eight isolates showed that they were sticky in shape, positive for Gram-staining, forming spores and the capsule, while the movement examination showed that they were positive for these tests (movement test). The biochemical tests and cultural characteristics showed that the eight isolates bear the characteristics of B. mucilaginosus. The results showed that the dissolution coefficient of potassium for the different isolates ranged between 2.28 and 1.14, while the type of sugar added to the culture medium increased the efficiency of bacterial isolates for potassium solubility. The study demonstrated the bacteria's efficiency in the rhizosphere region in dissolving potassium, which helps the plant use it easily. [ABSTRACT FROM AUTHOR]

Tomato is one of the premier vegetables in the world and is widely cultivated for higher yield and economic importance; thus, the area under cultivation is increasing. Pandoraea species can be a risky pathogenic bacterium to tomato plants, impacting the yield. They are gram-negative, motile, and rod-shaped. In 2022, the University of Limpopo conducted a study to identify and name the Pandoraea bacterium found in a tomato field located in Limpopo Province, South Africa. Molecular methods were employed, and the Chelex approach was utilized to extract the 16S rDNA marker, enabling the identification of bacteria present in the soil of tomato fields in South Africa. After conducting tests using specific primers to amplify the 16S rDNA, we have identified the bacterium as Pandoraea. Our analysis indicates that the strain of Pandoraea found in South Africa shares a 90% similarity with a population from Belgium (LR536859). Furthermore, maximum likelihood phylogenetic analysis indicates that this species is grouped with other Pandoraea species, with highly supported (100) bootstrap values. While the 16S rDNA method successfully identified this species, we recommend utilizing other DNA markers for a more comprehensive understanding of the Pandoraea phylogeny. [ABSTRACT FROM AUTHOR]

The identification of microorganisms at the species level has always constituted a diagnostic challenge for clinical microbiology laboratories. The aim of the present study has been the evaluation in a real-time assay of the performance of Autobio in comparison with the Bruker mass spectrometry system for the identification of bacteria and yeasts. A total of 535 bacteria and yeast were tested in parallel with the two systems by direct smear or fast formic acid extraction for bacteria and yeasts, respectively. Discordant results were verified by 16S, ITS rRNA or specific gene sequencing. Beyond giving comparable results for bacteria with respect to the MBT smart system, Autof MS2600 mass spectrometer provided excellent accuracy for the identification of yeast species of clinical interest. [ABSTRACT FROM AUTHOR]

Matrix-Assisted Desorption/Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) in the last decade has revealed itself as a valid support in the workflow in the clinical microbiology laboratory for the identification of bacteria and fungi, demonstrating high reliability and effectiveness in this application. Its use has reduced, by 24 h, the time to obtain a microbiological diagnosis compared to conventional biochemical automatic systems. MALDI-TOF MS application to the detection of pathogens directly in clinical samples was proposed but requires a deeper investigation, whereas its application to positive blood cultures for the identification of microorganisms and the detection of antimicrobial resistance are now the most useful applications. Thanks to its rapidity, accuracy, and low price in reagents and consumables, MALDI-TOF MS has also been applied to different fields of clinical microbiology, such as the detection of antibiotic susceptibility/resistance biomarkers, the identification of aminoacidic sequences and the chemical structure of protein terminal groups, and as an emerging method in microbial typing. Some of these applications are waiting for an extensive evaluation before confirming a transfer to the routine. MALDI-TOF MS has not yet been used for the routine identification of parasites; nevertheless, studies have been reported in the last few years on its use in the identification of intestinal protozoa, Plasmodium falciparum, or ectoparasites. Innovative applications of MALDI-TOF MS to viruses' identification were also reported, seeking further studies before adapting this tool to the virus's diagnostic. This mini-review is focused on the MALDI-TOF MS application in the real life of the diagnostic microbiology laboratory. [ABSTRACT FROM AUTHOR]

