Wastewater-borne viruses and bacteria, surveillance and biosensors at the interface of academia and field deployment.

Wastewater is a complex, but an ideal, matrix for disease monitoring and surveillance as it represents the entire load of enteric pathogens from a local catchment area. It captures both clinical and community disease burdens. Global interest in wastewater surveillance has been growing rapidly for infectious diseases monitoring and for providing an early warning of potential outbreaks. Although molecular detection methods show high sensitivity and specificity in pathogen monitoring from wastewater, they are strongly limited by challenges, including expensive laboratory settings and prolonged sample processing and analysis. Alternatively, biosensors exhibit a wide range of practical utility in real-time monitoring of biological and chemical markers. However, field deployment of biosensors is primarily challenged by prolonged sample processing and pathogen concentration steps due to complex wastewater matrices. This review summarizes the role of wastewater surveillance and provides an overview of infectious viral and bacterial pathogens with cutting-edge technologies for their detection. It emphasizes the practical utility of biosensors in pathogen monitoring and the major bottlenecks for wastewater surveillance of pathogens, and overcoming approaches to field deployment of biosensors for real-time pathogen detection. Furthermore, the promising potential of novel machine learning algorithms to resolve uncertainties in wastewater data is discussed.

Anti-cancer effects of plant-derived Micromonospora sp. M2 against A549 and MCF-7 cell lines.

The huge diversity of secondary bioactive metabolites, such as antibiotic and anticancer compounds produced by Micromonospora sp., makes it an attractive target for study. Here, we explored the anti-proliferative activities of Micromonospora sp. M2 extract (MBE) in relation to its pro-oxidative activities in A549 and MCF7 cell lines. Anti-proliferative effects were assessed by treating cells with MBE. We found that treatment with MBE decreased cell proliferation and increased intracellular reactive oxygen species, and that these observations were facilitated by the suppression of the PI3K-AKT pathway, alterations to the Bcl/Bad ratio, and increased caspase activity. These observations also demonstrated that MBE induced apoptotic cell death in cell lines. In addition, the phosphorylation of P38 and c-Jun N-terminal kinase (JNK) were upregulated following MBE treatment in both cell lines. Collectively, these results indicate that MBE acts as an anticancer agent via oxidative stress and JNK/mitogen-activated protein kinase pathway activation, enhancing apoptotic cell death in cell lines.

Incident infection risks depending on oral antidiabetic exposure in insulin-treated type 2 diabetes patients.

Dipeptidyl peptidase-4 inhibitors (DPP4is) and sodium glucose cotransporter-2 inhibitors (SGLT2is) have been speculated to have a potential to increase infection risks in type 2 diabetes mellitus (T2DM) patients. We performed a cohort study using the Korean health insurance data to investigate infection risks with each drug class relative to metformin in insulin-treated T2DM patients. After propensity score matching, we included 1,498 and 749 patients in DPP4i + insulin vs metformin + insulin and 300 and 549 patients in SGLT2i + insulin vs metformin + insulin, respectively. In stratified analyses per patient factor, none of the odds ratios (ORs) were associated with a statistical significance across respiratory, genital, and urinary tract infections (UTIs), except that of the male stratum for respiratory infections (OR 0.77, p = 0.04). With regard to SGLT2is, a higher risk of genital infections was analyzed with their use than with metformin therapy (OR 1.76, p = 0.03). In stratified analyses, the OR for genital infections remained significant in the baseline cardiovascular disease stratum (OR 2.29, p = 0.01). No increased UTI risk was detected with SGLT2is compared against metformin. In this study on insulin-receiving T2DM patients, DPP4is were not associated with increased infection risks, whereas SGLT2is led to a higher risk for genital infections, but not for UTIs, relative to metformin.

Management of multiple frostbite casualties at a burn center: San Antonio, Texas, 12-20 February 2021.

