Draft genome sequence of the human pathogen Halomonas stevensii S18214T

Adverse effects of thiamethoxam on the behavior, biochemical responses, hepatopancreas health, transcriptome and intestinal flora of juvenile Chinese mitten crab (Eriocheir sinensis)

Frequent detection of thiamethoxam in global surface waters has provoked great concern in environmental safety, as thiamethoxam exhibits high toxicity to aquatic arthropods. However, little systematic investigation has been conducted on the chronic toxicity of thiamethoxam to crustaceans. This study exposed Eriocheir sinensis to thiamethoxam (0, 0.5, 5 and 50 μg/L) in water for 28 days. No significant difference in mortality was observed among all groups. A high concentration of thiamethoxam (50 μg/L) impaired the righting ability of E. sinensis. Thiamethoxam significantly increased antioxidant enzyme activities (superoxide dismutase, total antioxidant capacity and glutathione peroxidase) and malondialdehyde levels. Simultaneously, detoxification enzyme activities (aminopyrine N-demethylase, erythromycin N-demethylase and glutathione-S-transferase) increased under chronic thiamethoxam stress. In addition, thiamethoxam caused immune and hepatopancreas damage. Moreover, thiamethoxam induced intestinal flora dysbiosis by altering the microbiome structure. The reduced complexity of the gut microbiota further illustrated that thiamethoxam could disrupt the stability of the microbiota ecological network. The transcriptomic results revealed that the number of downregulated DEGs increased in a dose-dependent manner, and most downregulated DEGs were enriched in energy metabolism-related pathways. These results indicate that thiamethoxam can adversely affect the crab behavior, biochemistry, intestinal microflora and transcriptomic responses.

Exploring the resistome, virulome and microbiome of drinking water in environmental and clinical settings

Aquatic ecosystems harbor a vast pool of antibiotic resistance genes (ARGs), which can suffer mutation, recombination and selection events. Here, we explored the diversity of ARGs, virulence factors and the bacterial community composition in water samples before (surface raw water, RW) and after (disinfected water, DW) drinking water conventional treatment, as well as in tap water (TW) and ultrafiltration membranes (UM, recovered from hemodialysis equipment) through metagenomics. A total of 852 different ARGs were identified, 21.8% of them only in RW, which might reflect the impact of human activities on the river at the sampling point. Although a similar resistance profile has been observed between the samples, significant differences in the frequency of clinically relevant antibiotic classes (penam and peptide) were identified. Resistance determinants to last resort antibiotics, including sequences related to mcr, optrA and poxtA and clinically relevant beta-lactamase genes (i.e. bla_KPC, bla_GES, bla_IMP, bla_VIM, bla_SPM and bla_NDM) were detected. 830 coding sequences (CDSs - related to 217 different ARGs) were embedded in contigs associated with mobile genetic elements, specially plasmids, of which 68% in RW, DW and TW, suggesting the importance of water environments in resistance dissemination. Shifts in bacterial pathogens genera were observed, such as a significant increase in Mycobacterium after treatment and distribution. In UM, the potentially pathogenic genus Halomonas predominated. Its draft genome was closely related to H. stevensii, hosting mainly multidrug efflux pumps. These results broaden our understanding of the global ARGs diversity and stress the importance of tracking the ever-expanding environmental resistome.

Halomonas montanilacus sp. nov., isolated from hypersaline Lake Pengyanco on the Tibetan Plateau

A Gram-stain-negative, catalase- and oxidase-positive, aerobic, rod-shaped, motile strain (PYC7WT) was isolated from Lake Pengyanco on the Tibetan Plateau. Comparisons based on 16S rRNA gene sequences showed that strain PYC7WT belongs to the genus Halomonas , with Halomonas malpeensis YU-PRIM-29T and Halomonas johnsoniae T68687T as its closest neighbours (96.8 and 96.6 % 16S rRNA gene sequence similarity, respectively), and only 93.1 % 16S rRNA gene sequence similarity to Halomonas elongata ATCC 33173T. The predominant respiratory quinone of strain PYC7WT is Q-9, with Q-8 as a minor component. The major fatty acids are C18 : 1  ω6c and / or C18 : 1  ω7c, C16 : 0, C16 : 1  ω6c and/or C16 : 1  ω7c, and C12 : 0 3OH. The polar lipids of strain PYC7WT include phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol and two unidentified phospholipids. Genome sequencing revealed a genome size of 4.79 Mbp and a G+C content of 62.9 mol%. DNA–DNA hybridization values of strain PYC7WT showed 45, 30 and 38 % relatedness with Halomonas johnsoniae DSM 21197T, Halomonas hamiltonii DSM 21196T and Halomonas stevensii DSM 21198T, respectively. Combining phenotypic, biochemical, genotypic and DNA–DNA hybridization data, we propose that strain PYC7WT represents a novel species within the genus Halomonas and to have the name Halomonas montanilacus sp. nov.; PYC7WT (=CICC 24506T= KCTC 62529T) is the type strain.

