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The aim of this study was to identify the species and antimicrobial susceptibility of bacteria involved in parietal fibrinous peritonitis (PFP). We studied 156 peritoneal fluid samples from cows presenting PFP after caesarean section. Bacteria were cultured in selective media and their antimicrobial susceptibility was tested by disk diffusion assay. Bacteria were isolated in the majority (129/156; 83%) of samples. The majority (82/129; 63%) of positive samples contained one dominant species, while two or more species were cultured in 47/129 (36%) samples. Trueperella pyogenes (T. Pyogenes) (107 strains) was the most identified species, followed by Escherichia coli (E. coli) (38 strains), Proteus mirabilis (P. mirabilis) (6 strains), and Clostridium perfringens (C. perfringens) (6 strains). Several other species were sporadically identified. Antimicrobial susceptibility was tested in 59/185 strains, predominantly E. coli (38 strains) and P. mirabilis (6 strains). Antibiotic resistance, including resistance to molecules of critical importance, was commonly observed; strains were classified as weakly drug resistant (22/59; 37%), multidrug resistant (24/59; 41%), extensively drug resistant (12/59; 20%), or pan-drug resistant (1/59; 2%). In conclusion, extensive antibiotic resistance in the isolated germs might contribute to treatment failure. Ideally, antimicrobial therapy of PFP should be based upon bacterial culture and susceptibility testing. [ABSTRACT FROM AUTHOR]

This study investigated the eggs of Polish-bred edible snails of the Cornu genus as a food and aimed to determine the presence of microorganisms in them of the Salmonella and Listeria genera and ascertain the number of coagulase-positive staphylococci. Raw material, semi-finished products, and the final product were collected during the production cycle. Testing for the presence of Salmonella spp. and Listeria spp. and measuring of the pathogenic staphylococci contamination level were carried out in accordance with ISO standards. Commercial biochemical tests were used for species identification of bacteria of the Enterobacteriaceae family and Staphylococcus genus. An API kit and a PCR protocol were utilised for species confirmation of the microorganisms of the Listeria genus. Neither Salmonella nor coagulase-positive staphylococci were found in any of the studied material. Bacteria of the Listeria genus were found in samples taken at every stage of production; however L. monocytogenes was confirmed in samples of the final product. The absence of Salmonella spp. and Staphylococcus aureus in samples of the final product indicates that the required hygiene standard was maintained in the production process of edible snail eggs. Nevertheless, the presence of L. monocytogenes in eggs of common garden snails may pose a potential risk to consumer health. [ABSTRACT FROM AUTHOR]

Fast identification of pathogenic bacteria is an essential need for patient's diagnostic in hospitals and environmental monitoring of water and air quality. Bacterial cells consist of a very high amount of biological molecules whose content changes in response to different environmental conditions. The similarity between the molecular compositions of different bacterial cells limits the possibility to find unique markers to enable differentiation among species. Although many biological molecules in the cells absorb at the UV-Vis region, only a few of them can be detected in whole cells by their intrinsic fluorescence. Among these molecules are the amino acids phenylalanine, tyrosine, and tryptophan. In this work, we develop a rapid method for bacterial identification by synchronous fluorescence. We show that we can quantify the concentration for the 3 amino acids without any significant interference from other fluorophores in the cells and that we can differentiate among 6 pathogenic bacterial species by using the concentrations of their amino acids as a bacterial fingerprint. Fluorescent amino acids exist in all living cells. Therefore, this method has the potential to be applicative for the rapid identification of cells from all kinds of organisms. [ABSTRACT FROM AUTHOR]

Avian influenza surveillance is a requirement for commercial trade in ostrich products, but influenza A viruses (IAVs) have proven difficult to isolate from ostrich tracheal swabs that test positive using molecular methods. We hypothesized that microbes unique to the ostrich trachea propagate in the transport medium after sampling and affect viral viability. We cultured tracheal swabs from 50 ostriches on 4 farms in South Africa, and recovered and identified 13 bacterial, 1 yeast, and 2 fungal species. Dietzia sp. had not been identified previously in the oropharyngeal tract of a bird, to our knowledge. The bacteria were tested for antimicrobial susceptibility, and most aerobic species, except for Streptococcus sp. and Pseudomonas sp., were sensitive to enrofloxacin; all were susceptible to sulfonamide. Virus inhibition experiments determined that ostrich-source Streptococcus sp., Pantoea sp., and Citrobacter freundii produced extracellular metabolites that caused a substantial reduction in the IAV titers of 99.9%. Streptomyces, Corynebacterium, Staphylococcus, Arthrobacter gandavensis, Pseudomonas putida, and Acinetobacter spp. similarly reduced the viability of IAV from 77.6% to 24.1%. Dietzia appeared to have no effect, but Rothia dentocariosa, Rhodotorula spp., and Clostridium spp. slightly increased the viability of IAV by 25.9, 34.9, and 58.5%, respectively. [ABSTRACT FROM AUTHOR]

Abstract Background Streptococcus halichoeri infections have been reported in grey seals, a European badger, a Stellar sea lion and humans, but its presence in companion and fur animals is unknown. Since 2010, S. halichoeri-like bacteria (SHL) have been isolated from fur animals and dogs in Finland. Our aim was to retrospectively investigate laboratory records for SHL from canine and fur animal infections, characterize the isolates and compare their genetic relatedness in relation to three reference strains: CCUG 48324T, originating from a grey seal, and strains 67100 and 61265, originally isolated from humans. Results A total of 138 and 36 SHLs from canine and fur animal infections, respectively, were identified in the laboratory records. SHL was commonly associated with skin infections, but rarely as the only species. A set of 49 canine and 23 fur animal SHLs were further characterized. MALDI-TOF confirmed them as being S. halichoeri. The growth characteristics were consistent with the original findings, but isolates were catalase positive. In total, 17 distinct API 20 Strep patterns were recorded among all 75 isolates tested, of which pattern 5563100 was the most common (n = 30). Antimicrobial resistance to erythromycin and clindamycin was common in canine isolates, but rare in fur animal isolates. Three clusters were observed by PFGE, and 16S rRNA sequencing revealed 98.1–100% similarities with the human strains and 98.1–99.5% with the seal strain. A phylogenetic tree of concatenated 16S rRNA and rpoB revealed closely related isolates with two clades. Fifteen canine isolates were identical to the human strains based on concatenated 16S rRNA and rpoB sequencing. Conclusions Streptococcus halichoeri appears to be quite a common bacterial species in the skin of dogs and fur animals. The clinical significance of S. halichoeri is uncertain, as it was rarely isolated as a monoculture. No apparent temporal or spatial clustering was detected, but isolates from different sources were genetically very similar. Because many canine isolates were genetically similar to the human reference strains, transmission between dogs and humans may be possible. WGS sequencing of strains from different sources is needed to further investigate the epidemiology and virulence of S. halichoeri.

