Species-level Identification Research Articles

Whole Genome Sequence-Based Identification of Clostridium estertheticum Complex Strains Supports the Need for Taxonomic Reclassification Within the Species Clostridium estertheticum.

Isolates within the Clostridium estertheticum complex (CEC) have routinely been identified through the 16S rRNA sequence, but the high interspecies sequence similarity reduces the resolution necessary for species level identification and often results in ambiguous taxonomic classification. The current study identified CEC isolates from meat juice (MJS) and bovine fecal samples (BFS) and determined the phylogeny of species within the CEC through whole genome sequence (WGS)-based analyses. About 1,054 MJS were screened for CEC using quantitative real-time PCR (qPCR). Strains were isolated from 33 MJS and 34 BFS qPCR-positive samples, respectively. Pan- and core-genome phylogenomics were used to determine the species identity of the isolates. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) were used to validate the species identity. The phylogeny of species within the CEC was determined through a combination of these methods. Twenty-eight clostridia strains were isolated from MJS and BFS samples out of which 13 belonged to CEC. At 95% ANI and 70% dDDH thresholds for speciation, six CEC isolates were identified as genomospecies2 (n=3), Clostridium tagluense (n=2) and genomospecies3 (n=1). Lower thresholds of 94% ANI and 58% dDDH were required for the classification of seven CEC isolates into species C. estertheticum and prevent an overlap between species C. estertheticum and Clostridium frigoriphilum. Combination of the two species and abolishment of current subspecies classification within the species C. estertheticum are proposed. These data demonstrate the suitability of phylogenomics to identify CEC isolates and determine the phylogeny within CEC.

Third-party Annotations: Linking PlutoF platform and the ELIXIR Contextual Data ClearingHouse for the reporting of source material annotation gaps and inaccuracies

Third-party annotations are a valuable resource to improve the quality of public DNA sequences. For example, sequences in International Nucleotide Sequence Databases Collaboration (INSDC) often lack important features like taxon interactions, species level identification, information associated with habitat, locality, country, coordinates, etc. Therefore, initiatives to mine additional information from publications and link to the public DNA sequences have become common practice (e.g. Tedersoo et al. 2011, Nilsson et al. 2014, Groom et al. 2021). However, third-party annotations have their own specific challenges. For example, annotations can be inaccurate and therefore must be open for permanent data management. Further, every DNA sequence (except sequences from type material) can carry different species names, which must be databased as equal scientific hypotheses. PlutoF platform provides such data management services for third-party annotations. PlutoF is an online data management platform and computing service provider for biology and related disciplines. Registered users can enter and manage a wide range of data, e.g., taxon occurrences, metabarcoding data, taxon classifications, traits, and lab data. It also features an annotation module where third-party annotations (on material source, geolocation and habitat, taxonomic identifications, interacting taxa, etc.) can be added to any collection specimen, living culture or DNA sequence record. The UNITE Community is using these services to annotate and improve the quality of INSDC rDNA Internal Transcribed Spacer (ITS) sequence datasets. The National Center for Biotechnology Information (NCBI) is linking its ITS sequences with their annotations in PlutoF. However, there is still missing an automated solution for linking annotations in PlutoF with any sequence and sample record stored in INSDC databases. One of the ambitions of the BiCIKL Project is to solve this through operating the ELIXIR Contextual Data ClearingHouse (CDCH). CDCH offers a light and simple RESTful Application Programming Interface (API) to enable extension, correction and improvement of publicly available annotations on sample and sequence records available in ELIXIR data resources. It facilitates feeding improved or corrected annotations from databases (such as secondary databases, e.g., PlutoF, which consume and curate data from repositories) back to primary repositories (databases of the three INSDC collaborative partners). In the Biodiversity Community Integrated Knowledge Library (BiCIKL) Project, the University of Tartu Natural History Museum is leading the task of linking the two components—the web interface provided by the PlutoF platform and CDCH APIs—to allow user-friendly and effortless reporting of errors and gaps in sequenced material source annotations. The API and web interface will be promoted to those communities (such as taxonomists, those abstracting from the literature, and those already using the community curated data) with the appropriate knowledge and tools who will be encouraged to report their enhanced annotations back to primary repositories.