BACKGROUND: Frostbite is an insidious disease that normally affects people of cold climates. Winter Storm Uri, which occurred from February 12-20, 2021, created unique metrological conditions for Texas. It caused prolonged sub-freezing temperatures and led to rolling blackouts, affecting 2.8 million Texans including 300,000 people in San Antonio. We report 13 frostbite patients admitted to one burn center during this event. OBJECTIVE: We aimed to determine the at-risk population for frostbite, to categorize their injury severity, and to describe their treatment. A secondary aim was to describe the rehabilitation management of these patients. METHODS: This is a single-center retrospective study. Each patient's injuries were assessed by a topographical grading system. Comparisons were made among those who were admitted to the intensive care unit (ICU), admitted to the progressive care unit (PCU), and treated as outpatients. RESULTS: Thirteen patients were identified. Ten (76.9 %) considered themselves homeless, and 9 (69.2 %) were directly exposed to the elements. The median delay between time of injury and presentation to a medical facility was 3 days (IQR 1-6). Only 3 patients presented to a medical facility within 24 h. Six (46 %) sustained grade 2 injuries, 2 (15 %) sustained grade 3 injuries, and 5 (38%) sustained grade 4 injuries. Only one patient met criteria to receive tissue plasminogen activator (tPA), which was discontinued due to hematochezia. Patients admitted to the ICU, when compared to patients admitted to the ward, had a longer length of stay (median 73 days v. 12 days, p = 0.0215), and required more amputations at below-the-knee or higher levels (3 v. 0, p-value 0.0442). CONCLUSION: In a region unaccustomed and perhaps unprepared to deal with winter storms, the population is particularly vulnerable to frostbite. Lack of awareness of frostbite injuries likely led to the delay in the presentation of patients, which prevented the timely use of tPA. Increasing public awareness may increase readiness.

Solitalea lacus sp. nov., isolated from pond sediment.

A Gram-stain-negative, strictly aerobic, oxidase-positive, catalase-negative, motile by gliding, creamy white-pigmented bacterium, designated strain S2-8T, isolated from a sediment sample from a Wiyang pond in the Republic of Korea, was subjected to polyphasic taxonomic analysis. Growth was observed at 10-40 °C (optimum: 30 °C), pH 7-8 and 0-0.5% NaCl. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain S2-8T belonged to the family Sphingobacteriaceae in the phylum Bacteroidota and was closely related to Solitalea longa HR-AVT, Solitalea canadensis DSM 3403T and Solitalea koreensis R2A36-4T with 97.2, 96.7 and 93.7 % 16S rRNA gene sequence similarities, respectively. Average nucleotide identity and digital DNA-DNA hybridization values for these type strains were 72.0-75.2% and 21.2-21.9 %, respectively. The major respiratory quinone is menaquinone-7. The major fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (comprising C16 : 1 ω7c and/or C16 : 1 ω6c). The major polar lipids were phosphatidylethanolamine, two unidentified amino acids and four unidentified lipids. The G+C content of genomic DNA was 37.9 mol%. Based on polyphasic taxonomic analysis, it was observed that strain S2-8T is a novel species belonging to the genus Solitalea, for which the name Solitalea lacus sp. nov. is proposed. The type strain is S2-8T (= KACC 22266T= JCM 34533T).

Fibrivirga algicola gen. nov., sp. nov., an algicidal bacterium isolated from a freshwater river.

An aerobic, gram-stain-negative, pink-colored, non-motile and rod-shaped algicidal bacterium, designated as JA-25T was isolated from freshwater in Geumgang River, Republic of Korea. Strain JA-25T grew at 15-30 °C and pH 6-9, and did not require NaCl. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain JA-25T belongs to the family 'Spirosomaceae' and is most closely related to Fibrella aestuarina BUZ 2T (93.6%). Strain JA-25T showed < 90% sequence similarity to other members of the family 'Spirosomaceae'. The average nucleotide identity(ANI), in silico DNA-DNA hybridization and average amino acid identity(AAI) values based on the genomic sequences of JA-25T and F. aestuarina BUZ 2T were 74.4, 20.5, and 73.6%, respectively. Strain JA-25T showed an algicidal effect on the marine flagellate alga Heterocapsa triquetra, but no effect on fresh water cyanobacterium (Nostoc). In genome analysis, RIPP-like peptides were detected and predicted to resemble the indolmycin biosynthetic gene cluster, which possibly influence its algicidal effect. Furthermore, a bacteriorhodopsin gene with photoheterotrophic characteristics was detected. The genomic DNA G + C content was 52.5 mol%. The major cellular fatty acids were summed feature 3 (C16:1 ω6c/C16:1 ω7c), C16:1 ω5c, C16:0 (> 10%). The major respiratory quinone was menaquinone 7 and major polar lipids were phosphatidylethanolamine, two unidentified aminolipids, two phospholipids, and five unidentified lipids. Considering the phylogenetic inference, phenotypic, and chemotaxonomic data, strain JA-25T should be classified as a novel species in the novel genus Fibrivirga, with the proposed name Fibrivirga algicola sp. nov. The type strain is JA-25T (= KCCM 43334T = NBRC 114259T).