Garcinia kola (Colanut) is a well-known indigenous plant with several pharmacological activities that is widely consumed in most Northern parts of Nigeria. It is traditionally believed to serve as a remedy in the management of diarrhoeagenic bacterial infections. This study investigated the prevalence of pathogenic bacteria on the surface of colanuts sold within Kaduna North Local Government Area, Kaduna State. A total of sixty-four (64) bacteria were isolated from the samples, and were identified based on their cultural, Gram reaction, and biochemical characterizations. The pathogens were tested against selected antibiotics using Agar well diffusion method. The isolates were confirmed to be Salmonella specie (46%), Escherichia coli (32%) and Staphylococcus aureus (22%). People who consume colanut without proper washing are at high risk of contracting infections caused by the aforementioned pathogens. [ABSTRACT FROM AUTHOR]

Background: It is a polysaccharide substance produced by a group of microorganisms that helps it adhere to living and non-living surfaces and it is responsible for many diseases, as it has a role in staphylococcal diseases such as pneumonia, urinary tract infection and endocarditis. Although lipoteichoic acid is a component of biofilm. However, it has a role in preventing biofilm formation Materials and Methods: The methods of this study included isolated and identification of bacteria from UTI samples and identified by morphology characters and biochemical test to identify S.aureus. Then discover their ability to formbiofilm and Use lipoteichoic acid in different concentration as antibiofilm Results: The results of identification of bacterial isolatesshowed the colonies grown on blood agar causing the typical B hemolytic state, these samples not grown on MacConkey agar and under the microscope showed gram positive cocci, a cluster like grape, these samples were identified as Staphylococcus when grown on mannitol medium converted it to yellowish color and appeared round, smooth, raised, mucous and gelatinous. The staphylococcusaureus formed biofilms with different concentrations, where the fourth isolate was the lowest percentage (0.065), while the second and fifth isolates were given (0.120 and 0.153) and the first isolation was given (0.220), however the highest percentage was given by the third isolation (0.357). So this study showed that the concentrations of LTA (200) µg/mlare MIC. The results of this work showed that after 24 hours of treatment with LTA it impeded the formation of biofilms of Staphylococcus aureus and the result after treatment was the concentration 50 and 100µg/ml gave less percentage of inhibition, while 500µg/ml appeared 100% of inhibition, so (200,300 and 400 gave 61%, 80% and90% inhibition to biofilm respectively. [ABSTRACT FROM AUTHOR]

Over the past year, the world's attention has focused on combating COVID-19 disease, but the other threat waiting at the door—antimicrobial resistance should not be forgotten. Although making the diagnosis rapidly and accurately is crucial in preventing antibiotic resistance development, bacterial identification techniques include some challenging processes. To address this challenge, we proposed a deep neural network (DNN) that can discriminate antibiotic-resistant bacteria using surface-enhanced Raman spectroscopy (SERS). Stacked autoencoder (SAE)-based DNN was used for the rapid identification of methicillin-resistant Staphylococcus aureus (MRSA) and methicillin-sensitive S. aureus (MSSA) bacteria using a label-free SERS technique. The performance of the DNN was compared with traditional classifiers. Since the SERS technique provides high signal-to-noise ratio (SNR) data, some subtle differences were found between MRSA and MSSA in relative band intensities. SAE-based DNN can learn features from raw data and classify them with an accuracy of 97.66%. Moreover, the model discriminates bacteria with an area under curve (AUC) of 0.99. Compared to traditional classifiers, SAE-based DNN was found superior in accuracy and AUC values. The obtained results are also supported by statistical analysis. These results demonstrate that deep learning has great potential to characterize and detect antibiotic-resistant bacteria by using SERS spectral data. [ABSTRACT FROM AUTHOR]

Salmonella enterica (S. enterica) is an important foodborne pathogen, causing food poisoning and human infection, and critically threatening food safety and public health. Salmonella typing is essential for bacterial identification, tracing, epidemiological investigation, and monitoring. Serotyping and multilocus sequence typing (MLST) analysis are standard bacterial typing methods despite the low resolution. Core genome MLST (cgMLST) is a high-resolution molecular typing method based on whole genomic sequencing for accurate bacterial tracing. We investigated 250 S. enterica isolates from poultry, livestock, food, and human sources in nine provinces of China from 2004 to 2019 using serotyping, MLST, and cgMLST analysis. All S. enterica isolates were divided into 36 serovars using slide agglutination. The major serovars in order were Enteritidis (31 isolates), Typhimurium (29 isolates), Mbandaka (23 isolates), and Indiana (22 isolates). All strains were assigned into 43 sequence types (STs) by MLST. Among them, ST11 (31 isolates) was the primary ST. Besides this, a novel ST, ST8016, was identified, and it was different from ST40 by position 317 C → T in dnaN. Furthermore, these 250 isolates were grouped into 185 cgMLST sequence types (cgSTs) by cgMLST. The major cgST was cgST235530 (11 isolates), and only three cgSTs contained isolates from human and other sources, indicating a possibility of cross-species infection. Phylogenetic analysis indicated that most of the same serovar strains were putatively homologous except Saintpaul and Derby due to their multilineage characteristics. In addition, serovar I 4,[5],12:i:- and Typhimurium isolates have similar genomic relatedness on the phylogenetic tree. In conclusion, we sorted out the phenotyping and genotyping diversity of S. enterica isolates in China during 2004–2019 and clarified the temporal and spatial distribution characteristics of Salmonella from different hosts in China in the recent 16 years. These results greatly supplement Salmonella strain resources, genetic information, and traceability typing data; facilitate the typing, traceability, identification, and genetic evolution analysis of Salmonella ; and therefore, improve the level of analysis, monitoring, and controlling of foodborne microorganisms in China. [ABSTRACT FROM AUTHOR]

Background and Aim: Due to the diversified lifestyle and fancy ecology associated with Chitra deer (Axis axis), deer farming has become popular in Bangladesh. Diseases may be the common constrain of successful deer farming. This study aims to investigate the pathological, bacteriological, and nucleic acid based technologies to identify specific causes of morbidity and mortality of captive deer. Materials and Methods: Two deer farms and a park deer (designated as farm A, B, and C) entailing 87, 54, and 20 deer, respectively, showed illness and death constitute the study materials. A total of 42 deer died during this investigation. Following death, routine post-mortem examination, histopathology, impression smear staining, isolation, and identification of bacteria were carried out. Polymerase chain reaction (PCR) and reverse transcription PCR were carried out to safeguard the etiology. Results: Clinically, farm A and B showed the acute phase of illness and park deer showed chronic illness. Case fatality rates were 90%, 92%, and 100% in farms A, B, and C deer, respectively. Pasteurella multocida and Streptococcus pneumoniae were identified from the visceral organs of farm A deer. Farm B deer was infected with Clostridium perfringens type A. Park deer was infected with Mycobacterium tuberculosis and hydatid cyst. Conclusion: The infectivity in farm A deer was due to stress as induced by punishing weather. The infectivity in farm B deer was due to feeding a higher volume of protein in the diet. The park C deer may optate infection from companion man and animals living around. The diseases of captive deer identified mainly were zoonotic. It needs extensive veterinary services and specialized technologies to identify these diseases, monitor the infectivity and eliminate the public health important diseases at early onset. [ABSTRACT FROM AUTHOR]

The resonance Raman spectra of bacterial carotenoids have been employed to identify bacterial strains and their intensity changes as a function of ultraviolet (UV) radiation dose have been used to differentiate between live and dead bacteria. In addition, the resonance-enhanced Raman spectra enabled us to detect bacteria in water at much lower concentrations (∼108 cells/mL) than normally detected spectroscopically. A handheld spectrometer capable of recording resonance Raman spectra in situ was designed, constructed, and was used to record the spectra. In addition to bacteria, the method presented in this paper may also be used to identify fungi, viruses, and plants, in situ, and detect infections within a very short period of time. Graphical Abstract [ABSTRACT FROM AUTHOR]