Microbial contamination and foodborne infections are a significant global public health concern. For this reason, the detection, monitoring, and characterization of pathogens represent a significant challenge in quality control settings. Standard approaches, such as culture methods and biochemical tests, are known to be very time-consuming and intensive. Conversely, molecular technologies based on the genomic identification of bacteria are quick and low-cost. Listeria monocytogenes is an opportunistic pathogen and a major concern especially in food industries. It is important to understand and implement multiple quality control measures to control Listeria infection risk and prevent the contamination of products. Standardized detection and confirmation tests such as the API Listeria test, MALDI-TOF MS, and PCR analysis are available. The aim of our work is to provide a specific molecular method, designed according to the EN UNI ISO 16140-3:2021, for the specific detection, monitoring, and characterization of Listeria spp. and Listeria monocytogenes contamination. The verification of this new rapid approach by real-time PCR (qPCR) overcomes the limitations of culture-based techniques, meeting all the verification criteria required by ISO guidelines, including implementation and item confirmation. This system offers a powerful approach to the real-time assessment of food safety, useful for industry self-monitoring and regulatory inspection. [ABSTRACT FROM AUTHOR]

Background:Raoultella planticola is an uncommon gram-negative organism found in the environment. Patients and Methods: The patient, an 81-year-old female who had undergone total cystectomy and bilateral ureteral stoma surgery, presented to the hospital with a fever. It was determined that Raoultella planticola was responsible for the bacteremia. Results: Rapid identification of bacteria using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) in blood culture samples and appropriate antibacterial treatment was begun and the patient was discharged three days later. Conclusions: This case emphasizes the presence of a rare pathogen as the cause of bacteremia and underscores the importance of utilizing rapid methods for bacterial identification to establish an accurate diagnosis. [ABSTRACT FROM AUTHOR]

Streptococcus suis is a zoonotic pathogen that causes a major health problem in the pig production industry worldwide. Spain is one of the largest pig producers in the world. This work aimed to investigate the genetic and phenotypic features of invasive S. suis isolates recovered in Spain. A panel of 156 clinical isolates recovered from 13 Autonomous Communities, representing the major pig producers, were analysed. MLST and serotyping analysis revealed that most isolates (61.6%) were assigned to ST1 (26.3%), ST123 (18.6%), ST29 (9.6%), and ST3 (7.1%). Interestingly, 34 new STs were identified, indicating the emergence of novel genetic lineages. Serotypes 9 (27.6%) and 1 (21.8%) prevailed, followed by serotypes 7 (12.8%) and 2 (12.2%). Analysis of 13 virulence-associated genes showed significant associations between ST, serotype, virulence patterns, and clinical features, evidencing particular virulence traits associated with genetic clusters. The pangenome was generated, and the core genome was distributed in 7 Bayesian groups where each group included a variable set of over- and under-represented genes of different categories. The study provides comprehensive data and knowledge to improve the design of new vaccines, antimicrobial treatments, and bacterial typing approaches. [ABSTRACT FROM AUTHOR]

Even though marine biofouling is the most common life form of microorganisms, it is understudied, especially on the Moroccan coast. This work aimed at the molecular identification of bacteria from the biofilm of the marine environment of the central Atlantic coast of Morocco. It assessed the resistance of bacteria to antibiotics and heavy metals, whilst also highlighted the reciprocal relationship between the environment and bacteria and their impact on human health. The study was conducted by analysing the formation of young biofilms on glass, plastic, and metal, as well as examining natural biofouling recovered from different materials (wood, metal and plastic) found in the intertidal zone of the Anza coast, city of Agadir. Bacteria were recuperated, purified and identified via biochemical and 16S rRNA methods. Then resistances to antibiotics and heavy metals were determined by the antibiogram method, and microdilution, respectively. The results showed a rich bacterial biodiversity of marine biofilms, which vary according to the support material of the biofilm (wood, metals or plastics). The abundance of bacteria was significantly (p < 0.05) higher on plastic (44.75%) than on wood (30.5%) and metal (24.75%). The biofilms harboured pathogenic species, such as Staphylococcus pasteuri, Klebsiella pneumoniae and Salmonella enterica. The resistance varied among bacterial species. However, all bacteria were resistant to amoxicillin, amikacin, gentamicin, manganese and zinc. These results constitute new data. Whilst the biofilms of the Anza coast are home to rich bacterial biodiversity, some bacteria pose health and environmental hazards due to their pathogenicity to antibiotics and heavy metals. [ABSTRACT FROM AUTHOR]

