Abyssivirga alkaniphila gen. nov., sp. nov., an alkane-degrading, anaerobic bacterium from a deep-sea hydrothermal vent system, and emended descriptions of Natranaerovirga pectinivora and Natranaerovirga hydrolytica.
A strictly anaerobic, mesophilic, syntrophic, alkane-degrading strain, L81T, was isolated from a biofilm sampled from a black smoker chimney at the Loki's Castle vent field. Cells were straight, rod-shaped, Gram-positive-staining and motile. Growth was observed at pH?6.2-9.5, 14-42?°C and 0.5-6?% (w/w) NaCl, with optima at pH?7.0-8.2, 37?°C and 3% (w/w) NaCl. Proteinaceous substrates, sugars, organic acids and hydrocarbons were utilized for growth. Thiosulfate was used as an external electron acceptor during growth on crude oil. Strain L81T was capable of syntrophic hydrocarbon degradation when co-cultured with a methanogenic archaeon, designated strain LG6, isolated from the same enrichment. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain L81T is affiliated with the family Lachnospiraceae, and is most closely related to the type strains of Natranaerovirga pectinivora (92?% sequence similarity) and Natranaerovirga hydrolytica (90%). The major cellular fatty acids of strain L81T were C15?:?0, anteiso-C15?:?0 and C16?:?0, and the profile was distinct from those of the species of the genus Natranaerovirga. The polar lipids were phosphatidylglycerol, diphosphatidylglycerol, three unidentified phospholipids, four unidentified glycolipids and two unidentified phosphoglycolipids. The G+C content of genomic DNA was determined to be 31.7?mol%. Based on our phenotypic, phylogenetic and chemotaxonomic results, strain L81T is considered to represent a novel species of a new genus of the family Lachnospiraceae, for which we propose the name Abyssivirga alkaniphila gen. nov., sp. nov. The type strain of Abyssivirga alkaniphila is L81T (=DSM 29592T=JCM 30920T). We also provide emended descriptions of Natranaerovirga pectinivora and Natranaerovirga hydrolytica.
The rates of sulfate reduction (SR) and the diversity of sulfate-reducing bacteria (SRB) were studied in the sediments of the Posol'skaya banka elevation in the southern part of Lake Baikal. SR rates varied from 1.2 to 1641 nmol/(dm3 day), with high rates (> 600 nmol/(dm3 day)) observed at both deep-water stations and in subsurface silts. Integral SR rates calculated for the uppermost 50 cm of the sediments were higher for gas-saturated and gas hydrate-bearing sediments than in those with low methane content. Enrichment SRB cultures were obtained in Widdel medium for freshwater SRB. Analysis of the 16S rRNA gene fragments from clone libraries obtained from the enrichments revealed the presence of SRB belonged to Desulfosporosinus genus, with D. lacus as the most closely related member (capable of sulfate, sulfite, and thiosulfate reduction), as well as members of the order Clostridiales.
The gut microbiota of honeybees (Apis) and bumblebees (Bombus) include the symbiotic bacterial genus Gilliamella. This genus shows a high degree of functional and genomic diversity and separates into distinct lineages. Gilliamella apicola wkB1T, which was isolated from Apis, was the first species to be described. Recently four new species, isolated from Bombus, were identified. In this paper, we compare several genomes/strains from previous studies spanning this diversity, which gives insight into the phylogenetic relationship among different Gilliamella species. We show that one lineage, isolated only from Apis, is different from other gilliamellas described, based on average nucleotide identity calculation (about 80?%) and phenotypic characterizations. We propose the new species name for this lineage: Gilliamella apis sp. nov. We present the characterization of the type strain NO3T (=DSM 105629T=LMG 30293T), a strain isolated from the Western honeybee Apis mellifera, which clusters within this lineage. Cells of strain NO3T grow best in a microaerophilic atmosphere with enhanced CO2 levels at 36?°C and pH 7.0-7.5. Cells also grow well in anaerobic conditions, but not in aerobic conditions. Cells are approximately 1?µm in length and rod-shaped, and the genomic G+C content is 34.7?mol%. Differential characteristics between strain NO3T and the different type strains of Gilliamella were revealed based on API kit tests and genomic content comparisons. The main respiratory quinone of strain NO3T was ubiquinone-8, and the predominant fatty acids were C18?:?1?7c/C18?:?1?6c, C16?:?0, consistent with the genus Gilliamella.