The use of matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) mass spectrometry has proven to be rapid and accurate for the majority of clinical isolates. Some gaps remain concerning rare, emerging, or highly pathogenic species, showing the need to continuously expand the databases. In this multicenter study, we evaluated the accuracy of the VITEK MS v3.2 database in identifying 1172 unique isolates compared to identification by DNA sequence analysis. A total of 93.6% of the isolates were identified to species or group/complex level. A remaining 5.2% of the isolates were identified to the genus level. Forty tests gave a result of no identification (0.9%) and 12 tests (0.3%) gave a discordant identification compared to the reference identification. VITEK MS is also the first MALDI-TOF MS system that is able to delineate the four members of the Acinetobacter baumannii complex at species level without any specific protocol or special analysis method. These findings demonstrate that the VITEK MS v3.2 database is highly accurate for the identification of bacteria and fungi encountered in the clinical laboratory as well as emerging species like Candida auris and the highly pathogenic Brucella species. [ABSTRACT FROM AUTHOR]

Background: This study aimed to produce carotenoids of two bacterial strains obtained and isolated from Caatinga soil in Northeastern Brazil and to evaluate their antioxidant and photoprotective activities. The morphological identification of bacteria was performed by Gram staining and molecularly confirmed through the 16S rRNA gene. The production of carotenoids was performed on two 2³ factorial designs to analyze the influence of independent variables (temperature range, luminosity, agitation, spiral presence, and bacterial isolate type) for maximum carotenoid yield. The selected condition has been transferred to a bioreactor (10L). The identification of carotenoids was performed by liquid chromatography (HPLC) and mass spectrometry (LC-MS). Antioxidant activity was determined by inhibiting the bcarotene/linoleic acid system and the effectiveness as sunscreen was measured through its sun protection factor (SPF). Results: The results revealed that the isolates FT-7.22 and FT-5.12 were identified as Kocuria palustris; producers of a rare C50 carotenoid sarcinaxanthin. This is the first report on the production of carotenoids by this species from the Caatinga Domain. The pigment that was obtained from the Tryptic Soy Broth (TSB) medium in the best conditions of the factorial designs (increased agitation, aeration, and light exposure) exhibited a significant increase in the carotenoid production. The isolated FT-7.22 reached a higher sarcinaxanthin concentration (112,480 lg/L), and it exhibited promising antioxidant (76.53 ± 0.09%) and photoprotective activities (SPF = 9.36 ± 0.52). Conclusions: This study demonstrated the ability of K. palustris to produce carotenoid sarcinaxanthin with antioxidant and photoprotective activities so that it can be applied in cosmetic formulations. [ABSTRACT FROM AUTHOR]

Black Tiger Shrimp (Penaeus monodon) is one of the leading export commodities in Bangladesh. The industry, however, is frequently beset with quality deterioration and microbial diseases owing to various reasons. Here, we analyzed the sensory and nutritional qualities of shrimp, the total bacterial count, and molecular identification of pathogenic bacteria in samples collected from different supply chain actors (SCA), including the gher (farms), depots, wholesalers, retailers, and the processing industry in Khulna, Bangladesh. While the Sensory Quality Indices (SQI) of shrimps collected from farms, depots, and processing plants were found 'excellent and highly acceptable', the rating for wholesale and retail markets were 'good and acceptable'. Nutritionally, higher protein (21.59%), lipid (1.47%), and ash (1.97%) contents were found in shrimps collected from farms than that of other SCAs. Heterotrophic bacterial count (cfu/g) differed in various SCAs: farms 3.75±0.31 (×106), depots 3.95±0.92 (×106), wholesale markets 5.03±0.35 (×106), retail markets 4.82±0.40 (×106), and the processing industry 3.78±0.25 (×106). The presence of Ralstonia spp and Pseudomonas spp, confirmed by 16S rDNA sequencing were found in different SCAs. Overall, the quality of shrimp appeared better in farms than that of other SCAs, indicating that a lack of proper hygiene, sanitation, and post-harvest handling practices could be the likely impediments for quality deterioration. [ABSTRACT FROM AUTHOR]

Salmonella enterica serovar Gallinarum biovar Pullorum (bvP) and biovar Gallinarum (bvG) are the etiological agents of pullorum disease (PD) and fowl typhoid (FT) respectively, which cause huge economic losses to poultry industry especially in developing countries including India. Vaccination and biosecurity measures are currently being employed to control and reduce the S. Gallinarum infections. High endemicity, poor implementation of hygiene and lack of effective vaccines pose challenges in prevention and control of disease in intensively maintained poultry flocks. Comparative genome analysis unravels similarities and dissimilarities thus facilitating identification of genomic features that aids in pathogenesis, niche adaptation and in tracing of evolutionary history. The present investigation was carried out to assess the genotypic differences amongst S.enterica serovar Gallinarum strains including Indian strain S. Gallinarum Sal40 VTCCBAA614. The comparative genome analysis revealed an open pan-genome consisting of 5091 coding sequence (CDS) with 3270 CDS belonging to core-genome, 1254 CDS to dispensable genome and strain specific genes i.e. singletons ranging from 3 to 102 amongst the analyzed strains. Moreover, the investigated strains exhibited diversity in genomic features such as virulence factors, genomic islands, prophage regions, toxin-antitoxin cassettes, and acquired antimicrobial resistance genes. Core genome identified in the study can give important leads in the direction of design of rapid and reliable diagnostics, and vaccine design for effective infection control as well as eradication. Additionally, the identified genetic differences among the S. enterica serovar Gallinarum strains could be used for bacterial typing, structure based inhibitor development by future experimental investigations on the data generated. [ABSTRACT FROM AUTHOR]

Objective: The activity of β-glucuronidase produced by Escherichia coli subtypes in bile of patients with primary pigment stone of bile duct was compared, then the predominant serotype of Escherichia coli that caused the formation of pigment stones was explored. Methods: 70 patients with primary pigment stone of bile duct were selected. Bile duct bile were extracted under aseptic condition for bacterial culture during the operation, then made identification of bacteria and drug sensitivity test. Identification of Escherichia coli serotypes in bile by slide agglutination. According to the activity of β-glucuronidase and the reaction rate k of β-glucuronidase with substrate 4-nitrobenzene-β-D-glucoside (PNPG) was in direct proportion and in inverse proportion with OD600 value of reaction system to caculated activity of β-glucuronidase produced by various subtypes of Escherichia coli. Results: A total of 70 cases of bile duct bile specimen were obtained, 61 cases were positive for bacterial culture, the positive rate was 87.14%. A total of 73 strains were obtained, the culture results ranked first for Escherichia coli (34.25%). Amikacin, piperacillin/tazobactam, penem, tegacyclin, cefoperazone/sulbactam were the top five drugs in drug sensitivity test and tetracycline, levofloxacin, ampicillin, chloramphenicol, compound xinnuoming were the top five drugs of drug resistance rates. The serotypes of 25 strains of Escherichia coli were identified, a total of 13 serotypes of Escherichia coli were obtained, the top three were O30, O24 and O79. However, the slope k value of time-absorbance curve of Escherichia coli O24 serotype was significantly higher than that of other serotypes, it could be concluded that the activity of β-glucuronidase in Escherichia coli O24 serotype was high by combined with its OD600 value. Conclusion: The most common bacteria in the bile duct bile of patients with primary pigment stone of bile duct is Escherichia coli, its serotypes are O30, O24 and O79 mainly. Among them, the O24 serotype Escherichia coli has a high activity of producing β-glucuronidase. [ABSTRACT FROM AUTHOR]