External Morphology of Larvae of Belgica antarctica Jacobs, 1900 (Diptera, Chironomidae) Obtained from Two Locations in Maritime Antarctica.

Simple SummaryThe chironomid midge Belgica antarctica Jacobs is endemic to the western Antarctic Peninsula and South Shetland Islands. We provide the first detailed photomicrographic images of the fourth-instar larval head capsule and posterior parapods. We assessed variation in the morphology of larvae from two different collection locations off the coast of the western Antarctic Peninsula and compared it with that available in the literature. A number of differences were identified relating to the size of the larvae, the number of teeth on the mandibles, the number of antennal segments and the length of the antennal blade. Malformations of the mandible and mentum are reported for the first time in this species.The external morphology of the fourth-instar larva of the Antarctic endemic chironomid midge Belgica antarctica is described. Larvae were collected from Jougla Point (Wiencke Island) and an un-named island close to Enterprise Island, off the coast of the western Antarctic Peninsula. Light microscopy was used to examine and document photographically the structures of the mouthparts (mandible, mentum, premandible, labrum), antennae, pecten epipharyngis, clypeus, frontal apotome and posterior parapods. Measurements of the mouthparts are presented. The data obtained are compared with that available in the literature. A number of differences were identified relating to the size of the larvae, the number of teeth on the mandibles, the number of antennal segments and the length of the antennal blade. Malformations of the mandible and mentum are reported for the first time in this species. Features of larvae of taxonomic value that can be used to determine the species in larval stages are presented. These are of utility in using the larvae to reveal relationships with other species. Larvae are also important in ecological and genotoxicological studies, which require accurate species level identification.

Occurrence of Multiple, Extensive and Pan Drug-Resistant Pseudomonas aeruginosa and Carbapenemase Production from Presumptive Isolates Stored in a Biobank at Ethiopian Public Health Institute.

PurposePseudomonas aeruginosa is a common cause of nosocomial infections with associated morbidity and mortality because the organism is unresponsive to commonly available antimicrobials. This study was undertaken to determine the multiple drug-resistant (MDR), extensive drug-resistant (XDR) and pan drug-resistant (PDR) phenotype of P. aeruginosa and its carbapenemase production rate from presumptive isolates stored in the biobank at the Ethiopian Public Health Institute (EPHI).MethodsA cross-sectional study was conducted at the EPHI laboratory, Addis Ababa, Ethiopia from March to June 2021. Stored isolates of Pseudomonas spp. which had been characterized by manual identification methods were further processed for species-level identification (ID) and antimicrobial susceptibility testing (AST) using a Becton Dickinson (BD) Phoenix automated system. The isolates were analyzed for carbapenemase enzyme production using the modified Carbapenem Inactivation Method (mCIM). The data analysis was done using SPSS version 20 software.ResultsIn this study, 110 presumptive Pseudomonas isolates from a biobank were re-analyzed, 100 of them were found to be Pseudomonas and among these P. aeruginosa accounted for 98% and P. putida accounted for 2%. The majority of isolates were recovered from wound (46%) specimens followed by ear swabs (18%). The highest level of resistance was observed against ceftazidime (35%) and the lowest level of resistance was observed against amikacin (2%). Twenty-seven isolates were identified as candidates for carbapenemase enzyme production testing, of which only 3/27 (11%) isolates were detected as carbapenemase enzyme producers.ConclusionThis study shows an increasing rate of MDR and XDR isolates and the appearance of PDR in P. aeruginosa strains; this is a serious problem in Ethiopia. The lack of newer anti-pseudomonal antibiotics adds to the problem. In order to alleviate this, infection prevention activities should be promoted, and treatment of bacterial infections should be guided by antibiotic susceptibility test results.