A Gram-reaction-negative, rod-shaped, yellow-pigmented, motile by gliding bacterial strain, designated RU-4-M-4(T), was isolated from intertidal sediment of Sakhalin Island in Russia. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain RU-4-M-4(T) was related to the genus Algibacter and had highest 16S rRNA gene sequence similarity with Algibacter pectinivorans KACC 14153(T) (97.2%). The major cellular fatty acids were iso-C15 : 0 3-OH, C15: 0 and iso-C15 : 1 G. The predominant menaquinone was MK-6. The polar lipid profile contained phosphatidylethanolamine, three unidentified aminolipids and two unidentified lipids. The genomic DNA G+C content of strain RU-4-M-4(T) was 36.4 mol%. Combined data from phenotypic, phylogenetic and DNA-DNA relatedness studies demonstrated that strain RU-4-M-4(T) is a representative of a novel species of the genus Algibacter , for which we propose the name Algibacter amylolyticus sp. nov. (type strain RU-4-M-4(T)?=LMG 28383(T)?=DSM 29199(T)).
A novel alkaliphilic spore-forming bacterium was isolated from the benthic sediments of the highly mineralized steppe Lake Khilganta (Transbaikal Region, Russia). Cells of the strain, designated ?-07-2T, were straight to slightly curved rods, Gram-stain-positive and motile. Strain ?-07-2T grew in the pH range from 7.0 to 10.7 (optimum pH 9.6-10.3). Growth was observed at 25-47?°C (optimum 30?°C) and at an NaCl concentration from 5 to 150?g l-1 with an optimum at 40?g l-1. Strain ?-07-2T was a chemo-organoheterotroph able to reduce amorphous ferric hydroxide, Fe(III) citrate and elemental sulfur in the presence of yeast extract as the electron donor. It used tryptone, peptone and trypticase with Fe(III) citrate as the electron acceptor. The predominant fatty acids in cell walls were C16:1?8, iso-C15:0, C14?:?0 3-OH and C16?:?0. The DNA G+C content was 32.6?mol%. 16S rRNA gene sequence analysis revealed that strain ?-07-2T was related most closely to members of the genus Alkaliphilus within the family Clostridiaceae. The closest relative was Alkaliphilus peptidifermentans Z-7036T (96.4?% similarity). On the basis of the genotypic, chemotaxonomic and phenotypic data, strain ?-07-2T represents a novel species in the genus Alkaliphilus, for which the name Alkaliphilus namsaraevii sp. nov. is proposed. The type strain is ?-07-2T (=VKM ?-2746?=DSM 26418?).
The standard diagnostic methods for pertussis have several shortcomings. With the increased knowledge of the Bordetella pertussis genome a specific and conserved DNA sequence, present in about 70-80 copies in each genome, was selected for amplification with the polymerase chain reaction (PCR) technique in order to evaluate its diagnostic potential in children with suspected pertussis. The 400 basepair DNA sequence chosen was present and amplified in all 112 B. pertussis strains and in no other bacterial species examined. The specificity of the amplified material was documented by restriction enzyme cleavage. In nasopharyngeal aspirates a B. pertussis specific PCR product was visualized in 19/25 culture positive and in 5/50 culture negative children. In conclusion the present PCR assay for B. pertussis can be clinically useful and permit a specific diagnosis within 1 day after sampling. Further studies are requested to document its sensitivity, specificity and predictive value for positive and negative results.
