Genes Encoding 16S rRNA Research Articles

Prevalence and mechanisms of aminoglycoside resistance among drug-resistant Pseudomonas aeruginosa clinical isolates in Iran

BackgroundAminoglycosides have been a cornerstone of the treatment of nosocomial infections caused by Pseudomonas aeruginosa for over 80 years. However, escalating emergence of resistance poses a significant challenge. Therefore, this study aimed to investigate the prevailing patterns of aminoglycoside resistance among clinical isolates of P. aeruginosa in Iran; as well as the underlying resistance mechanisms observed in patients referred to Ardabil hospitals.MethodsA total of 200 isolates from five hospitals were evaluated. The resistance profiles of P. aeruginosa isolates to tobramycin, amikacin, and netilmicin were determined using the disk diffusion method. The capacity of aminoglycoside-resistant isolates to form biofilms was assessed through a phenotypic assay, and the results were confirmed using the gene amplification technique. The presence of genes associated with aminoglycoside resistance was detected using polymerase chain reaction (PCR). Quantitative reverse transcription PCR (qRT-PCR) was performed to measure the expression levels of genes encoding the MexXY-OprM efflux pump and PhoPQ two-component system (TCS).ResultsThe prevalence of aminoglycoside-resistant P. aeruginosa isolates was 48%, with 94.7% demonstrating multidrug resistance (MDR). All aminoglycoside-resistant P. aeruginosa strains exhibited biofilm-forming capabilities and harbored all the genes associated with biofilm production. Among the nine genes encoding 16S rRNA methylase and aminoglycoside-modifying enzymes, three genes were detected in these isolates: aac(6’)-Ib (85.4%), ant(2’’)-Ia (18.7%), and aph(3’)-VI (3.1%). Additionally, all aminoglycoside-resistant P. aeruginosa isolates carried mexY and phoP genes, although the expression levels of mexY and phoP were 75% and 87.5%, respectively.ConclusionGiven the considerably high prevalence of aminoglycoside-resistant P. aeruginosa strains, urgent measures are warranted to transition towards the use of novel aminoglycosides and to uphold vigilant surveillance of resistance patterns.

Бактерии-деструкторы с ростстимулирующими свойствами для использования в экологической

A topical research trend in ecological biotechnology is the search and study of microorganisms-destructor resistant to additional pollutants and growth-stimulating to remediant-plants. Four strains of hydrocarbon-oxidizing microorganisms isolated from soil samples were identified on the basis of cultural-morphological, physiological-biochemical properties and a comparative analysis of the gene encoding 16S rRNA. The bacteria Acinetobacter calcoaceticus UOM 22 and UOM 29, A. courvalinii UOM 35 showed a significant degree of oil biodegradation in a liquid medium at 24 and 8 °C (93.0–95.6% and 78.4–81.1%, respectively). In the same conditions these indicators were 44.8 and 33.7%, respectively for strain Rhodococcus erythropolis UOM 33. All microorganisms grew in the presence of aromatic hydrocarbons (including polycyclic hydrocarbons), were resistant to NaCl (5–7%) and lead ions (1.00–1.25 g/L). They were capable of nitrogen fixation and inorganic phosphate dissolution, indole-3-acetic acid synthesis (150–1416 ng/ml of culture liquid) and hydrolytic enzyme lipase production. We found that A. calcoaceticus UOM 22 and A. courvalinii UOM 35 strains increased the barley seeds germination by 8.6 and 10.5%, as well as A. calcoaceticus UOM 29 and A. courvalinii UOM 35 stimulated the barley root growth by 16.3 and 18.1% respectively. The results of the experiments indicate the possibility of using A. calcoaceticus UOM 22 and UOM 29, and A. courvalinii UOM 35 strains for cleaning oil-contaminated soils, including in combination with remediant-plants.