Detection of spores of causal fungi of dieback-type trunk diseases in young, asymptomatic vineyards and mature, symptomatic vineyards

Grapevine trunk diseases threaten grape production worldwide. In California, preventative practices (delayed pruning, fungicide applications after pruning) that reduce infections of pruning wounds by pathogen spores produced with rain are timed during the dormant season, when high spore-trap counts of the causal fungi are reported from studies in mature, symptomatic vineyards. Similar studies in young, asymptomatic vineyards are lacking. Given infrequent usage by California growers of preventative practices in young vineyards, empirical data on spore detection may provide convincing evidence to start preventing trunk diseases before symptoms appear. Active and passive spore traps were examined after rain from December to March for four years (2013–2017) in six young, asymptomatic (<5-years-old in year 1) and six mature, symptomatic (13–18-years-old in year 1) vineyards, in Lodi and Napa, California, USA wine-grape regions. We compared detection of spores of causal fungi of Botryosphaeria-, Eutypa-, and Phomopsis diebacks, which are common and widespread trunk diseases in California. From 769 samples, we isolated 15 species in culture, with DNA sequencing of 2 bar-coding loci for species-level identification. Detections (defined as presence of a species at least once per timepoint per site) were sparse in years 1 and 2, and so statistical analyses of detections pooled across timepoints and sites were restricted to years 3 and 4. Most common among all 12 sites and both trap types were Diplodia seriata and Diaporthe chamaeropis. Our novel species-level detections of six Diaporthe species fill a gap in the knowledge of which species can spread during California's dormant season. Overall, detections in young sites in years 3 and 4 (10 and 29 detections, respectively) were significantly lower than those of mature sites (31 and 57 detections, respectively). The presence of spores in young sites, even with no symptomatic vines, suggests preventative practices are needed in young vineyards. Nonetheless, our findings of more detections in mature sites reinforces higher usage by growers of preventative practices in mature, symptomatic vineyards.

Characterizing parasitic nematode faunas in faeces and soil using DNA metabarcoding

BackgroundGastrointestinal parasitic nematodes can impact fecundity, development, behaviour, and survival in wild vertebrate populations. Conventional monitoring of gastrointestinal parasitic nematodes in wild populations involves morphological identification of eggs, larvae, and adults from faeces or intestinal samples. Adult worms are typically required for species-level identification, meaning intestinal material from dead animals is needed to characterize the nematode community with high taxonomic resolution. DNA metabarcoding of environmental samples is increasingly used for time- and cost-effective, high-throughput biodiversity monitoring of small-bodied organisms, including parasite communities. Here, we evaluate the potential of DNA metabarcoding of faeces and soil samples for non-invasive monitoring of gastrointestinal parasitic nematode communities in a wild ruminant population.MethodsFaeces and intestines were collected from a population of wild reindeer, and soil was collected both from areas showing signs of animal congregation, as well as areas with no signs of animal activity. Gastrointestinal parasitic nematode faunas were characterized using traditional morphological methods that involve flotation and sedimentation steps to concentrate nematode biomass, as well as using DNA metabarcoding. DNA metabarcoding was conducted on bulk samples, in addition to samples having undergone sedimentation and flotation treatments.ResultsDNA metabarcoding and morphological approaches were largely congruent, recovering similar nematode faunas from all samples. However, metabarcoding provided higher-resolution taxonomic data than morphological identification in both faeces and soil samples. Although concentration of nematode biomass by sedimentation or flotation prior to DNA metabarcoding reduced non-target amplification and increased the diversity of sequence variants recovered from each sample, the pretreatments did not improve species detection rates in soil and faeces samples.ConclusionsDNA metabarcoding of bulk faeces samples is a non-invasive, time- and cost-effective method for assessing parasitic nematode populations that provides data with comparable taxonomic resolution to morphological methods that depend on parasitological investigations of dead animals. The successful detection of parasitic gastrointestinal nematodes from soils demonstrates the utility of this approach for mapping distribution and occurrences of the free-living stages of gastrointestinal parasitic nematodes.Graphical abstract