Rapid bacterial typing is a valuable and necessary tool in the prevention and detection of outbreaks. The purpose of this study was to adapt a multilocus variable number of tandem repeats analysis (MLVA) for analysis on a benchtop capillary electrophoresis instrument and compare the modified assay with multilocus sequence typing (MLST) for typing cefpodoxime-resistant Escherichia coli (E. coli). Further, we identified the causative resistance mechanisms and epidemiological type of infection for isolates producing extended-spectrum ß-lactamases (ESBLs). A collection of E. coli resistant to cefpodoxime was typed by MLST and a modified MLVA assay using a benchtop capillary electrophoresis instrument. Resistance mechanisms were identified by polymerase chain reaction (PCR) and sequencing. Patient history was examined to establish the epidemiological type of infection for ESBL-producing E. coli. MLVA yielded typing results homologous with MLST and it correctly identified E. coli sequence type (ST) 131 that was accounting for 45 % of all ESBL-producing isolates in the sample collection. The majority (76.7 %) of ESBL-producing isolates was healthcare-related and only 23.3 % of the ESBL-producing isolates were community-onset infections (COI), regardless of the ST. Patients with COI were significantly more often of female gender and younger age compared to healthcare-associated infections (HCAI) and hospital-onset infections (HOI). In conclusion, the modified MLVA is a useful tool for the rapid typing of E. coli and it identified ST131 as the predominating ESBL-producing lineage in Copenhagen. Healthcare-related infections were the predominant infection setting of ESBL-producing E. coli and the demographic characteristics differed between patients with COI and healthcare-related infections.
The analysis of meningococcal strains of different serogroups, isolated from the liquor of patients in Moscow, which was carried out with the method of multilocus sequencing-typing (MLST), was presented. At the periods of epidemic morbidity rises in Moscow the prevalence of group A meningococcal strains, belonging to subgroups III with sequence-types 5 (in the 1970s) and 7 (in 1996), was noted, and at a period between epidemics strains of genetic subgroups VI and X were isolated. Meningococcal strains, groups B and C, isolated in 1995 - 2002, had, as a rule, unique sequence-types, differing both one from another and from N. meningitidis sequence-types detected in other countries. Among group B meningococci the prevalence of strains belonging to clonal complex ST-18 was noted, while for group C meningococcci strains belonging to clonal complex ST-41/44 were most typical. Such genetic variability of circulating meningococci was regarded as characteristic of the period between epidemics, observed in Moscow since the end of the 1980s.
Anaplasma phagocytophilum is the causative agent of an emerging tick-borne disease, human granulocytic anaplasmosis. While the bacterium has been reported from questing ticks in neighboring Sweden, Norway and Russia, the few surveys regarding questing ticks in Finland have thus far been negative. In the current study, the prevalence of A. phagocytophilum in Ixodes ricinus populations was evaluated in several study localities around southwestern Finland during 2013-2014. Some of these populations were previously screened and found negative for A. phagocytophilum in 2000. A total of 3158 I. ricinus collected by blanket dragging were screened for Anaplasma spp. using qPCR. Anaplasma were detected in 9.2% of adult ticks (n = 87) and 3.1% of nymphs (n = 979). All larval samples were negative for infection. All Anaplasma-positive samples were identified as A. phagocytophilum by sequencing. This is, to the best of our knowledge, the first report of the pathogen from questing ticks in Finland. Furthermore, the pathogen was detected from several localities found negative during the previous screening 13 years earlier.
The bacterium Francisella tularensis is recognized for its virulence, infectivity, genetic homogeneity, and potential as a bioterrorism agent. Outbreaks of respiratory tularemia, caused by inhalation of this bacterium, are poorly understood. Such outbreaks are exceedingly rare, and F. tularensis is seldom recovered from clinical specimens.
A localized outbreak of tularemia in Sweden was investigated. Sixty-seven humans contracted laboratory-verified respiratory tularemia. F. tularensis subspecies holarctica was isolated from the blood or pleural fluid of 10 individuals from July to September 2010. Using whole-genome sequencing and analysis of single-nucleotide polymorphisms (SNPs), outbreak isolates were compared with 110 archived global isolates.
There were 757 SNPs among the genomes of the 10 outbreak isolates and the 25 most closely related archival isolates (all from Sweden/Finland). Whole genomes of outbreak isolates were >99.9% similar at the nucleotide level and clustered into 3 distinct genetic clades. Unexpectedly, high-sequence similarity grouped some outbreak and archival isolates that originated from patients from different geographic regions and up to 10 years apart. Outbreak and archival genomes frequently differed by only 1-3 of 1 585 229 examined nucleotides.
The outbreak was caused by diverse clones of F. tularensis that occurred concomitantly, were widespread, and apparently persisted in the environment. Multiple independent acquisitions of F. tularensis from the environment over a short time period suggest that natural outbreaks of respiratory tularemia are triggered by environmental cues. The findings additionally caution against interpreting genome sequence identity for this pathogen as proof of a direct epidemiological link.