Multidrug-resistant Klebsiella pneumoniae clinical isolates producing NDM- and OXA-type carbapenemase in Nepal

ObjectivesThe emergence of multidrug-resistant Klebsiella pneumoniae has become a serious problem in medical settings worldwide. MethodsA total of 46 isolates of multidrug-resistant K. pneumoniae were obtained from 2 hospitals in Nepal from October 2018 to April 2019. ResultsMost of these isolates were highly resistant to carbapenems, aminoglycosides, and fluoroquinolones with the minimum inhibitory concentrations (MICs) of more than 64 µg/mL. These isolates harboured carbapenemase-encoding genes, including blaNDM-1, blaNDM-5, blaOXA-181 and blaOXA-232, and 16S rRNA methyltransferase-encoding genes, including armA, rmtB, rmtC, and rmtF. Multilocus sequence typing revealed that 44 of 46 isolates were high-risk clones such as ST11 (2%), ST14 (4%), ST15 (11%), ST37 (2%), ST101 (2%), ST147 (28%), ST231 (13%), ST340 (4%), and ST395 (28%). In particular, ST395 isolates, which spread across medical settings in Nepal, co-harboured blaNDM-5 and rmtB on IncFII plasmids and co-harboured blaOXA-181/-232 and rmtF on ColKP3 plasmids. Several isolates harboured blaOXA-181 or blaNDM-5 on their chromosomes and multi-copies of blaNDM-1 or genes encoding 16S rRNA methyltransferases on their plasmids. ConclusionsThe presented study demonstrates that the high-risk clones of multidrug-resistant K. pneumoniae spread in a clonal manner across hospitals in Nepal.

Composition of the sputum bacterial microbiome of patients with different pathomorphological forms of non-small-cell lung cancer.

Recent studies have shown that the bacterial microbiome of the respiratory tract influences the development of lung cancer. Changes in the composition of the microbiome are observed in patients with chronic inflammatory processes. Such microbiome changes may include the occurrence of bacteria that cause oxidative stress and that are capable of causing genome damage in the cells of the host organism directly and indirectly. To date, the composition of the respiratory microbiome in patients with various histological variants of lung cancer has not been studied. In the present study, we determined the taxonomic composition of the sputum microbiome of 52 patients with squamous cell carcinoma of the lung, 52 patients with lung adenocarcinoma and 52 healthy control donors, using next-generation sequencing (NGS) on the V3-V4 region of the bacterial gene encoding 16S rRNA. The sputum microbiomes of patients with different histological types of lung cancer and controls did not show significant differences in terms of the species richness index (Shannon); however, the patients differed from the controls in terms of evenness index (Pielou). The structures of bacterial communities (beta diversity) in the adenocarcinoma and squamous cell carcinoma groups were also similar; however, when analyzed according to the matrix constructed by the Bray-Curtis method, there were differences between patients with squamous cell carcinoma and healthy subjects, but not between those with adenocarcinoma and controls. Using the LEFse method it was possible to identify an increase in the content of Bacillota (Streptococcus and Bacillus) and Actinomycetota (Rothia) in the sputum of patients with squamous cell carcinoma when compared with samples from patients with adenocarcinoma. There were no differences in the content of bacteria between the samples of patients with adenocarcinoma and the control ones. The content of representatives of the genera Streptococcus, Bacillus, Peptostreptococcus (phylum Bacillota), Prevotella, Macellibacteroides (phylum Bacteroidota), Rothia (phylum Actinomycetota) and Actinobacillus (phylum Pseudomonadota) was increased in the microbiome of sputum samples from patients with squamous cell carcinoma, compared with the control. Thus, the sputum bacterial microbiome of patients with different histological types of non-small-cell lung cancer has significant differences. Further research should be devoted to the search for microbiome biomarkers of lung cancer at the level of bacterial species using whole-genome sequencing.

Composition of bacterial microbiome in sputum of patients with localized forms of pulmonary tuberculosis

Recent studies have shown that the respiratory bacterial microbiome has an impact on the development of pulmonary tuberculosis. Changes in the composition of the microbiome have been associated with the pathogenesis of Mycobacterium tuberculosis infection, response to therapy, and clinical outcomes of the disease. To date, the composition of the respiratory microbiome has not been studied in patients with localized forms of pulmonary tuberculosis. Methods. In the present study, the taxonomic composition of the sputum microbiome of 14 patients with localized forms of pulmonary tuberculosis (tuberculomas) and 14 healthy donors in the comparison group was analyzed by sequencing (NGS) of the V3 – V4 region of the bacterial gene encoding 16S rRNA. Results. The sputum microbiomes of the patients and the control group did not have significant differences in the species richness index (Shannon). However, the patients showed a decrease in the uniformity index, another parameter of alpha diversity. Bacterial community structures (beta diversity) did not differ significantly between patients with localized forms of tuberculosis and healthy subjects. In patients with limited forms of tuberculosis, contrary to the decrease in the content of representatives of the phyla Fusobacteria, TM7, Tenericutes, Spirochaetes, and SR1, and of the genera Dialister, Mycoplasma, and Filifactor in the sputum, no clear dominance of any bacterial taxon was observed. Conclusion. Certain alpha and beta diversity parameters that characterize the sputum microbiome of patients with localized forms of pulmonary tuberculosis need to be confirmed in independent large-scale studies to further understand the role of the sputum microbiota in the development of localized forms of pulmonary tuberculosis. Determination of Prevotella titers in the sputum of these patients holds promise for the diagnosis of localized forms of pulmonary tuberculosis and the search for their genomic markers.