Review of Spider Ecology During Carrion Decomposition, with a Field Study on Density and Taxa Richness in Pitfall Trap Captures of Geophilic Spiders (Aranea: Anyphaenidae, Corinnidae, Linyphiidae, Lycosidae, Salticidae)

AbstractDuring a recent pig carrion succession study in northwest Florida, United States, we noticed an abundance of spiders but found that literature on spider ecology at carrion is sparse and scattered. We compiled a literature review of 569 carrion succession studies, of which 37 studies specifically mentioned the presence of spiders, with less than a third providing species-level identifications and only half providing family-level identifications. Nineteen spider families have been reported at carrion in the literature. Spiders are recognized as generalist, opportunistic predators in carrion succession studies, but only 38% of the studies that mentioned spiders during carrion succession included any ecological information. Data on spiders in the present experiment were compared to background samples, finding that the difference in abundance was statistically significant for all spider species combined. Seven species of spiders from five families were identified from both background and carrion succession samples; statistical differences in abundance were found for three species: the linyphiid Florinda coccinea and the lycosids Tigrosa annexa and Pirata seminolus. The family Corinnidae is reported from carrion for the first time. This research reviews the existing literature on spider ecology during carrion succession, provides additional data on species identity and abundance, and demonstrates the potential significance of spiders in carrion ecology and forensic investigations.

Validation, Implementation, and Clinical Utility of Whole Genome Sequence-Based Bacterial Identification in the Clinical Microbiology Laboratory

The application of next-generation sequencing extends from microbial identification to epidemiologic insight and antimicrobial resistance prediction. Despite this potential, the roadblock for clinical laboratories lies in implementation and validation of such complex technology and data analysis. Herein, a validation study used whole-genome sequencing (WGS) for pan-bacterial identification (ID) in a clinical laboratory, and assessed its clinical relevance. A diverse set of 125 bacterial isolates, including a subset without genus (25) and/or species (10) ID, were analyzed by de novo assembly and reference genome mapping. The 16S rRNA, rpoB, and groEL genes were used for ID. Using WGS, 100% (89 of 89) and 89% (79 of 89) of isolates were identified at the genus and species-levels, respectively. WGS also provided improved results for 71% (25/35) isolates originally reported with genus-only or descriptive IDs. Chart review identified cases in which improved genus and/or species-level ID by WGS may have had a positive impact on patient care. Reasons included the use of an ineffective antibiotic owing to unclear ID, use of antibiotics when not clinically indicated, and help with an outbreak investigation. The implementation of next-generation sequencing in a clinical microbiology setting is a challenging but necessary task. This study provides a model for the validation and implementation of bacterial ID by WGS in such a setting.

Expansion of the Cassava Brown Streak Disease Epidemic in Eastern Democratic Republic of Congo.

Cassava plays a key role in ensuring food security and generating income for smallholder farmers throughout Central Africa, particularly in the Democratic Republic of Congo (DRC). This status is threatened, however, by cassava brown streak disease (CBSD), which has expanded its incidence and range in eastern DRC. The study described here comprises the first extensive assessment of temporal change in the occurrence of CBSD and its causal viruses in DRC, based on surveys conducted during 2016 and 2018. Cassava fields were inspected in Ituri, Nord-Kivu, Sud-Kivu, Tanganyika, and Haut-Katanga provinces within eastern DRC to record foliar incidence and severity of CBSD. Leaf samples were collected for virus detection and species-level identification. New occurrences of CBSD, confirmed by virus diagnostic tests, were recorded in two provinces (Haut-Katanga and Sud-Kivu) and nine previously unaffected territories, covering an area of >62,000 km2, and at up to 900 km from locations of previously published reports of CBSD in DRC. Overall, average CBSD incidence within fields was 13.2% in 2016 and 16.1% in 2018. In the new spread zone of Haut-Katanga, incidence increased from 1.7 to 15.9%. CBSD is now present in provinces covering 321,000 km2, which is approximately 14% of the total area of DRC. This represents a major expansion of the CBSD epidemic, which was only recorded from one province (Nord-Kivu) in 2012. Both Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus were detected in Ituri, Nord-Kivu, and Sud-Kivu, but only CBSV was detected in Haut-Katanga. Overall, these results confirm the increasing threat that CBSD poses to cassava production in DRC and describe an important expansion in the African pandemic of CBSD.