Recently, the interest in donkey milk has increased considerably because it proved high nutritive and functional values of their ingredients. Its chemical composition is widely studied, but its microbiota, especially lactic acid bacteria, remains less studied. This study focuses on analyzing, isolating, and identifying lactic acid bacteria and evaluating their capacity to produce biomolecules with antibacterial activity. Among 44 strains identified, 43 are Gram-positive, and most are catalase-negative and cocci-shaped. Five strains were selected to evaluate their antibacterial activity against Listeria monocytogenes, Staphylococcus aureus, and Escherichia coli. Different induction methods allowed to amplify the antibacterial effects against these pathogenic strains. [ABSTRACT FROM AUTHOR]

Lactic acid bacteria (LAB) have long been consumed by people in several fermented foods such as dairy products. A study was conducted on lactating dairy cows to isolate and characterize LAB from dairy products found in and around Bahir-Dar city, North Western Ethiopia. Milk and milk products were randomly collected from dairy farms, milk vending shops, individual households, and supermarkets for bacteriological investigations. A total of sixteen samples were taken from different sources and cultured on different selective media: de Man, Rogosa, and Sharpe (MRS) agar for Lactobacillus spp.; M17 agar for Lactococcus spp.; Rogasa SL agar for Streptococci spp.; and MRS supplemented with cysteine (0.5%) for Bifidobacteria spp. Different laboratory techniques were implemented for LAB isolation and identification. A total of 41 bacterial isolates were grouped under five different genera of LAB and Bifidobacteria spp. were identified based on the growth morphology on the selective media, growth at a different temperature, gas production from glucose, carbohydrate fermentation, and other biochemical tests. LAB genera such as Lactobacillus, Lactococcus, Leuconostoc, Pediococcus, Streptococcus, and Bifidobacterium spp. were isolated and identified from raw milk, cheese, and yogurt. Based on the current study, the majority of the LAB (24.38%) was isolated from cheese and yogurt. Among these, Lactobacillus, Lactococcus (21.94%), Streptococcus (19.51%), Leuconostoc (14.64%), Bifidobacteria (12.19%), and Pediococcus (7.31%) spp. were also identified from these products. Furthermore, based on the bacterial load count and different identification methodologies, our study revealed that Lactobacillus spp. were the dominant LAB isolated from milk and milk products. As a result, since there are few studies on the isolation and identification of lactic acid bacteria from dairy products in Ethiopia, more research studies are needed to complete the identification and characterization to species level and their possible role as probiotics. [ABSTRACT FROM AUTHOR]

Background: Seasonal anestrus, which is controlled by the photoperiod in ewes, limits the ability to the fertility of ewe every time. Therefore, using hormones by vaginal devices is the most effective way of increasing fertility in order to form oestrus during the anestrus period and obtain a high rate of pregnancy. But, vaginal devices may cause a change in the profile and number of bacteria in the uterus and vagina, and thus create an environment suitable for infection. For this reason, identification of bacteria that are the source of infection can be achieved by performing antibiotic susceptibility tests and interpreting them correctly. The purpose of this study was to characterize the effect of intravaginal device-type and treatment-duration on vaginal bacteria count and type and determine the antibiotic susceptibility of vaginal bacterias in ewes after a program of oestrus synchronization. Methods: A total of 90 clinically healthy Kivircik ewes were selected. In order to provide oestrus synchronization during anestrus season (June), CIDR was inserted intravaginally to 45 ewes, the other 45 ewes were progestogen sponges inserted. In both groups remained inserted for 5, 9 and 13 days. While vaginal devices were withdrawal both groups ewes were exposed to intramuscular 350 IU PMSG injection. The mucous samples were collected from all ewes 0, 5, 9 and 13 days at time the IVS or CIDR withdrawal. In samples, bacterial concentration, bacterial identification and antibiotic susceptibility were determined. Result: The changes in the vaginal flora caused by the vaginal devices favored the development of opportunistic microbiota that could potentially be pathogenic. In the study, after vaginal device withdrawal, the bacteria species most frequently observed in both IVS and CIDR groups were E. coli. According to the results of this study, the first choice of antibiotics for vaginal infections caused by G-agents in ewes should be any of AXC, CEP and CTZ compared to other antibiotics. [ABSTRACT FROM AUTHOR]

Pseudaminic acid (Pse) is a significant prokaryotic monosaccharide found in important Gram‐negative and Gram‐positive bacteria. This unique sugar serves as a component of cell‐surface‐associated glycans or glycoproteins and is associated with their virulence. We report the synthesis of azidoacetamido‐functionalized Pse derivatives as part of a search for Pse‐derived metabolic labeling reagents. The synthesis was initiated with d‐glucose (Glc), which served as a cost‐effective chiral pool starting material. Key synthetic steps involve the conversion of C1 of Glc into the terminal methyl group of Pse, and inverting deoxyaminations at C3 and C5 of Glc followed by backbone elongation with a three‐carbon unit using the Barbier reaction. Metabolic labeling experiments revealed that, of the four Pse derivatives, ester‐protected C5 azidoacetamido‐Pse successfully labeled cells of Pse‐expressing Gram‐positive and Gram‐negative strains. No labeling was observed in cells of non‐Pse‐expressing strains. The ester‐protected and C5 azidoacetamido‐functionalized Pse is thus a useful reagent for the identification of bacteria expressing this unique virulence‐associated nonulosonic acid. [ABSTRACT FROM AUTHOR]

Meat from wildlife species (bushmeat) represents a major source of dietary protein in low- and middle-income countries where humans and wildlife live in close proximity. Despite the occurrence of zoonotic pathogens in wildlife, their prevalence in bushmeat remains unknown. To assess the risk of exposure to major pathogens in bushmeat, a total of 3784 samples, both fresh and processed, were collected from three major regions in Tanzania during both rainy and dry seasons, and were screened by real-time PCR for the presence of DNA signatures of Bacillus anthracis (B. anthracis), Brucella spp. (Brucella) and Coxiella burnetii (Coxiella). The analysis identified DNA signatures of B. anthracis (0.48%), Brucella (0.9%), and Coxiella (0.66%) in a total of 77 samples. Highest prevalence rates of B. anthracis, Brucella, and Coxiella were observed in wildebeest (56%), dik-dik (50%), and impala (24%), respectively. Fresh samples, those collected during the rainy season, and samples from Selous or Serengeti had a greater relative risk of being positive. Microbiome characterization identified Firmicutes and Proteobacteria as the most abundant phyla. The results highlight and define potential risks of exposure to endemic wildlife diseases from bushmeat and the need for future investigations to address the public health and emerging infectious disease risks associated with bushmeat harvesting, trade, and consumption. [ABSTRACT FROM AUTHOR]