Phenotypic identification of bacteria by staining technique and biochemical tests. This practical was carried out to identify Proteus vulgaris using biochemical test, this test includes, citrate utilization, indole, carbohydrate fermentation, methyl red, voges Proskauer, motility, production of hydrogen sulphide, catalase, and oxidase tests. Results obtained shows that Proteus vulgaris was positive to indole, motility, methyl red and urease. Proteus vulgaris was unable to utilize citrate for carbon and energy, and does not synthesis the enzyme amylase to break down starch. The bacteria fermented glucose to produce acid and gas. [ABSTRACT FROM AUTHOR]

Spiny lobster is a member of crustaceans that has high economic value. The demand for export markets in Asian, European and American countries as well as locally, is quite high with an expensive selling price. However, there are obstacles that often occur in spiny lobster rearing cultivation, namely infectious diseases that will cause high mortality. The purpose of this study was to investigate infectious diseases in rearing spiny lobster Panulirus spp. that were kept in floating net cages at Tanjung Putus, Lampung. The research method involved sampling five spiny lobsters in floating net cages, observation of clinical symptoms, bacterial isolation, identification of bacteria, detection of Milky Hemolymph Disease of Spiny Lobster (MHD-SL) through polymerase chain reaction (PCR) analysis and histopathology. The sampling location was at PT. Saibatin Perikanan Indonesia. The bacteria Vibrio parahaemolyticus and Vibrio alginolyticus were detected. Five lobsters were infected by MHD-SL, characterized by milky white hemolymph. All five lobster samples were positively infected with Milky Hemolymph Disease of Spiny Lobster (MHD-SL) through PCR analysis. Histopathological observations showed pathological microanatomical changes in the lobster hepatopancreas tissue, indicating that the tissue changes, in the form of encapsulation and infiltration were due to Rickettsia-like bacteria (RLB) infection. The management of spiny lobster stocking density, maintenance biosecurity, and increased lobster immunity must be implemented in order to prevent MHD-SL disease in floating net cages. [ABSTRACT FROM AUTHOR]

Paratuberculosis (Johne's disease) is a chronic granulomatous small intestine disease caused by MAP. Diagnosing and isolating infected animals is the most important measure for controlling the disease. Therefore, this study aimed to molecularly identify mycobacterium isolated from ELISA- positive cows with Johne's disease by nested PCR from the samples from Markazi Province, Iran. For this purpose, 2938 samples were decontaminated and then cultured on the Herrold egg culture medium containing mycobactin and no mycobactin. After DNA extraction, PCR for 16S rRNA was first performed, followed by nested PCR on positive samples. Of 2938 samples, 87 were positive, and 26 were suspected. All positive isolates were observed in Ziehl-Neelsen staining in microscopic expansion. A 543-bp band was observed in 26 tested samples and mycobacterium strains in PCR for 16S rRNA, indicating the presence of mycobacterium in the above samples. Nested PCR was performed for all isolates and positive and negative control strains. A 398-bp band was obtained in the first stage, and a 298-bp fragment was obtained in the second stage, indicating the presence of MAP in the samples. Accordingly, nested PCR is suggested as a proper method for the quick and definitive diagnosis of disease cases. [ABSTRACT FROM AUTHOR]