Quantifying Late Pennsylvanian Multivariate Morphological Change in the Fusulinid GenusTriticitesfrom the Central and Southwestern United States

ABSTRACTFusulinid Foraminifera are important for biostratigraphic correlation of strata in the Upper Paleozoic of the central and southwestern United States due to their high abundance and diversity in shallow marine carbonates. These correlations rely on consistent species-level identifications as well as geographically consistent morphological variation within species. However, many taxonomically important characters are described qualitatively, which can lead to conflicting identifications among taxonomists and cause biostratigraphic disagreements. Quantitative morphometric comparisons among species can increase the consistency of identifications among workers and capture temporal and geographic morphological gradients. Here, we used 14 linear measurements to describe the morphology of 18 biostratigraphically important species within the genus Triticites. Canonical variates analysis (CVA) showed that whereas specimens of a given species occupy similar areas of morphospace, species overlap considerably and, thus, these linear measurements poorly differentiate among species. However, species morphology covaried with geological age and multivariate analyses focused on age differences reveal an increase in the size of the initial chamber (proloculus) and a relative decrease in test expansion along the long axes over time. These morphological changes are consistent with an adaptation to shallow water conditions following the fall in relative sea-level across the Virgilian-Newwellian/Bursumian transition. Given the consistency of the morphological shift among North American basins, these morphological changes may be more useful for the recognition of the Virgilian-Newwellian/Bursumian transition than species-level biozones because they do not depend on consistent species identification.

Detection of emerging tick-borne disease agents in the Alpes-Maritimes region, southeastern France

Lyme borreliosis is a zoonotic tick-borne infection representing the most frequent vector-borne disease in the northern hemisphere. The Mediterranean rim is generally described as unsuitable for the European vector, Ixodes ricinus. We conducted an epidemiological study to assess whether I. ricinus was present and study its infection status for tick-borne bacteria. Ticks originating from southeastern France were obtained from flagging sampling and removed from animals and tick-bitten patients. Species level identification used morphological keys and MALDI-TOF MS. Quantitative PCR and sequencing assays were used to detect and identify tick-associated bacteria (Borrelia, Rickettsia, Anaplasmataceae, Bartonella, Coxiella burnetii) in each specimen. A total of 1232 ticks were collected in several localities. Among these, 863 were identified as I. ricinus (70%). Bacterial screening allowed identification of Lyme group Borrelia among I. ricinus ticks originating from various regional areas. Other emerging tick-borne pathogens like Borrelia miyamotoi and Rickettsia species were also detected. The Alpes-Maritimes region, part of the French Riviera, harbours I. ricinus ticks infected with Lyme group Borrelia and several other tick-borne bacterial agents. Clinicians and outdoor activity participants should be aware of the local Lyme borreliosis transmission risk.

Isolation and characterization of phosphate solubilizing bacteria from the rhizospheric soil of Ponthenpuzha forest, Pathanamthitta (District), Kerala

Phosphorous is considered as a major parameter for crop yield. Its availability to plant is independent of its abundance. For the plants to utilize phosphorous, it is to be converted to absorbable form. Here, the part rendered by phosphate solubilizing bacteria is significant for it plays a crucial role in the formation of plant usable phosphate from organic forms. In the present work, an effort had been made to isolate and identify phosphate solubilising bacterial isolate from the rhizhospheric soils of various plants in Ponthenpuzha forest. One of the isolate from Cymbopogon citrates responded positively to Pikovskaya’s medium by producing a halo zone during in vitro culture. Colony features and 16S rRNA sequence analysis identified the isolate as Burkholderia sps. We have reported the presence of genus Burkholderia in the rhizospheric zone of Cymbopogon citratus. Further studies are warranted for species level identification of the isolate.