Background: Burkholderia pseudomallei is the bacterial causative agent of melioidosis, a difficult disease to diagnose clinically with high mortality if not appropriately treated. Definitive diagnosis requires isolation and identification of the organism. With the increased adoption of MALDI-TOF MS for the identification of bacteria, we established a method for rapid identification of B. pseudomallei using the Vitek MS, a system that does not currently have B. pseudomallei in its in-vitro diagnostic database. Results: A routine direct spotting method was employed to create spectra and SuperSpectra. An initial B. pseudomallei SuperSpectrum was created at Shoklo Malaria Research Unit (SMRU) from 17 reference isolates (46 spectra). When tested, this initial SMRU SuperSpectrum was able to identify 98.2 % (54/55) of Asian isolates, but just 46.7 % (35/75) of Australian isolates. Using spectra (430) from different reference and clinical isolates, two additional SMRU SuperSpectra were created. Using the combination of all SMRU SuperSpectra with seven existing SuperSpectra from Townsville, Australia 119 (100 %) Asian isolates and 31 (100 %) Australian isolates were correctly identified. In addition, no misidentifications were obtained when using these 11 SuperSpectra when tested with 34 isolates of other bacteria including the closely related species Burkholderia thailandensis and Burkholderia cepacia. Conclusions: This study has established a method for identification of B. pseudomallei using Vitek MS, and highlights the impact of geographical differences between strains for identification using this technique. [ABSTRACT FROM AUTHOR]

The identification of bacteria plays an essential role in multiple areas of research. Those areas include experimental biology, food and water industries, pathology, microbiology, and evolutionary studies. Although there exist methodologies for identification, a transition to a whole-genome sequence-based taxonomy is already undergoing. Next-Generation Sequencing helps the transition by producing DNA sequence data efficiently. However, the rate of DNA sequence data generation and the high dimensionality of such data need faster computer methodologies. Machine learning, an area of artificial intelligence, has the ability to analyze high dimensional data in a systematic, fast, and efficient way. Therefore, we propose a sequential deep learning model for bacteria identification. The proposed neural network exploits the vast amounts of information generated by Next-Generation Sequencing, in order to extract an identification model for whole-genome bacteria sequences. After validating the identification model, the bidirectional recurrent neural network outperformed other classification approaches. [ABSTRACT FROM AUTHOR]

• A retrospective single-centre study was undertaken including 147 samples from 92 patients. • The overall percentage agreement was 98% for detection of typical bacteria. • Significant thresholds in culture were compared with nucleic acid copy number. • Median turnaround time was significantly shorter for the FilmArray Pneumonia Panel Plus than for culture. This study aimed to evaluate the performance of FilmArray Pneumonia Panel Plus (FA-PP) for the detection of typical bacterial pathogens in respiratory samples from patients hospitalized in intensive care units (ICUs). FA-PP was implemented for clinical use in the microbiology laboratory in March 2020. A retrospective analysis on a consecutive cohort of adult patients hospitalized in ICUs between March 2020 and May 2020 was undertaken. The respiratory samples included sputum, blind bronchoalveolar lavage (BBAL) and protected specimen brush (PSB). Conventional culture and FA-PP were performed in parallel. In total, 147 samples from 92 patients were analysed; 88% had coronavirus disease 2019 (COVID-19). At least one pathogen was detected in 46% (68/147) of samples by FA-PP and 39% (57/147) of samples by culture. The overall percentage agreement between FA-PP and culture results was 98% (93–100%). Bacteria with semi-quantitative FA-PP results ≥105 copies/mL for PSB samples, ≥106 copies/mL for BBAL samples and ≥107 copies/mL for sputum samples reached clinically significant thresholds for growth in 90%, 100% and 91% of cultures, respectively. FA-PP detected resistance markers, including mecA/ C, bla CTX-M and bla VIM. The median turnaround time was significantly shorter for FA-PP than for culture. FA-PP may constitute a faster approach to the diagnosis of bacterial pneumonia in patients hospitalized in ICUs. [ABSTRACT FROM AUTHOR]

In recent years, Surface Enhanced Raman Spectroscopy (SERS) has been considered the best tool for the detection and identification of the least concentration of analytes and micro-organisms, such as bacteria. In this article, we have successfully obtained the SERS signal of Escherichia coli and Methylene Blue (MB) using Zinc Tin Oxide (ZTO) nanostructures as the SERS substrate. The ZTO SERS substrates were grown by a simple thermal evaporation method and annealed at various temperatures ranging from 600 to 800 °C before using them for bacteria identification. After the structural verification and morphological analysis using XRD and SEM, ZTO samples were used as SERS substrates for the detection of E. coli and MB by placing a drop of each solution on the ZTO. SERS data strongly identified the presence of MB and E. coli Raman peaks. Furthermore, it was found that intensity of signals (for both E. coli and MB) was found to be improved from SERS substrates that are pre-annealed at higher temperature. The intensity of Raman peaks for E. coli and MB was increased by 60 000 and 120 000 counts as the annealing temperature increased to 600 and 800 °C, respectively. An enhancement factor of 1.44 × 104 was observed for MB. Results obtained in this study indicate that zinc oxide based nanostructured SERS chips are potential candidates for rapid identification of many pathogens. [ABSTRACT FROM AUTHOR]

A urinary tract infection (UTI) is an infection in any part of urinary system (kidneys, ureters, bladder and urethra). Most infections involve the lower urinary tract, the bladder and the urethra. Women are at greater risk of developing a UTI than are men. In this study, (50) urine sample were collected from (50) patients with suspected urinary tract infection, during the period from December (2017) to March (2018). The results of this study revealed that (70%) of samples was positive for bacterial culture, while (30%) of sample have no growth. The bacterial culture shown that (18) (51.43%) of bacterial isolates was E. coli followed by Staphylococcus aureus (8) (22.86%) and Klebsiella spp (17.14%) (6), Proteus spp .(8.57%) (3). In-vitro, the susceptibility of bacteria towards some antibiotics included in this study revealed that the Ciprofloxacin, Gentamicin, and Chloramphenicol are the most effective antibiotics to different types of pathogenic bacteria. [ABSTRACT FROM AUTHOR]

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As an approach to the exploration of cold-active enzymes, in this study, we isolated a cold-active protease produced by psychrotrophic bacteria from glacial soils of Thajwas Glacier, Himalayas. The isolated strain BO1, identified as Bacillus pumilus, grew well within a temperature range of 4–30 °C. After its qualitative and quantitative screening, the cold-active protease (Apr-BO1) was purified. The Apr-BO1 had a molecular mass of 38 kDa and showed maximum (37.02 U/mg) specific activity at 20 °C, with casein as substrate. It was stable and active between the temperature range of 5–35 °C and pH 6.0–12.0, with an optimum temperature of 20 °C at pH 9.0. The Apr-BO1 had low Km value of 1.0 mg/ml and Vmax 10.0 µmol/ml/min. Moreover, it displayed better tolerance to organic solvents, surfactants, metal ions and reducing agents than most alkaline proteases. The results exhibited that it effectively removed the stains even in a cold wash and could be considered a decent detergent additive. Furthermore, through protein modelling, the structure of this protease was generated from template, subtilisin E of Bacillus subtilis (PDB ID: 3WHI), and different methods checked its quality. For the first time, this study reported the protein sequence for psychrotrophic Apr-BO1 and brought forth its novelty among other cold-active proteases. [ABSTRACT FROM AUTHOR]