Rapid and accurate identification of bacteria is of great importance to public health in various fields, including medical diagnostics, food safety, and environmental monitoring. However, most existing bacterial detection methods have very narrow detectable concentration ranges and limited detection information, which easily leads to wrong diagnosis and treatment. This work presents a novel high-throughput microfluidic electrical impedance-based multidimensional single-bacterium profiling system for ultrawide concentration range detection and accurate differentiation of viability and Gram types of bacteria. The electrical impedance-based microfluidic cytometry is capable of multi-frequency impedance quantification, which allows profiling of the bacteria size, concentration, and membrane impedance as an indicator of bacterial viability and Gram properties in a single flow-through interrogation. It has been demonstrated that this novel impedance cytometry has an ultrawide bacterial counting range (102–108 cells per mL), and exhibits a rapid and accurate discrimination of viability and Gram types of bacteria in a label-free manner. Escherichia coli (E. coli) has been used as an analog species for the accuracy assessment of the electrical impedance-based bacterial detection system in an authentic complex beverage matrix within 24 hours. The impedance-based quantifications of viable bacteria are consistent with those obtained by the classical bacterial colony counting method (R2 = 0.996). This work could pave the way for providing a novel microfluidic cytometry system for rapid and multidimensional bacterial detection in diverse areas. [ABSTRACT FROM AUTHOR]

In and around the Treatment Storage and Disposal Facility (TSDF), Duindigal, Ramky site, Hyderabad, Telangana, ten samples were collected. To assess the ability of the bacterial isolates to remove contaminants, the following parameters were chosen for this study: pH, TDS, BOD, COD, TN, and TP. Two of the ten isolates showed promising degradation capabilities. The 16S rRNA gene sequence was used to apply genotypic techniques to the two strains that performed the best. Alcaligenes faecalis and Brevibacterium iodinum are the two bacterial strains that we found using NCBI BLAST analysis. To optimize the growth rate of the isolates, some parameters like pH, temperature, incubation time and peptone concentrations were optimized and got enhanced results. These findings have expanded the possibility of identifying industrially significant bacteria from solid waste disposal sites, and these isolates may be an essential source for the identification of enzymes with practical applications in industry. [ABSTRACT FROM AUTHOR]

The Region of Arica and Parinacota (Atacama Desert) offers several unexplored remote sites with unique characteristics that would allow for the formulation of new bioproducts for agriculture. Among them, Jurasi Hot Springs, Polloquere Hot Springs, and Amuyo Lagoons represent a group of open pools fed by thermal water springing from the mountains. Their microbiomes remain unspecified, providing a unique opportunity to characterize the endemic community of these sites and develop new bioproducts for sustainable agriculture. Bacteria were isolated from the sediments of these geothermal sites and characterized by sequencing the 16S rRNA gene, microbiological characterization, and agricultural functional characterization. A total of 57 bacteria were isolated from three geothermal sites north of the Atacama Desert. The sequence analysis showed that the isolates belong to several bacterial genera, including Pantoea, Bacillus, and Pseudomonas, among others. The functional characterization revealed the presence of PGP traits, hydrolytic enzymes, and biocontrol activity against phytopathogenic fungi. These bacteria possess the potential to develop new biobased products for agriculture in arid conditions. [ABSTRACT FROM AUTHOR]

Abstract Background The rapid expansion of Whole-Genome Sequencing has revolutionized the fields of clinical and food microbiology. However, its implementation as a routine laboratory technique remains challenging due to the growth of data at a faster rate than can be effectively analyzed and critical gaps in bioinformatics knowledge. Results To address both issues, CamPype was developed as a new bioinformatics workflow for the genomics analysis of sequencing data of bacteria, especially Campylobacter, which is the main cause of gastroenteritis worldwide making a negative impact on the economy of the public health systems. CamPype allows fully customization of stages to run and tools to use, including read quality control filtering, read contamination, reads extension and assembly, bacterial typing, genome annotation, searching for antibiotic resistance genes, virulence genes and plasmids, pangenome construction and identification of nucleotide variants. All results are processed and resumed in an interactive HTML report for best data visualization and interpretation. Conclusions The minimal user intervention of CamPype makes of this workflow an attractive resource for microbiology laboratories with no expertise in bioinformatics as a first line method for bacterial typing and epidemiological analyses, that would help to reduce the costs of disease outbreaks, or for comparative genomic analyses. CamPype is publicly available at https://github.com/JoseBarbero/CamPype .