Rapid detection and identification of bacteria directly from whole blood with light scattering spectroscopy based biosensor

Bacterial infections are one of the major causes of death worldwide. The identification of a bacterial species that is the source of an infection generally takes a long time, and often exceeds the treatment window for seriously ill patients. Many of these deaths are preventable if the bacterial species can be identified quickly. Here we present an optical spectroscopic method for rapid detection and identification of bacteria directly from whole blood using a light scattering spectroscopy technique. This technique was originally developed to detect pre-cancerous changes in epithelial tissues, characterize changes in tissue on the cellular scale, and characterize biological structures comparable to or smaller than a single wavelength. We demonstrate here that not only can an inexpensive light scattering spectroscopy-based biosensor rapidly detect and identify four bacteria species in the blood, responsible for the majority of death causing infections, but that species-level identification can potentially be made based on approximately one thousand bacterial cells per milliliter of blood. Observing entire colonies or performing susceptibility testing is therefore not required.

Morphometric and molecular identification ofArgulus japonicus(Thiele 1900) in vulnerable Himalayan snow trout,Schizothorax richardsonii(Gray 1832)

Argulus is a crustacean branchiuran parasite that causes severe problems in aquaculture throughout the world. Conventionally, Argulus spp. are identified through the morphological descriptions. In the recent years, polymerase chain reaction amplification with nuclear ribosomal RNA sequence coupled with morphological description is becoming standard for the species-level identification of Argulus spp. The present study investigated Argulus sp. in snow trout, Schizothorax richardsonii, using morphological and molecular tools. Morphologically, the parasite had branched dorsal ridges of the carapace, clubbed shaped anterior respiratory area, curved shaped posterior respiratory area, three relative sharp teeth and chitinous shovel peg on the fourth swimming appendages. Females Argulus sp. were larger in size than males in their length and width. Morphological characteristics and 18s rRNA study revealed that the parasite species was Argulus japonicus. A phylogenetic tree was constructed to examine relationships between these A. japonicus sequences and existing archived sequences. The maximum distribution of pathogenic argulid was observed in the dorsal fin, followed by the ventral fin and pectoral fin. The present study contributes to the first species-level morphological and molecular identification of A. japonicus in vulnerable Himalayan snow trout, S. richardsonii.

Isolation and Identification of Optochin-Resistant Viridans Group Streptococci from the Sputum Samples of Adult Patients in Jakarta, Indonesia.

Aim To investigate optochin-resistant viridans group streptococci (VGS) strains isolated from the sputum sample of adult patients with different clinical symptoms. Materials and Methods Optochin-resistant VGS isolates were identified by matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS). recA sequencing was used to confirm identified isolates at the genus level by MALDI-TOF MS. Finding. We identified 79% of tested isolates (148/187) at the species-level identification using the MALDI-TOF MS tool. We identified that the most common species isolated from sputum specimens were S. oralis (44.9%) followed by S. mitis (25.7%), S. infantis (9.1%), S. parasanguinis (7.5%), S. peroris (3.7%), S. anginosus (2.7%), and S. sanguinis (2.1%). Discussion. The S. oralis strains were majority of optochin-resistant VGS isolates obtained from sputum of adult patients in Jakarta, Indonesia. MALDI-TOF MS showed potential for the rapid identification tool to identify optochin-resistant VGS isolates. Although there were discrepancies in identifying isolates at the genus/species level, the performance could be improved by expanding its database.