The study aimed to isolate and identify lactic acid bacteria (LAB) from silages and their application to improve the fermentation quality of alfalfa. Forty-nine LAB strains were isolated from silages, and two strains were screened for growth and acid production rates. Then two strains were selected for Physiological and morphological tests and 16S rRNA sequencing. They were Gram-positive and Catalase-negative and were able to grow at pH 3.5 and at 45 °C, were unable to grow different NaCl concentrations as 3.0% and 6.5%. Strain BDy3-10 was identified as Lactobacillus rhamnosus, while TSy1-3 was identified as L. buchneri. The selected strains were evaluated on fermentation of alfalfa silage. The highest crude protein content occurred in the BDy3-10 treatment group. The contents of neutral detergent fiber and acid detergent fiber in the TSy1-3 treatment were significantly lower than other treatment (P < 0.05). Compared to the control treatment, inoculation treatments deceased pH during ensiling (P < 0.001) and provided the most increased lactic acid content after ensiling for 10 days (P < 0.001). The acetic acid contents of all the inoculation groups were significantly increased (P < 0.001) during ensiling, and were lower than that of control group (P < 0.001). So, the TSy1-3 treatment most effectively improved the fermentation quality of alfalfa silage in warm and humid climate area. [ABSTRACT FROM AUTHOR]

Rapid and reliable pathogen identification is compulsory to confirm ventilator-associated pneumonia (VAP) in order to initiate appropriate antibiotic treatment. In the present proof of concept, the effectiveness of rapid microorganism identification with a targeted bottom-up proteomics approach was investigated in endotracheal aspirate (ETA) samples of VAP patients. To do so, a prototype selected-reaction monitoring (SRM)-based assay was developed on a triple quadrupole mass spectrometer tracking proteotypic peptide surrogates of bacterial proteomes. Through the concurrent monitoring of 97 species-specific peptides, this preliminary assay was dimensioned to characterize the occurrence of six most frequent bacterial species responsible for over more than 65% of VAP. Assay performance was subsequently evaluated by analyzing early and regular 37 ETA samples collected from 15 patients. Twenty-five samples were above the significant threshold of 105 CFU/mL and five samples showed mixed infections (both pathogens ≥ 105 CFU/mL). The targeted proteomics assay showed 100% specificity for Acinetobacter baumannii, Escherichia coli, Haemophilus influenzae, Pseudomonas aeruginosa, Staphylococcus aureus, and Streptococcus pneumoniae. No false bacterial identification was reported and no interference was detected arising from the commensal flora. The overall species identification sensitivity was 19/25 (76%) and was higher at the patient level (84.6%). This successful proof of concept provides a rational to broaden the panel of bacteria for further clinical evaluation. [ABSTRACT FROM AUTHOR]

Microbial biofilms pose a great threat for patients requiring indwelling medical devices (IMDs), as it is difficult to remove them. It is, therefore, crucial to follow an appropriate method for the detection of biofilms. The present study focuses on the detection of biofilm formation among the isolates from IMDs. We also aimed to explore the antibiogram of biofilm producers. This prospective analysis included 104 prosthetic samples. After isolation and identification of bacteria following standard methodology, an antibiogram of the isolates was produced following the disc diffusion method. Detection of biofilms was performed by tissue culture plate (TCP), tube adherence (TA) and Congo red agar methods. Over a period of study, 104 IMDs were removed from 78 patients with implantable devices infections. Eighty bacterial strains were isolated and identified, with coagulase-negative staphylococci being the predominant bacteria with 57.5% (46/80). There was a positive correlation between biofilm production and antimicrobial resistance, with the-strongest biofilm producers resistant to more than one antibiotic. For the detection of biofilm production, TA method can be an economical and effective alternative to TCP method. A greater understanding of biofilm detection in pathogen bacteria will help in the development of newer and more effective treatments. The detection of biofilm formation and antibiotic susceptibility patterns helps in choosing the correct antibiotic therapy. [ABSTRACT FROM AUTHOR]

The Indonesian Pesticide Regulations state that Malathion and Profenofos have been restricted in their use for agriculture because of is bioaccumulative in ecological systems. Cleaning technology using microorganisms is an effective solution for cleaning pesticide residues. This study aims to identify the bacteria that degrade and the degradation process of Malathion and Profenophos into non-toxic compounds. The research method was experimental, identification of bacteria by 16S-rRNA gene analysis, degradation ability by GC MS. The results of phylogenetic tree analysis showed that the tested bacteria were closely related to Oceanobacillus iheyenis (RPL1) and Exiquobacterium profundum (RPL5) with a similarity level of 87% and 99%. The two bacteria are used as a consortium of test bacteria. The results of degradation based on the observation chromatogram T = 0 showed that the Malathion compound C10H19O6PS2 or butanedioic acid [(dimethoxyphosphinothioyl) thio]) was detected at peak 4, real-time = 19,675, area% = 7.37 and Profenofos compound C11H15BrClO3PSO-(4-Bromo-2-chlorophenyl) o-ethyl s-propyl thiophosphate, peak 8, real-time = 23,957, area% = 6.91. Likewise, the chromatogram results at T = 96 were still detected Malathion ((dimethoxyphosphinothioyl) thio) at peak 14, real-time = 19,675, area% = 2.25, and Profenofos (o-(4-Bromo-2-chlorophenyl)) o - ethyl. s - propyl thiophosphate) peak = 22 real-time = 23,951, area% = 2.2. However, the observation of T = 192 hours, Malathion and Profenofos compounds were not detected. The conclusion showed that the consortium bacteria were able to completely degrade Malathion and Profenophos within 192 hours. [ABSTRACT FROM AUTHOR]

Recent advancements in DNA-based approaches have led to the identification of uncommon and rare bacterial pathogens. In this study, by utilizing a DNA-based approach, a total of 1043 clinical specimens were processed for the identification of actinobacteria targeting the 16S rRNA and gyrB genes. Drug susceptibility testing was also conducted using micro-broth dilution and PCR. Two isolates of Nocardia flavorosea and Rhodococcus erythropolis were reported for the first time in Iran. Also, Nocardiopsis dassonvillei, Streptomyces olivaceus, and Streptomyces griseus were reported for the first time in Asia. Infections caused by Nocardia caishijiensis and Prauserella muralis have also been reported in this study. The first Asian case of pulmonary infection caused by Nocardia ignorata and the first global case of brain abscess caused by Nocardia ninae and Nocardia neocaledoniensis have been reported in this study. Overall 30 isolates belonging to 6 genera (Nocardia, Streptomyces, Rodoccoccus, Nocardiopsis, Rothia, and Prauserella) were detected in 30 patients. All 30 isolates were susceptible to amikacin and linezolid. Three isolates including Nocardia otitidiscaviarum (n = 2) and Nocardia flavorosea (n = 1) were resistant to trimethoprim-sulfamethoxazole which were the first trimethoprim-sulfamethoxazole resistant clinical actinomycetes in Iran. Isolation of rare species of actinomycetes particularly Nocardia spp. requires urgent action before they spread clinically particularly among immunocompromised patients. [ABSTRACT FROM AUTHOR]