Peritoneal dialysis-related peritonitis due to Halomonas hamiltonii: A first case report

INTRODUCTION

Halomonas hamiltonii is a Gram-negative, halophilic, motile, and nonspore-forming rod bacterium. Although most Halomonas sp. are commonly found in saline environments, it has rarely been implicated as a cause of human infection. Herein, the authors present a case report of continuous ambulatory peritoneal dialysis (CAPD)-related peritonitis attributed to H hamiltonii.

CASE PRESENTATION

An 82-year-old male patient who had been receiving CAPD therapy presented to an emergency department with complaints of abdominal pain and cloudy dialysate that had persisted for 2 days. The peritoneal dialysate was compatible with CAPD peritonitis, with white blood cell count of peritoneal effluent of 810/mm and neutrophils predominated (60%). Two days after culture on blood agar medium, nonhemolytic pink mucoid colonies showed, with cells showing Gram-negative, nonspore-forming rods with a few longer and larger bacilli than usual were found. We also performed biochemical tests and found negative responses in K/K on the triple sugar iron test and H2S and equivocal (very weak) response in the motility test, but positive responses to catalase, oxidase, and urease tests. The partial sequence of the 16S rRNA gene of a bacterium detected by peritoneal fluid culture was utilized for a Basic Local Alignment Search Tool search, which revealed that the organism was H hamiltonii. Intraperitoneal antibiotics were administered for 21 days, and the patient was discharged without clinical problems.

CONCLUSION

We present here the first case report of CAPD-related peritonitis caused by H hamiltonii, which was identified using molecular biological techniques. Although guidelines do not exist for the treatment of infections caused by this organism, conventional treatment for Gram-negative organisms could be effective.

Halophiles, coming stars for industrial biotechnology

Industrial biotechnology aims to produce chemicals, materials and biofuels to ease the challenges of shortage on petroleum. However, due to the disadvantages of bioprocesses including energy consuming sterilization, high fresh water consumption, discontinuous fermentation to avoid microbial contamination, highly expensive stainless steel fermentation facilities and competing substrates for human consumption, industrial biotechnology is less competitive compared with chemical processes. Recently, halophiles have shown promises to overcome these shortcomings. Due to their unique halophilic properties, some halophiles are able to grow in high pH and high NaCl containing medium under higher temperature, allowing fermentation processes to run contamination free under unsterile conditions and continuous way. At the same time, genetic manipulation methods have been developed for halophiles. So far, halophiles have been used to produce bioplastics polyhydroxyalkanoates (PHA), ectoines, enzymes, and bio-surfactants. Increasing effects have been made to develop halophiles into a low cost platform for bioprocessing with advantages of low energy, less fresh water consumption, low fixed capital investment, and continuous production.

Microbiology and epidemiology of Halomonas species

Halomonas has been organized as a genus since 1980, and comprises halophilic and/or halotolerant Gram-negative aerobic bacteria, typically found in saline environments. The genus is enlarging: at present, 76 species are taxonomically recognized, with more to be added. Increasing industrial uses have been found, largely in bioremediation and the production of desirable compounds. Originally seen as environmental contaminants, pathogenicity was initially not recognized; however, disease in algae, animals and humans has now been described. As the biotechnological use of these species increases, and the ability to isolate and recognize them improves, one might expect further pathogenic encounters with humans to be described.

Genome sequences published outside of Standards in Genomic Sciences, October - November 2012

The purpose of this table is to provide the community with a citable record of publications of ongoing genome sequencing projects that have led to a publication in the scientific literature. While our goal is to make the list complete, there is no guarantee that we may have omitted one or more publications appearing in this time frame. Readers and authors who wish to have publications added to subsequent versions of this list are invited to provide the bibliographic data for such references to the SIGS editorial office.

Genome sequences published outside of Standards in Genomic Sciences, July - October 2012

The purpose of this table is to provide the community with a citable record of publications of ongoing genome sequencing projects that have led to a publication in the scientific literature. While our goal is to make the list complete, there is no guarantee that we may have omitted one or more publications appearing in this time frame. Readers and authors who wish to have publications added to subsequent versions of this list are invited to provide the bibliographic data for such references to the SIGS editorial office.