Species Level Identification of Yeast and Yeast Like Fungus for Prompt Infection Control Measures in Prevention of Outbreaks: With Special Reference to Candida auris in Pre-covid Era

Species Level Identification of Yeast and Yeast Like Fungus for Prompt Infection Control Measures in Prevention of Outbreaks: With Special Reference to Candida auris in Pre-covid Era

Identification key to nymphal and adult mealybugs (Hemiptera: Pseudococcidae) associated with dragon fruits in Indonesia

Abstract. Rezeki MS, Harahap IS, Sartiami D, Irmansyah, Watson GW. 2021. Identification key to nymphal and adult mealybugs (Hemiptera: Pseudococcidae) associated with dragon fruits in Indonesia. Biodiversitas 22: 3113-3118. Dragon fruit (Hylocereus spp.), belonging to Cactaceae family, is one of the horticultural commodities being developed in Indonesia for export. Phytosanitary regulations require that fruits for export must be free from diseases and pests, including mealybugs (Hemiptera: Pseudococcidae). Mealybug species commonly found on dragon fruits in Indonesia are Ferrisia virgata (Cockerell), Phenacoccus solenopsis Tinsley, Planococcus minor (Maskell) and Pseudococcus jackbeardsleyi Gimpel &amp; Miller. Species-level identification of these insects in the nymphal phase is difficult due to the limited number of identification keys available, so it has been necessary to create an identification key to nymphs of mealybug species found on dragon fruit. A dichotomous identification key was constructed based on microscopic morphological characteristics of the cuticle. Thus, the four species can be differentiated based on general and unique characteristics of each species in the nymphal and adult stages. The diagnostic features that can be used to separate the four species in the nymphal phase are the presence or absence of: discoidal pores around the eyes; anal lobe bars; tubular ducts on the dorsum; and a denticle on each tarsal claw.

Isolation and characterization of marine bioluminescent bacteria for toxicity bioassays and biotechnological applications.

Toxic heavy metals pollution posed severe health hazards to the environment and biodiversity. Therefore, the development of rapid and non-invasive bioassays is in the race to monitor toxic chemicals using novel approaches. This study isolated and characterized an intense blue luminescence-producing marine bacteria, Vibrio campbellii STF1, for biosensing applications. Species-level identification of this strain was confirmed based on various phenotypic tests and multilocus sequence approach using 16s rRNA, toxR, and luxA gene sequence analysis. Fatty acid methyl ester analysis revealed the presence of three predominant fatty acids C15:0 anteiso (21.73%), C17:0 anteiso (11.27%), and C19:0 anteiso (9.08%) in STF1. Luciferase enzyme from V. campbellii STF1 was extracted, partially purified, and molecular masses (alpha subunit 40 kDa and beta subunit 37 kDa) were determined by SDS-PAGE gel for in vivo assays. MALDI-TOF-MS analysis of V. campbellii cells' protein extracts showed distinct mass spectral peaks at m/z of 2615, 3948, and 4232 da. V. campbellii STF1 is resistant to heavy metal lead, while other metals such as cadmium, copper, and mercury inhibited its growth and luminescence. Crude ethyl acetate extraction of V. campbellii demonstrated antibacterial activity against Shigella dysenteriae type 5 with a maximum inhibition zone of 27.0±1.0 mm.

Favorable Outcome in Patients with Pre-Transplant Gut Colonization with Intrinsically Vancomycin-Resistant Enterococci