Mutations in Genes Encoding 23S rRNA and FadD32 May be Associated with Linezolid Resistance in Mycobacteroides abscessus.

Linezolid is one of the antibiotics used to treat the Mycobacteroides abscessus infection. However, linezolid-resistance mechanisms of this organism are not well understood. The objective of this study was to identify possible linezolid-resistance determinants in M. abscessus through characterization of step-wise mutants selected from a linezolid-susceptible strain, M61 (minimum inhibitory concentration [MIC]: 0.25 mg/L). Whole-genome sequencing and subsequent PCR verification of the resistant second-step mutant, A2a(1) (MIC: >256 mg/L), revealed three mutations in its genome, two of which were found in the 23S rDNA (g2244t and g2788t) and another one was found in a gene encoding the fatty-acid-CoA ligase FadD32 (c880t→H294Y). The 23S rRNA is the molecular target of linezolid and mutations in this gene are likely to contribute to resistance. Furthermore, PCR analysis revealed that the c880t mutation in the fadD32 gene first appeared in the first-step mutant, A2 (MIC: 1 mg/L). Complementation of the wild-type M61 with the pMV261 plasmid carrying the mutant fadD32 gene caused the previously sensitive M61 to develop a reduced susceptibility to linezolid (MIC: 1 mg/L). The findings of this study uncovered hitherto undescribed mechanisms of linezolid resistance in M. abscessus that may be useful for the development of novel anti-infective agents against this multidrug-resistant pathogen.

Bacterial diversity associated with Millepora alcicornis and Phyllogorgia dilatata corals and prospection for genes encoding bioactive molecules

Coral reefs are marine environments with notable biodiversity, considered rich in organisms that produce active molecules. The microorganisms present in coral tissue play different roles that are not yet fully understood. The study of the microbiota can explain how microorganisms influence the health of corals and their participation in defense mechanisms. In this study, the cultivable bacterial communities of Millepora alcicornis and Phyllogorgia dilatata corals were analyzed following the steps of isolation, morphological characterization, and molecular identification by amplification of the gene encoding 16S rRNA. Of the 135 bacterial isolates, 121 of which were from M. alcicornis and 14 from P. dilatata, most belonged to the phyla Proteobacteria and Firmicutes, with the majority from the genera Vibrio and Bacillus. Coral metagenomic DNA was extracted and the gene encoding 16S rRNA was analyzed. The isolates were evaluated, in vitro, for antimicrobial activity against ATCC strains of Escherichia coli and Staphylococcus aureus, and 29 isolates from M. alcicornis showed activity against at least one of the bacteria evaluated. Using specific pairs of primers, 27 isolates showed amplification for at least one pair of primers designed for amplification of genes involved in the synthesis of non-ribosomal peptides (NRPs) and polyketides (PKs). However, only in some cases was a relationship detected between the isolates that showed antimicrobial activity in vitro and the isolates where amplification of genes involved in the synthesis of NRPs and PKs was observed.

Reduced abundance of butyric acid-producing bacteria in the ileal mucosa-associated microbiota of ulcerative colitis patients.