Bacterial infection is a life-threatening situation, and its rapid diagnosis is essential for treatment. Apart from medical applications, rapid identification of bacteria is vital in the food industry or the public health system. There are various bacterial identification techniques, including molecular-based methods, immunological approaches, and biosensor-based procedures. The most commonly used methods are culture-based methods, which are time-consuming. The objective of this study is to find a fingerprint of bacteria to identify them. Three strains of bacteria were selected, and seven different concentrations of each bacterium were prepared. The bacteria were then treated with two different molar concentrations of the fluorescent fluorophore, dichlorodihydrofluorescein diacetate for 30 minutes. Then, using the fluorescence mode of a multimode reader, the fluorescence emission of each bacterium is scanned twice during 60 minutes. Plotting the difference between two scans versus the bacteria concentration results in a unique fluorescence pattern for each bacterium. Observation of the redox state of bacteria, during 90 minutes, results in a fluorescence pattern that is clearly a fingerprint of different bacteria. This pattern is independent of fluorophore concentration. Mean Squares Errors (MSE) between the fluorescence patterns of similar bacteria is less than that of different bacteria, which shows the method can properly identify the bacteria. In this study, a new label-free method is developed to detect and identify different species of bacteria by measuring the redox activity and using the fluorescence fluorophore, dichlorodihydrofluorescein diacetate. This robust and low-cost method can properly identify the bacteria, uses only one excitation and emission wavelength, and can be simply implemented with current multimode plate readers. • The pattern of the redox state of bacterium is a fingerprint of that bacterium. • The mechanism of H2-DCF-DA conversion depends on the redox state of the bacteria and its enzymes. • Using H2-DCF-DA and scanning the sample twice, results in a fingerprint of each bacterium. [ABSTRACT FROM AUTHOR]

In this study, the isolation and identification of bacteria that form biofilms on various food products sold on open-air market stalls in Aydın Province were aimed. Bacteria were isolated from food surfaces in aseptic conditions and isolated after incubation in the Tryptic Soy Agar medium at 37°C for 24-48 hours. DNA isolations of the isolated bacteria were performed and the PCR products obtained were used for sequencing. The Congo Red Agar method was used to qualitatively analyze biofilm formation. According to this method, bacteria forming black colonies were evaluated as biofilm-positive and were subjected to quantitative analysis using the Microplate method. A total of 67 bacteria were isolated from the sampled food items, of which 7 were strong and 2 were moderate biofilm producers, showing that more importance should be given to food hygiene. [ABSTRACT FROM AUTHOR]

FTIR (Fourier transform infrared spectroscopy) is one analytical technique of the absorption of infrared radiation. FTIR can also be used as a tool to characterize profiles of biomolecules in bacterial cells, which can be useful in differentiating different bacteria. Considering that different bacterial species have different molecular compositions, it will then result in unique FTIR spectra for each species and even bacterial strains. Having this important tool, here, we have developed a methodology aimed at refining the analysis and classification of the FTIR absorption spectra obtained from samples of Staphylococcus aureus, with the implementation of machine learning algorithms. In the first stage, the system conforming to four specified species groups, Control, Amoxicillin induced (AMO), Gentamicin induced (GEN), and Erythromycin induced (ERY), was analyzed. Then, in the second stage, five hidden samples were identified and correctly classified as with/without resistance to induced antibiotics. The total analyses were performed in three windows, Carbohydrates, Fatty Acids, and Proteins, of five hundred spectra. The protocol for acquiring the spectral data from the antibiotic-resistant bacteria via FTIR spectroscopy developed by Soares et al. was implemented here due to demonstrating high accuracy and sensitivity. The present study focuses on the prediction of antibiotic-induced samples through the implementation of the hierarchical cluster analysis (HCA), principal component analysis (PCA) algorithm, and calculation of confusion matrices (CMs) applied to the FTIR absorption spectra data. The data analysis process developed here has the main objective of obtaining knowledge about the intrinsic behavior of S. aureus samples within the analysis regions of the FTIR absorption spectra. The results yielded values with 0.7 to 1 accuracy and high values of sensitivity and specificity for the species identification in the CM calculations. Such results provide important information on antibiotic resistance in samples of S. aureus bacteria for potential application in the detection of antibiotic resistance in clinical use. [ABSTRACT FROM AUTHOR]