Rapid screening of infected people plays a crucial role in interrupting infection chains. However, the current methods for identification of bacteria are very tedious and labor intense. Fast on-site screening for pathogens based on volatile organic compounds (VOCs) by ion mobility spectrometry (IMS) could help to differentiate between healthy and potentially infected subjects. As a first step towards this, the feasibility of differentiating between seven different bacteria including resistant strains was assessed using IMS coupled to multicapillary columns (MCC-IMS). The headspace above bacterial cultures was directly drawn and analyzed by MCC-IMS after 90 min of incubation. A cluster analysis software and statistical methods were applied to select discriminative VOC clusters. As a result, 63 VOC clusters were identified, enabling the differentiation between all investigated bacterial strains using canonical discriminant analysis. These 63 clusters were reduced to 7 discriminative VOC clusters by constructing a hierarchical classification tree. Using this tree, all bacteria including resistant strains could be classified with an AUC of 1.0 by receiver-operating characteristic analysis. In conclusion, MCC-IMS is able to differentiate the tested bacterial species, even the non-resistant and their corresponding resistant strains, based on VOC patterns after 90 min of cultivation. Although this result is very promising, in vivo studies need to be performed to investigate if this technology is able to also classify clinical samples. With a short analysis time of 5 min, MCC-IMS is quite attractive for a rapid screening for possible infections in various locations from hospitals to airports. Key Points • Differentiation of bacteria by MCC-IMS is shown after 90-min cultivation. • Non-resistant and resistant strains can be distinguished. • Classification of bacteria is possible based on metabolic features. [ABSTRACT FROM AUTHOR]

Identification of bacteria by mass spectrometry offers the potential of a high-throughput non-targeted method to determine the presence of Salmonella. While MALDI-TOF mass spectrometry can identify Salmonella at the genus and species level, few studies have reported subtyping beyond the species level due to the diversity and complexity of Salmonella that includes more than 2600 serovars. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) approaches enable profiling of a greater number of proteins over a larger dynamic range and offer the potential to detect small differences between closely related isolates. We evaluate the discriminatory power of bottom-up LC-MS/MS with a collection of nineteen isolates that differ at the genus, species, subspecies, or strain level. Isolates were classified by matching the sequence of identified peptides to reference proteomes translated from genomes with known taxonomic ranks. The degree of proteomic similarity between the tested isolates and reference strains correlated with how closely they were related. All tested Salmonella isolates were easily distinguished from their close relatives, E. coli and Shigella, and readily grouped by species and subspecies. Additionally, each Salmonella isolate most closely matched to its correct serovar. This approach presents a simple and effective proteomic approach to identification of Salmonella genus, species, and subspecies. [ABSTRACT FROM AUTHOR]

Currently, traditional and newer molecular and mass spectrometry techniques of identifying bacteria from biological samples requires lengthy sample preparation, growth and labelling/staining assays. Thus, there is a pressing clinical need for an adjunct method that accurately identifies bacteria in real time. Here we report on the evaluation of confocal microscopy for the identification of clinically important and multi-drug resistant (MDR) bacteria in real time, using their intrinsic fluorescence features, i.e., emission spectra and fluorescence lifetime. The results demonstrate that difference in emission spectra and fluorescence lifetimes can be used as a fingerprint for identification of 12 bacterial species and MDR strains in real-time. Photostability or time-traces of bacteria demonstrated that these parameters could be used for tracking and recording without a need for labelling. Further, dilution experiments demonstrated that using intrinsic fluorescence S. aureus, Klebsiella pneumoniae and Escherichia coli bacteria can be detected and identified at clinically relevant concentrations as low as 2 × 102 CFU/mL. This non-invasive, non-labelling optical methodology may serve as the basis for development of a device that would quickly and accurately identify bacteria in biological samples. Thus, this intrinsic fluorescence technique would provide clinicians information, within minutes from sampling, to base accurate and specific treatments for patients. [ABSTRACT FROM AUTHOR]

The rapid increase of OXA-244-producing Escherichia coli , predominantly driven by genetically clustered isolates of sequence type (ST)38, has been observed in at least nine European countries, including Germany. However, the reasons for the spread of OXA-244-producing E. coli remain unclear. Here, we aim to evaluate the possibility of prolonged carriage. We identified a total of six different patients with repeated detection of OXA-244-producing E. coli isolates, which were subjected to both short and long-read whole-genome sequencing (WGS). Besides allelic differences using core genome multilocus sequence typing (cgMLST) analyses, we obtained numbers of single-nucleotide polymorphisms (SNPs) to calculate individual base-pair substitution (BPS) rates. To assess possible re-exposure and risk factors for prolonged carriage, case interviews were conducted. The time between detections ranged from eleven months to more than three years. Initial isolates originated in three+ out of six cases from clinical samples, whereas remaining samples were from screening, mostly in the inpatient setting. As expected, cgMLST analyses showed low numbers of allelic differences between isolates of each case ranging from 1 to 4, whereas numbers of SNPs were between 2 and 99 (mean = 36), thus clearly highlighting the discrepancy between these different bacterial typing approaches. For five out of six cases, observed BPS rates suggest that patients can be colonized with OXA-244-producing E. coli , including ST38 cluster isolates, for extensively long times. Thus, we may have previously missed the epidemiological link between cases because exposure to OXA-244-producing E. coli could have occurred in a time frame, which has not been evaluated in previous investigations. Our results may help to guide future epidemiological investigations as well as to support the interpretation of genetic diversity of OXA-244-producing E. coli , particularly among ST38 cluster isolates. [ABSTRACT FROM AUTHOR]

The detection limit of FT-IR-based bacterial typing was systematically studied by combining improved sample preparation procedures and optimized analytical models. [Display omitted] • Detection limit of FT-IR-based bacterial typing was investigated to be 108 CFU/mL. • A simplified and reliable sample preparation method for FT-IR bacterial typing was developed. • HCA and ANN strategies with optimized parameters were applied for FT-IR data analysis. Accurate and efficient bacterial typing methods are crucial to microbiology. Fourier transform infrared (FT-IR) spectroscopy enables highly distinguishable fingerprint identification of closely related bacterial strains by producing highly specific fingerprints of bacteria, which is increasingly being considered as an alternative to genotypic methods, such as pulsed field gel electrophoresis (PFGE) and whole genome sequencing (WGS), for bacterial typing. Compared with genotypic methods, FT-IR has significant advantages of convenient operation, fast speed, and low cost. Fundamental research into the detection limit based on optimized analytical conditions for FT-IR bacterial typing, which can avoid excessive bacterial culture time or sampling volume, is particularly important, especially in clinical practice. However, the corresponding parameters have not been fully investigated. In this study, we developed a simplified and reliable procedure for sample preparation, optimized the data analysis procedure, and evaluated the FT-IR detection limit based on the above conditions. In particular, we combined the film mold and calcium fluoride plate for sample preparation. We evaluated the detection limit (about 108 CFU/mL) after parameter optimization using hierarchical cluster analysis (HCA) and artificial neural network (ANN). The optimization and evaluation of these key fundamentals will better promote future application of FT-IR-based bacterial typing. [ABSTRACT FROM AUTHOR]

Culture plating is worldwide accepted as the gold standard for quantifying viable foodborne pathogens. However, it is time-consuming (1–2 days) and requires specialized laboratory and personnel. This study reported a deep learning enhanced digital microfluidic platform for multiplex detection of viable foodborne pathogens. The new method used a Time-Lapse images driven EfficientNet-Transformer Network (TLENTNet) to type and quantify the bacteria through spatiotemporal features of bacterial growth and digital enumeration of bacterial culture. First, the bacterial sample was prepared with LB medium and injected into a pre-vacuumed microfluidic chip with an array of 800 microwells to encapsulate at most one bacterium in each well. Then, a programmed sliding microscopic platform was used to scan all microwells every 15 min, capturing time-lapse images of bacterial growth within each microwell. Finally, the TLENTNet was used to facilitate bacterial typing and quantification. Under optimal conditions, this platform was able to detect four bacterial species (S. typhimurium, E. coli O157:H7 , S. aureus and B. cereus) with an average accuracy of 97.72% and a detection limit of 63 CFU/mL in 7 h. [ABSTRACT FROM AUTHOR]