Compositional changes in the microbiota are associated with various inflammatory diseases, including ulcerative colitis (UC). Aim: This study aimed to investigate the mucosa-associated microbiota (MAM) in patients with UC and its difference related with disease activity and classification. Brush samples were collected from the terminal ileum and sigmoid colon during endoscopic procedures. The microbiota of samples was profiled using the Illumina MiSeq platform. The V3-V4 regions of the gene encoding 16S rRNA (460 bp) were amplified using PCR. Fifty UC patients and twenty healthy controls were enrolled. UC patients displayed significantly reduced α-diversity in both the ileum and sigmoid colon compared to controls. A difference in β-diversity in the unweighted analysis was observed between the two groups. The abundance of Lactobacillus and Veillonella was significantly higher and that of Butyricicoccus, Ruminococcus and Lachnospiraceae was significantly lower in the ileum of UC patients than in controls. The abundance of Odoribacter in the ileum was significantly lower in left-sided colitis and pancolitis patients than in proctitis patients and lower in patients with highly severe disease activity than with mild disease activity. The reduction in abundance of butyric acid-producing bacteria, especially Odoribacter, in ileal MAM may play an important role in the pathophysiology of UC.

Hydrocarbon biodegradation by Proteus and Serratia strains isolated from oil-polluted water in Bonny Community, Niger Delta, Nigeria

Two indigenous hydrocarbon utilizing bacteria strains, designated as TKZ and QGR were isolated in oil rich Niger Delta of Nigeria. Determination of the nucleotide sequence of the gene encoding 16S rRNA allowed TKZ and QGR to be identified as Proteus vulgaris and Serratia marcescens. Hydrocarbon degradation potential of the strains was confirmed on hydrocarbon mineral salts medium (1 %, v/v) at 37 °C. Assessment of oil degradation capability of the isolates was monitored using gas chromatographic analysis (GC). The ability of the strains to utilize benzene, diesel, kerosene, and naphthalene was also studied. The results show maximal increase in optical densities at 540 nm and total viable counts was proportional with decrease in pH of the culture media. Percentage degradation in the culture medium showed that the two isolates exhibited biodegradation efficiency above 90 % for kerosene. The two bacterial strains also possess a plasmid of about 9.1 kb size which is suspected to influence the bacterium’s hydrocarbon degradation potential.

Spread of Carbapenem-Resistant Klebsiella pneumoniae Clinical Isolates Producing NDM-Type Metallo-β-Lactamase in Myanmar.

ABSTRACTA total of 38 isolates of carbapenem-resistant Klebsiella pneumoniae harboring blaNDM were obtained during surveillance of 10 hospitals in Myanmar. Of these 38 isolates, 19 (50%) harbored genes encoding 16S rRNA methylases, such as armA or rmtB. The K. pneumoniae strains tested belonged to 17 sequence types (STs), including the high-risk clonal lineages ST101 and ST147. The ST101 and ST147 isolates carried IncFII plasmids harboring blaNDM-5 and IncFIB(pQil) plasmids harboring blaNDM-1, respectively. These results indicate that IncFII plasmids harboring blaNDM-5 and IncFIB(pQil) plasmids harboring blaNDM-1 have been spreading in K. pneumoniae ST101 and ST147 isolates, respectively, in Myanmar.IMPORTANCE The emergence of carbapenem-resistant K. pneumoniae has become a serious problem in medical settings worldwide. The present study demonstrated that carbapenem-resistant K. pneumoniae strains have been spreading in medical settings in Myanmar. In particular, plasmid genes encoding NDMs and 16S rRNA methylases have been spreading in K. pneumoniae high-risk clones.

Assessing multiple fecal sources to surf zone waters of two recreational beaches by bacterial community analysis

Fecal sources to recreational surf zone waters should be identified to protect public health. While watershed origins of human and other fecal sources are often discoverable by quantitative polymerase chain reaction (qPCR) of fecal markers using spatially stratified samples, similarly assessing wastewater treatment plant (WWTP) outfall and other offshore contributions to surf zones is challenged by individual marker fate and transport. Here, bacterial communities were assessed for relatedness between all hypothesized fecal sources and surf zone waters for two urban California recreational beaches, by sequencing genes encoding 16S rRNA and analyzing data using SourceTracker and FEAST. Ambient marine bacterial communities dominated the surf zone, while fecal (human, dog, or gull) or wastewater (sewage or treated WWTP effluent) bacterial communities were present at low proportions and those from recycled water were absent. Based on the relative abundances of bacterial genera specifically associated with human feces, the abundances of HF183 in bacterial community sequences, and FEAST and SourceTracker results when benchmarked to HF183, the major sources of HF183 to surf zone waters were human feces and treated WWTP effluent. While surf zone sequence proportions from human sources (feces, sewage and treated WWTP effluent) appeared uncorrelated to previously obtained qPCR HF183 results, the proportions of human fecal and potential human pathogen sequences in surf zone waters were elevated when there were more swimmers (i.e. during weekday afternoons, holidays and busy weekends, and race events), thus confirming previously-published qPCR-based conclusions that bather shedding contributed low levels of human fecal contamination. Here, bacterial community sequencing also showed evidence that treated WWTP effluent from an offshore outfall was entering the surf zone, thereby resolving a prior uncertainty. Thus, bacterial community sequencing not only confirms qPCR HF183-based human marker detections, but further allows for confirming fecal sources for which individual marker quantification results can be equivocal.