Limnovirga soli gen. nov., sp. nov., isolated from river sediment.

A cream-coloured, Gram-stain-negative, rod-shaped bacterium, designated strain KSC-6T, was isolated from soil sampled at the Gapcheon River watershed in Daejeon, Republic of Korea. The organism does not require NaCl for growth and grows at pH 6.0-8.0 (optimum, pH 7.0) and 10-37 °C (optimum, 25 °C). Phylogenetic trees based on the 16S rRNA gene sequences reveal that strain KSC-6T belongs to the family Chitinophagaceae within the order Chitinophagales and is most closely related to Panacibacter ginsenosidivorans Gsoil 1550T (95.9% similarity). The genomic DNA G+C content was 38.9 mol%. The major cellular fatty acids (>8 %) of strain KCS-6T were iso-C15:0, iso-C15 : 1 G and iso-C17 : 0 3-OH. The predominant respiratory quinone was menaquinone 7 and the predominant polar lipids were phosphatidylethanolamine, five unidentified aminolipids and two unidentified lipids. Based on genome analyses, low digital DNA-DNA hybridization, average nucleotide identity and average amino acid identity values with closely related genera, and differential chemotaxonomic and physiological properties, we suggest that strain KCS-6T represents a novel species in a new genus in the family Chitinophagaceae, for which the name Limnovirga soli gen. nov., sp. nov. (type strain KCS-6T=KCCM 43337T=NBRC 114336T) is proposed.

Draft Genome Sequence of Rubricoccus marinus SG-29T, a Marine Bacterium within the Family Rhodothermaceae, Which Contains Two Different Rhodopsin Genes.

Here, we report the draft genome sequence of Rubricoccus marinus SG-29T, a bacterium isolated from the western North Pacific Ocean. R. marinus SG-29T possesses two different types of rhodopsin genes and belongs to the family Rhodothermaceae, with which halophilic, thermophilic, and marine bacteria are associated.

Algibacter aquaticus sp. nov., a slightly alkaliphilic marine Flavobacterium isolated from coastal surface water.

A rod-shaped, pale yellow-pigmented, aerobic, Gram-staining-negative strain with gliding motility, designated as strain SK-16T, was isolated from the coastal surface water of a semi-enclosed coastal inlet in Misaki, Japan. Analysis of 16S rRNA gene sequences revealed that SK-16T represented a member of the family Flavobacteriaceae and was closely related to the genus Algibacter, with sequence similarities ranging from 95.9 to 94.3 % to the type strains of species of the genus Algibacter. The major cellular fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH, iso-C15 : 0 G and iso-C15 : 0 3-OH. Major polar lipids were phosphatidylethanolamine, an aminophospholipid and an unidentified phospholipid. The DNA G+C content of SK-16T was 32.3 mol% and MK-6 was the only predominant isoprenoid quinone. On the basis of the results of phenotypic, genotypic, chemotaxonomic and phylogenetic studies, it was suggested that SK-16T represents a novel species within the genus Algibacter, with the newly proposed name Algibacteraquaticus. The type strain is SK-16T (=NBRC 110220T=KCTC 32974T).

Complete Genome Sequence of the Intracellular Bacterial Symbiont TC1 in the Anaerobic Ciliate Trimyema compressum.