Heavy metals from solid waste deposits that are toxic, mutagenic, and carcinogenic contaminate natural water supplies and agricultural environments. The purpose of this project is to separate and characterize naturally occurring bacteria that can reduce and detoxify heavy metals (lead, cadmium, nickel, zinc, manganese, iron, copper, chromium, and mercury) from solid waste dumping sites. Ten strains in total were isolated from the samples; the two best-performing isolates, Shewanella oneidensis strain AGB 4 (Isolate 5) and Bacillus pumilus strain AGB 11 (Isolate 6) were recognized up to the genus level based on their 16S rRNA identification studies. These isolates demonstrated resistance to every heavy metal that was examined in the solid waste. The MICs for the two isolates varied in relation to the amounts of the heavy metals listed above. The solid waste isolates grew best at pH 7.0, 30°C and an incubation period of 24 hours. Utilizing an atomic absorption spectrophotometer to measure degradation potential, Shewanella oneidensis demonstrated the most removable capability for copper (60%) and the lowest removable capability for lead, arsenic and mercury (45%) and Bacillus pumilus demonstrated a reduction of 48% in mercury and arsenic and 65% in copper. Bacillus pumilus and Shewanella oneidensis may be able to break down heavy metals through plasmids, which could be used to change plasmids so they can carry the ability to accumulate heavy metals. Thus, determining the resistance to heavy metals and biodegradation potential of two bacteria could serve as a foundational investigation for the development of viable local biological remediation agents in solid waste deposit sites. [ABSTRACT FROM AUTHOR]

Sepsis is a critical disease caused by the abrupt increase of bacteria in human blood, which subsequently causes a cytokine storm. Early identification of bacteria is critical to treating a patient with proper antibiotics to avoid sepsis. However, conventional culture-based identification takes a long time. Polymerase chain reaction (PCR) is not so successful because of the complexity and similarity in the genome sequence of some bacterial species, making it difficult to design primers and thus less suitable for rapid bacterial identification. To address these issues, several new technologies have been developed. Recent advances in nanotechnology have shown great potential for fast and accurate bacterial identification. The most promising strategy in nanotechnology involves the use of nanoparticles, which has led to the advancement of highly specific and sensitive biosensors capable of detecting and identifying bacteria even at low concentrations in very little time. The primary drawback of conventional antibiotics is the potential for antimicrobial resistance, which can lead to the development of superbacteria, making them difficult to treat. The incorporation of diverse nanomaterials and designs of nanomaterials has been utilized to kill bacteria efficiently. Nanomaterials with distinct physicochemical properties, such as optical and magnetic properties, including plasmonic and magnetic nanoparticles, have been extensively studied for their potential to efficiently kill bacteria. In this review, we are emphasizing the recent advances in nano-biotechnologies for bacterial identification and anti-bacterial properties. The basic principles of new technologies, as well as their future challenges, have been discussed. [ABSTRACT FROM AUTHOR]

Matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry (MALDI‐TOF MS) is an excellent tool for bacterial identification. It allows high throughput, sensitive and specific applications in clinical diagnostics and environmental research. Currently, there is no optimal standardized protocol for sample preparation and culture conditions to profile bacteria. The performance of MALDI‐TOF MS is affected by several variables, such as sample preparation, culture media and culture conditions, incubation time/growth stage, incubation temperature, high salt content, blood in the culture media, and others. This review thus aims to clarify why a uniformed protocol is not plausible, to assess the effects these factors have on MALDI‐TOF MS identification score, and discuss possible optimizations for its methodology, in relation to specific bacterial representatives and strain requirements. [ABSTRACT FROM AUTHOR]