Isolation and identification of phosphate solubilizing bacteria from the rhizosphere of rice in organic and non-organic rice fields in Sukoharjo District, Indonesia

Abstract. Purwanti D, Setyaningsih R, Susilowati A. 2019. Isolation and identification of phosphate solubilizing bacteria from the rhizosphere of rice in organic and non-organic rice fields in Sukoharjo District, Indonesia. Bonorowo Wetlands 9: 108-115. One of the essential nutrients in the soil is phosphate. Phosphate fertilization is often inefficient because phosphate is bound and difficult for plants to absorb. The use of phosphate solubilizing bacteria (PSB) can be used as an alternative to the availability of P in the soil. This study aimed to obtain PSB isolates with high phosphate solubilization ability and identify these PSB isolates molecularly. Soil samples were taken from organic and non-organic rice (Oryza sativa L.) fields in Sukoharjo, Central Java, Indonesia, namely Grogol Village, Menuran Village, and Pondok Village. The research activity was carried out in several stages: isolation of PSB on Pikovskaya medium, characterization and testing of PSB in dissolving P, and Gram staining. PSB colonies with a phosphate solubilization index and showed different colony colors were taken, and then DNA was isolated. DNA isolation was carried out by extraction method using a DNA extraction kit. The gene encoding 16S rRNA amplified the obtained DNA samples. Sequencing was carried out using a genetic analyzer. Data analysis by comparing sequence data on the BLASTN program. Based on the isolation of rhizosphere samples from organic paddy fields, 14 isolates of PSB were obtained, and ten isolates of non-organic paddy were PSB. P13, P1, Q7, and Q8 isolates had the highest P solubilization ability with dissolution index (IP), namely 3.35, 2.13, 1.82, and 1.47. The 16S rRNA gene sequence analysis showed that isolates P1 and P13 had 99% similarity to Acinetobacter sp. ADP1 strain. The isolate Q7 had a 96% similarity with the genus Clavibacter strain NCPPB 382, ??while Q8 had a 99% similarity with Pseudomonas aeruginosa strain PAO1.

Persistence of a multidrug-resistant worldwide-disseminated methicillin-resistant Staphylococcus epidermidis clone harbouring the cfr linezolid resistance gene in a French hospital with evidence of interspecies transfer to several Staphylococcus aureus lineages.

Resistance to linezolid has become a worldwide concern since it is one of the last-resort antibiotics to treat multidrug-resistant staphylococcal and enterococcal infections. We investigated staphylococcal infections caused by 16 cfr-positive linezolid-resistant Staphylococcus epidermidis and Staphylococcus aureus isolates in a French university hospital from 2015 to 2018. Antimicrobial susceptibility of isolates was tested by broth microdilution and gradient strips. Genetic determinants of linezolid resistance (including cfr gene and 23S rRNA mutations) were assessed by PCR and WGS; the latter was also used to characterize the cfr-carrying plasmids in S. epidermidis and S. aureus, and to explore the clonal relationship of isolates. All linezolid-resistant staphylococcal isolates harboured the same cfr-carrying plasmid, sharing 99% identity with the previously described pSA737. The three S. aureus isolates belonged to different STs (ST8, ST72, ST2416); the 13 methicillin-resistant S. epidermidis (MRSE) belonged to ST2 and harboured both cfr and mutations in genes encoding 23S rRNA and ribosomal proteins. Phylogenetic analysis grouped the MRSE isolates into two clusters, one of which (n = 12 isolates) belonged to the recently reported multidrug-resistant worldwide-disseminated S. epidermidis lineages. The results presented herein highlight the persistence and efficient spread of a cfr-carrying plasmid in a hospital related both to the dissemination of a multidrug-resistant S. epidermidis clone and the in vivo interspecies transfer of cfr between S. epidermidis and S. aureus. The emergence of linezolid-resistant strains should be closely monitored, and the mechanisms involved systematically explored in order to limit the spread of plasmid-mediated resistance.