A free-living ciliate, Trimyema compressum, found in anoxic freshwater environments harbors methanogenic archaea and a bacterial symbiont named TC1 in its cytoplasm. Here, we report the complete genome sequence of the TC1 symbiont, consisting of a 1.59-Mb chromosome and a 35.8-kb plasmid, which was determined using the PacBio RSII sequencer.

Rubrivirga profundi sp. nov., isolated from deep-sea water, and emended description of the genus Rubrivirga.

A Gram-staining-negative, rod-shaped, facultatively anaerobic, non-motile and pale-red-pigmented bacterium, designated SAORIC-476T, was isolated from deep-sea water from the Pacific Ocean. 16S rRNA gene sequence analyses showed that strain SAORIC-476T was most closely related to Rubrivirga marinaSAORIC-28T (96.8 % similarity) and formed a robust phylogenetic clade with Rubrivirga marinaof the family Rhodothermaceae. Optimal growth of strain SAORIC-476T was observed at 25 °C, pH 7.5 and in the presence of 3.0 % (w/v) NaCl. The DNA G+C content of strain SAORIC-476T was 66.2 mol%, and the sole isoprenoid quinone was MK-7. The predominant cellular fatty acids were summed feature 9 (iso-C17 : 1ω9c and/or 10-methyl C16 : 0), iso-C17 : 0, C17 : 1ω8c and iso-C15 : 0. The major polar lipids constituted phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, three unknown phospholipids and four unknown polar lipids. On the basis of taxonomic data obtained in this study, it was concluded that strain SAORIC-476T represents a novel species of the genus Rubrivirga, for which the name Rubrivirga profundi sp. nov. is proposed. The type strain of Rubrivirga profundi is SAORIC-476T (=NBRC 110607T=KACC 18401T).

Complete mitochondrial genome of Cacospongia mycofijiensis (Dictyoceratida: Demospongiae): the first report for the sponge family Thorectidae.

We sequenced a complete mitochondrial genome of the marine sponge, Cacospongia mycofijiensis, which is the first report for the family Thorectidae in the class Demospongiae. The mitogenome was obtained from a de novo assembly of shotgun genome sequencing using Illumina Miseq technology, which reconstructed a circular genome with 97 × of sequence coverage. The assembled mitochondrial genome consisting of 16,227 bp includes 14 protein-coding genes, 2 rRNAs and 2 tRNAs. This complete mitogenome sequence will be useful especially for the phylogenic studies of Demospongiae.

Fabibacter misakiensis sp. nov., a marine bacterium isolated from coastal surface water.

A slightly curved-rod-shaped, pink-pigmented, Gram-stain-negative, aerobic bacterial strain with gliding motility, designated SK-8T, was isolated from coastal surface water of Misaki, Japan. Phylogenetic trees generated using 16S rRNA gene sequences revealed that strain SK-8T belonged to the genus Fabibacter and showed 96.0 % sequence similarity to the type strain of the most closely related species, Fabibacter pacificus DY53T. The novel isolate was phenotypically and physiologically different from previously described strains. The major cellular fatty acids were iso-C15 : 1 G, iso-C15 : 0 and iso-C17 : 0 3-OH. Major polar lipids were phosphatidylethanolamine, two aminophospholipids and an unidentified phospholipid. The DNA G+C content was 39.1 mol% and MK-7 was the only predominant isoprenoid quinone. On the basis of this taxonomic study employing a polyphasic approach, it was suggested that strain SK-8T represents a novel species of the genus Fabibacter, with the newly proposed name Fabibacter misakiensis sp. nov. The type strain is SK-8T ( = NBRC 110216T = KCTC 32969T).

Aureicoccus marinus gen. nov., sp. nov., a member of the family Flavobacteriaceae, isolated from seawater.