Ultraviolet (UV) light and foodborne pathogenic bacteriais are an important risk to the environment's safety. They endanger human health, and also lead to outbreaks of infectious disease, posing great threats to global public health security, national economy, and social stability. The appearance of carbon dot (CD) nanozymes offers a new perspective to solve the problems of detection of UV light and pathogenic bacteria in environment. This paper reports the preparation of CDs with dual enzyme-like activities (superoxide dismutase activity and UV-induced oxidase activity). The product can catalyze the oxidation of the substrate 3, 3′, 5, 5′-tetramethylbenzidine (TMB) under UV light (365 nm) to achieve rapid color development. Based on the excellent fluorescence properties of CDs, the colorimetric-fluorescence dual-channel real-time detection of UVA dose was realized, the mechanism underlying the catalytic oxidation of TMB by UV-induced oxidase CDs was also investigated. Furthermore, a portable CDs-TMB-PA hydrogel was prepared which could realize the real-time monitoring of UV in outdoor environment with the assistance of smartphone. Based on the pH dependency of the CD nanozymes and specific glycolytic response of the pathogenic bacteria Escherichia coli (E. coli) O157:H7, the direct, simple, quick, and sensitive typing and detection have been realized. This research offers new perspectives for studying CD nanozymes and their applications in UV and bacterial detection, demonstrating the remarkable potential of CD nanozymes in detecting environmental hazards. [Display omitted] • The yellow-green CDs with UV-induced oxidase activity have been prepared. • The dual-channel sensing system for the detection of UVA has been established. • The real-time monitoring of outdoor UV-light based on portable hydrogel. • The detection of E. coli triggered by glycolytic metabolism has been established. • The mechanism of UV-induced CDs catalytic oxidization of TMB was presented. [ABSTRACT FROM AUTHOR]

Cronobacter sakazakii has been documented as a cause of life-threating infections, predominantly in neonates. We conducted a multicenter study to assess the occurrence of C. sakazakii across Europe and the extent of clonality for outbreak detection. National coordinators representing 24 countries in Europe were requested to submit all human C. sakazakii isolates collected during 2017 to a study center in Austria. Testing at the center included species identification by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, subtyping by whole-genome sequencing (WGS), and determination of antimicrobial resistance. Eleven countries sent 77 isolates, including 36 isolates from 2017 and 41 historical isolates. Fifty-nine isolates were confirmed as C. sakazakii by WGS, highlighting the challenge of correctly identifying Cronobacter spp. WGS-based typing revealed high strain diversity, indicating absence of multinational outbreaks in 2017, but identified 4 previously unpublished historical outbreaks. WGS is the recommended method for accurate identification, typing, and detection of this pathogen.

Abstract Background A. baumannii is a common nosocomial pathogen known for its high transmission potential. A high rate of carbapenem-susceptible Acinetobacter calcoaceticus-Acinetobacter baumannii (ACB)-complex in clinical specimens led to the implementation of a pathogen-based surveillance on a 32-bed surgical intensive care unit (SICU) in a German tertiary care centre. Methods Between April 2017 and March 2018, ACB-complex isolates with an epidemiological link to the SICU were further assessed. Identification to the species level was carried out using a multiplex PCR targeting the gyrB gene, followed by RAPD, PFGE (ApaI) and whole genome sequencing (WGS, core genome MLST, SeqSphere+ software, Ridom). Additional infection prevention and control (IPC) measures were introduced as follows: epidemiological investigations, hand hygiene training, additional terminal cleaning and disinfection incl. UV-light, screening for carbapenem-susceptible A. baumannii and environmental sampling. Hospital-acquired infections were classified according to the CDC definitions. Results Fourty four patients were colonized/infected with one or two (different) carbapenem-susceptible ACB-complex isolates. Fourty three out of 48 isolates were classified as hospital-acquired (detection on or after 3rd day of admission). Nearly all isolates were identified as A. baumannii, only four as A. pittii. Twelve patients developed A. baumannii infections. Genotyping revealed two pulsotype clusters, which were confirmed to be cgMLST clonal cluster type 1770 (n = 8 patients) and type 1769 (n = 12 patients) by WGS. All other isolates were distinct from each other. Nearly all transmission events of the two clonal clusters were confirmed by conventional epidemiology. Transmissions stopped after a period of several months. Environmental sampling revealed a relevant dissemination of A. baumannii, but only a few isolates corresponded to clinical strains. Introduction of the additional screening revealed a significantly earlier detection of carbapenem-susceptible A. baumannii during hospitalization. Conclusions A molecular and infection surveillance of ACB-complex based on identification to the species level, classic epidemiology and genotyping revealed simultaneously occurring independent transmission events and clusters of hospital-acquired A. baumannii. This underlines the importance of such an extensive surveillance methodology in IPC programmes also for carbapenem-susceptible A. baumannii.

Optochin susceptibility testing is a major assay used for presumptive identification of Streptococcus pneumoniae. Still, atypical optochin-resistant (Optr) pneumococci have been reported and this phenotype has been attributed to nucleotide substitutions in the genes coding for the F0F1ATPase. While substitutions in the atpC gene (c-subunit of ATPase) are more common and better characterized, data on mutations in the atpA (a-subunit) are still limited. We have characterized five Optr isolates presenting alterations in the atpA (Trp206Cys in four isolates and Trp206Ser in one isolate), constituting the first report of such mutations in Brazil. Most of the Optr isolates consisted of heterogeneous populations. Except for Opt MICs and the nucleotide changes in the atpA gene, Optr and Opts subpopulations originating from the same culture had identical characteristics. In addition, we compared phenotypic and genetic characteristics of these atpA mutants with those of atpC mutants previously identified in Brazil. No structural alterations were detected among predicted proteins, regardless of mutations in the coding gene, suggesting that, despite the occurrence of mutations, protein structures tend to be highly conserved, ensuring their functionalities. Phylogenetic analysis revealed that atypical Optr strains are true pneumococci and Opt resistance does not represent any apparent selective advantage for clinical isolates. [ABSTRACT FROM AUTHOR]

Lignin is biopolymer synthesized by plants and it consists up to 30% dry mass weight of any woody tissue. It is also known as second most abundant source of carbon after cellulose but still has a major problem, i.e. very tough to degrade. Thus, in present work authors were studied about the degradation of lignin by bacteria. The paper reports isolation, screening and identification of lignin degrading bacteria from collected samples. The bacterial strains were isolated from a cave that is located in the Chhattisgarh state of India in the mountain range of Salewara which have a temperature range between 26-28°C. A total of 32 bacterial isolates were studied and their RAPD analysis was performed and it was observed that Brevundimonas diminuta, Bacillus thuringiensis and Bacillus cereus were isolated in lignin- rich media which showed evidence of high lignin degradation. [ABSTRACT FROM AUTHOR]