IntroductionGut colonization with vancomycin-resistantenterococci (VRE) (specifically, Enterococcus faecium and E. fecalis) is common both before and after allogeneic hematopoietic cell transplantation (allo-HCT), and has been variably associated with VRE bloodstream infections. Clinical infections with intrinsically low-level VRE(E. gallinarum and E. casseliflavus), which have the chromosomally encoded vanC gene, are rare. Additionally, the clinical impact of pre-HCT gut colonization with these bacteria is unknown. In this study, we evaluated the outcome significance of pre-HCT colonization with E. gallinarum and E. casseliflavus, collectively named “intrinsics” herein.MethodsWe retrospectively reviewed the medical records of all adult and pediatric (>1 year old) allo-HCT recipients with available pre-HCT rectal swab or stool culture results at our institution (2011-2017). Second transplant recipients were excluded. SpectraTM VRE chromogenic agar medium (ThermoFisher Scientific) was used for species-level identification, and vancomycin E-test was used for MIC determination. Cases with ≥1 positive pre-HCT result for E. gallinarum or E. casseliflavus and no positive test for VRE or vancomycin-intermediate enterococci (VIE) were defined as intrinsics. Patients with no previous positive test for intrinsics or VRE/VIE, and with at least 2 negative tests for all these, were defined as controls. Due to the rare occurrence of colonization with intrinsics and the preponderance of pediatric patients with this condition, we used a matched-pairs design. Each intrinsic case was matched to a control using the following hierarchical criteria: (i) Diagnosis (malignant vs. non-malignant), (ii) disease risk (standard vs. high vs. non-malignant), (iii) donor type (matched sibling vs. matched unrelated donor vs. cord blood), (iv) conditioning intensity (myeloablative vs. reduced-intensity), and (v) age (± 10 years). The Prentice-Wilcoxon test was used to evaluate the matched pairs on the primary endpoints of overall survival (OS). For relapse and RFS, we excluded patients with non-malignant disorders.ResultsTable 1 shows the characteristics of the control group and intrinsics (n = 18 in each group). The groups were similar in all studied variables. The median follow up was 15 months. The intrinsic group showed a significantly higher 2-year OS of 86 [52-96]% vs. controls with OS of 35 [8-65]% at 2 years (P < 0.01, Figure 1). This remarkable difference in OS was due to a significantly lower NRM in the intrinsic group (0% vs. 36 [8-65]%, P= 0.01). Other transplant outcomes (GVHD and relapse) in each group were similar. Both deaths in the intrinsic group were due to relapse. In contrast, deaths in the control group were due to organ failure in 45%, relapse in 33%, infection in 11%, and GVHD in 11%.ConclusionsIn matched-pair analysis of intrinsically vancomycin-resistantenterococcivs. controls, we observed a remarkably lower NRM among patients colonized pre-HCT with E. gallinarum or E. casseliflavus .The mechanisms for this finding remain to be further explored. We hypothesize that in addition to vanC, these organisms have other genes that collectively contribute to establishment of a protective microbiome against various etiologies of early post-transplant NRM. This may occur as a result of beneficial microbial secondary metabolites that modulate the host immune system, or be consequent to colonization resistance against pathogenic organisms. [Display omitted] DisclosuresNo relevant conflicts of interest to declare.

DESMIDS BIODIVERSITY IN FRESHWATER PONDS OF DISTRICT NAGAUR, WESTERN RAJASTHAN INDIA: A PRELIMINARY INVESTIGATION

The present study was carried out to investigate the desmids biodiversity in traditional freshwater reservoirs of Nagaur district, Western Rajasthan, India. The samples were collected in January 2021 from the freshwater small ponds which harvests rainwater located in and around Nagaur city. These samples were analyzed by following the standard method prescribed by A.P.H.A for assessing the various physicochemical parameters such as pH, TDS, Fluoride, Nitrate, Chloride, total alkalinity, and total hardness to check drinking water quality and for ecological assessment. Furthermore desmids species-level identification and description have been done with the help of standard literatures and monographs. Results of physicochemical parameters indicate the deteriorating drinking water quality of all four sampling sites. In the present study total of 16 species belong to 5 genera i.e. Netrium, Closterium, Cosmerium, Staurastrum, and Eustrum of desmids have been recorded for the first time from the freshwater ponds located in or around the Nagaur city. The higher biodiversity of Closterium and Cosmarium species at Jhada talab confirm its significant relationship with high calcium and nutrient-rich water quality. While low biodiversity of desmids at remaining all village ponds indicates that high pH and oligotrophic quality decreases the desmids biodiversity. Results of this study might be helpful to assess the geographic distribution of desmids flora of Nagaur district and establish water quality of protected freshwater habitats as well as in updating the list of current species of desmids in this sub-region.