A coccoid and amorphous-shaped, non-gliding, proteorhodopsin-containing, yellow bacterium, designated strain SG-18(T), was isolated from seawater in the western North Pacific Ocean near Japan. The strain was Gram-stain-negative, obligately aerobic, heterotrophic and oxidase-positive. It hydrolysed aesculin but not DNA, urea, gelatin or agar. Growth occurred in the presence of 1-5 % NaCl, with optimum growth at 2 % NaCl. The strain grew at 15-37 °C with an optimum temperature of 25-30 °C. The DNA G+C content of the genomic DNA of strain SG-18(T) was 47.0 mol% (HPLC). The predominant isoprenoid quinone was MK-6, and major cellular fatty acids were iso-C15 : 1 G, iso-C15 : 0, iso-C15 : 0 3-OH. Phylogenetic trees generated by using 16S rRNA gene sequences revealed that strain SG-18(T) belonged to the family Flavobacteriaceae and showed 92.7 % sequence similarity to the most closely related species, Croceitalea eckloniae DOKDO 025(T). On the basis of phenotypic and phylogenetic features, strain SG-18(T) is classified as representing a novel species of a new genus within the family Flavobacteriaceae, for which the name Aureicoccus marinus gen. nov., sp. nov. is proposed. The type strain of the type species is SG-18(T) ( = NBRC 108814(T) = KCTC 23967(T)).

Rubrivirga marina gen. nov., sp. nov., a member of the family Rhodothermaceae isolated from deep seawater.

Two aerobic, Gram-stain-negative, pale-red-pigmented and rod-shaped bacterial strains, designated SAORIC-26 and SAORIC-28(T), were isolated from seawater (3000 m depth) from the Pacific Ocean. Phylogenetic analysis based on their 16S rRNA gene sequences revealed that the novel isolates could be affiliated with the family Rhodothermaceae of the class Cytophagia. Strains SAORIC-26 and SAORIC-28(T) shared 99.7% pairwise sequence similarity with each other and showed less than 92.6% similarity with other cultivated members of the class Cytophagia. The strains were found to be non-motile, oxidase-positive, catalase-negative and able to hydrolyse gelatin and aesculin. The DNA G+C contents were determined to be 64.8-65.8 mol% and MK-7 was the predominant menaquinone. Summed feature 9 (iso-C17:1ω9c and/or C16:0 10-methyl), summed feature 3 (C16:1ω6c and/or C16:1ω7c) and iso-C15:0 were found to be the major cellular fatty acids. On the basis of this taxonomic study using a polyphasic approach, it was concluded that strains SAORIC-26 and SAORIC-28(T) represent a novel species of a new genus in the family Rhodothermaceae, for which the name Rubrivirga marina gen. nov., sp. nov. is proposed. The type strain of the type species of is SAORIC-28(T) (=KCTC 23867(T)=NBRC 108816(T)). An additional strain of the species is SAORIC-26.

Nonlabens marinus [corrected] sp. nov., a novel member of the Flavobacteriaceae isolated from the Pacific Ocean.

Two aerobic, Gram-negative, orange pigmented and irregular rod-shaped bacteria, designated S1-05 and S1-08(T), were isolated from seawater from the Pacific Ocean. Phylogenetic analysis based on their 16S rRNA gene sequences revealed that the novel isolates could be affiliated with the genus Nonlabens of the family Flavobacteriaceae. The strains S1-05 and S1-08(T) shared 100 % pairwise sequences similarity with each other and showed less than 96.8 % similarity with the cultivated members of the genus Nonlabens. The novel isolates are phenotypically and physiologically different from strains described previously. The strains were found to be non-motile, oxidase positive, catalase positive and hydrolyzed gelatin and aesculin. The G+C contents of the DNA were determined to 41.4 and 41.7 mol% and MK-6 the predominant menaquinone. Anteiso-C15:0 and iso-C15:0 were found to be the major two cellular fatty acids. On the basis of polyphasic taxonomic studies, it was concluded that strains S1-05 and S1-08(T) represent a novel species within the genus Nonlabens, for which the name Nonlabens marina sp. nov. is proposed. The type strain of N. marina is S1-08(T) (=KCTC 23432(T) = NBRC 107738(T)).

Advenella faeciporci sp. nov., a nitrite-denitrifying bacterium isolated from nitrifying-denitrifying activated sludge collected from a laboratory-scale bioreactor treating piggery wastewater.