Neonatal calf diarrhea (NCD) is a broad symptom encompassing many potential underlying causes. While alterations in the gut microbiota have been correlated with diarrhea, the effects of diarrhea on gut communities have not been sufficiently studied. To explore these effects and identify key microbiota involved, we profiled the fecal microbial community of 21 calves with varying health conditions using the 16S rRNA gene. In comparison to healthy calves, diarrheic calves exhibited significantly decreased diversity and evenness indices. There was a notable increase in the relative abundance of Proteobacteria and Actinobacteriota, and a significant decrease in the relative abundance of Bacteroidetes. At the genus level, there were increased relative abundances of Escherichia-Shigella and Lactobacillus. Notably, the abundance of Lactobacillus continued to increase during the recovery from diarrhea. Clinical observation and bacterial typing analysis revealed fecal microbiome dysbiosis as a significant characteristic of NCD. This work identifies dysbiosis as a key factor promoting diarrhea in neonatal calves, characterized by a low-diversity microbiome. The increased abundance of Lactobacillus might contribute to the curative properties of diarrhea. [ABSTRACT FROM AUTHOR]

The Gram-negative non-motile Klebsiella pneuomoniae is currently a major cause of hospital-acquired (HA) and community-acquired (CA) infections, leading to great public health concern globally, while rapid identification and accurate tracing of the pathogenic bacterium is essential in facilitating monitoring and controlling of K. pneumoniae outbreak and dissemination. Multi-locus sequence typing (MLST) is a commonly used typing approach with low cost that is able to distinguish bacterial isolates based on the allelic profiles of several housekeeping genes, despite low resolution and labor intensity of the method. Core-genome MLST scheme (cgMLST) is recently proposed to sub-type and monitor outbreaks of bacterial strains with high resolution and reliability, which uses hundreds or thousands of genes conserved in all or most members of the species. However, the method is complex and requires whole genome sequencing of bacterial strains with high costs. Therefore, it is urgently needed to develop novel methods with high resolution and low cost for bacterial typing. Surface enhanced Raman spectroscopy (SERS) is a rapid, sensitive and cheap method for bacterial identification. Previous studies confirmed that classification and prediction of bacterial strains via SERS spectral analysis correlated well with MLST typing results. However, there is currently no similar comparative analysis in K. pneumoniae strains. In this pilot study, 16 K. pneumoniae strains with different sequencing typings (STs) were selected and a phylogenetic tree was constructed based on core genome analysis. SERS spectra (N = 45/each strain) were generated for all the K. pneumoniae strains, which were then comparatively classified and predicted via six representative machine learning (ML) algorithms. According to the results, SERS technique coupled with the ML algorithm support vector machine (SVM) could achieve the highest accuracy (5-Fold Cross Validation = 100%) in terms of differentiating and predicting all the K. pneumoniae strains that were consistent to corresponding MLSTs. In sum, we show in this pilot study that the SERS-SVM based method is able to accurately predict K. pneumoniae MLST types, which has the application potential in clinical settings for tracing dissemination and controlling outbreak of K. pneumoniae in hospitals and communities with low costs and high rapidity. [ABSTRACT FROM AUTHOR]

Daphne mezereum of the Thymelaeaceae family is a medicinal shrub occurring naturally in Europe and under legal protection in Poland. In the present study, a protocol developed for mass propagation of February daphne from nodal explants is presented. Micropropagation is one of the in vitro techniques that allow the preservation of rare and valuable plants by developing efficient methods for their propagation. In the proliferation stage, explants were cultured in the Woody Plant Medium (WPM) with different cytokinins, and in the rooting stage on the semi-solid WPM medium with perlite, indole-3-butyric acid (IBA) in various concentrations was used. The maximum proliferation rate (five shoots per explant) was observed on the medium containing 4.14 μM of meta-Topolin (mT). When the regenerated shoots were rooted in vitro in the presence of IBA in various concentrations, that of 19.68 μM induced the highest number of roots per shoot (6.63) and the maximal root length (2.15 cm). It is also worth remembering that plants are often colonized by different groups of microorganisms, which also affect the diversity of the ecosystem. The endophytic bacteria inhabiting the D. mezereum shoots are Mycobacterium. [ABSTRACT FROM AUTHOR]