Strain M-07(T) was isolated from nitrifying-denitrifying activated sludge treating piggery wastewater. Phylogenetic analysis based on 16S rRNA gene sequences demonstrated that strain M-07(T) belonged to the genus Advenella. 16S rRNA gene sequence similarity between M-07(T) and Advenella incenata CCUG 45225(T), Advenella mimigardefordensis DPN7(T) and Advenella kashmirensis WT001(T) was 96.5, 97.3 and 96.9%, respectively. The DNA G+C content of strain M-07(T) was 49.5 mol%, which was approximately 5 mol% lower than the range for the genus Advenella (53.5-58.0 mol%). The predominant cellular fatty acids of strain M-07(T) were C(16:0), summed feature 3 (comprising C(16:1)ω7c and/or iso-C(15:0) 2-OH), C(17:0) cyclo and summed feature 2 (comprising one or more of C(14:0) 3-OH, iso-C(16:1) I, an unidentified fatty acid with an equivalent chain-length of 10.928 and C(12:0) alde). The isoprenoid quinone was Q-8. On the basis of phenotypic characteristics, phylogenetic analysis and DNA-DNA relatedness, strain M-07(T) should be classified as a novel species of the genus Advenella, for which the name Advenella faeciporci sp. nov. is proposed. The type strain is M-07(T) ( = JCM 17746(T)  = KCTC 23732(T)).

Aureitalea marina gen. nov., sp. nov., a member of the family Flavobacteriaceae, isolated from seawater.

An irregular rod-shaped, non-gliding, yellow-pigmented bacterium was isolated from seawater from the western North Pacific Ocean near Japan. The strain, designated S1-66T, was Gram-negative, obligately aerobic, heterotrophic and oxidase-positive. Growth occurred in the presence of 1-4 % NaCl, with optimum growth at 2 % NaCl. The strain grew at 15-30 °C, with optimum growth at 20-25 °C. The G+C content of genomic DNA was 48.1 mol% (HPLC). The predominant isoprenoid quinone was MK-6 and the major cellular fatty acids were iso-C15:0 (26.4 %), iso-C15:1 (20.3 %) and iso-C17:0 3-OH (14.2 %). Phylogenetic trees generated by using 16S rRNA gene sequences revealed that strain S1-66T belongs to the family Flavobacteriaceae and showed 94.2 % sequence similarity to the most closely related type strain, Ulvibacter antarcticus IMCC3101T. On the basis of phenotypic and phylogenetic features, S1-66T is classified in a novel genus and species within the family Flavobacteriaceae, for which the name Aureitalea marina gen. nov., sp. nov. is proposed. The type strain of Aureitalea marina is S1-66T (=NBRC 107741T=KCTC 23434T).

Tunicatimonas pelagia gen. nov., sp. nov., a novel representative of the family Flammeovirgaceae isolated from a sea anemone by the differential growth screening method.

A Gram-negative, strictly aerobic, reddish-pink pigmented, non-motile, rod-shaped strain designated N5DB8-4(T), was isolated from an orange-striped sea anemone Diadumene lineata by a differential growth screening method. Phylogenetic analyses based on the 16S rRNA gene sequence revealed that the novel isolate was affiliated with the family Flammeovirgaceae of the phylum Bacteroidetes and that it showed highest sequence similarity (89.1%) to Porifericola rhodea N5EA6-3A2B(T). The strain could be differentiated phenotypically from recognized members of the family Flammeovirgaceae. The G+C content of the DNA is 52.6 mol%, the major respiratory quinone is menaquinone 7 (MK-7) and iso-C15:0, C16:1ω5c and iso-C15:1 G (the double-bond position indicated by capital letter is unknown) were the major fatty acids. From the distinct phylogenetic position and combination of genotypic and phenotypic characteristics, the strain represents a novel taxon for which the name Tunicatimonas pelagia gen. nov., sp. nov. is proposed. The type strain of Tunicatimonas pelagia is N5DB8-4(T) (=KCTC 23473(T )= NBRC 107804(T)).