Allochromatium tepidum, sp. nov., a hot spring species of purple sulfur bacteria.

We describe a new species of purple sulfur bacteria (Chromatiaceae, anoxygenic phototrophic bacteria) isolated from a microbial mat in the sulfidic geothermal outflow of a hot spring in Rotorua, New Zealand. This phototroph, designated as strain NZ, grew optimally near 45°C but did not show an absorption maximum at 915nm for the light-harvesting-reaction center core complex (LH1-RC) characteristic of other thermophilic purple sulfur bacteria. Strain NZ had a similar carotenoid composition as Thermochromatium tepidum, but unlike Tch. tepidum, grew photoheterotrophically on acetate in the absence of sulfide and metabolized thiosulfate. The genome of strain NZ was significantly larger than that of Tch. tepidum but slightly smaller than that of Allochromatium vinosum. Strain NZ was phylogenetically more closely related to mesophilic purple sulfur bacteria of the genus Allochromatium than to Tch. tepidum. This conclusion was reached from phylogenetic analyses of strain NZ genes encoding 16S rRNA and the photosynthetic functional gene pufM, from phylogenetic analyses of entire genomes, and from a phylogenetic tree constructed from the concatenated sequence of 1090 orthologous proteins. Moreover, average nucleotide identities and digital DNA:DNA hybridizations of the strain NZ genome against those of related species of Chromatiaceae supported the phylogenetic analyses. From this collection of properties, we describe strain NZ here as the first thermophilic species of the genus Allochromatium, Allochromatium tepidum NZT, sp. nov.

Isolation, characterization, and effectiveness of bacteriophage Pɸ-Bw-Ab against XDR Acinetobacter baumannii isolated from nosocomial burn wound infection.

Objective(s):With emergence of drug resistance, novel approaches such as phage therapy for treatment of bacterial infections have received significant attention. The purpose of this study was to isolate and identify effective bacteriophages on extremely drug-resistant (XDR) bacteria isolated from burn wounds. Materials and Methods:Pathogenic bacteria were isolated from hospitalized patient wounds in specialized burn hospitals in Iran, and their identification was performed based on biochemical testing and sequencing of the gene encoding 16S rRNA. Bacteriophages were isolated from municipal sewage, Isfahan, Iran. The phage morphology was observed by TEM. After detection of the host range, adsorption rate, and one-step growth curve, the phage proteomics pattern and restriction enzyme digestion pattern were analyzed.Results:All isolates of bacteria were highly resistant to antibiotics. Among isolates, Acinetobacter baumannii strain IAU_FAL101 (GenBank accession number: MW845680), which was an XDR bacterium, showed significant sensitivity to phage Pɸ-Bw-Ab. TEM determined the phage belongs to Siphoviridae. They had double-stranded DNA. This phage showed the highest antibacterial effect at 15 °C and pH 7. Analysis of the restriction enzyme digestion pattern showed Pɸ-Bw-Ab phage was sensitive to most of the used enzymes and based on SDS-PAGE, protein profiles were revealed 43 to 90 kDa.Conclusion:Considering the potential ability of the isolated phage, it had an antibacterial impact on other used bacterial spp and also strong antibacterial effects on XDR A. baumannii. Also, it had long latency and low burst size. This phage can be a suitable candidate for phage therapy.

Diversity of aerobic spore-forming bacteria isolated from fresh bee pollen intended for human consumption in Argentina

Bee pollen is the result of the agglutination of pollen grains collected from flowers and mixed with nectar and salivary secretions by honey bees. Bee pollen is a natural product exposed to environmental conditions and also provides a unique microhabitat for yeasts and bacterial communities. We analyzed 30 fresh bee pollen samples obtained from the main producing areas of Argentina to identify aerobic-spore-forming bacteria. We obtained 73 isolates belonging to 16 different species through isolation on selective and differential media, morphological and biochemical tests, and PCR and RFLP analysis of genes encoding 16S rRNA. Our data revealed that Bacillus cereus sensu stricto was the most predominant species (50%), followed by Bacillus megaterium (40%) and Bacillus subtilis (40%), respectively. In a minor proportion, Paenibacillus polymyxa (20%), Paenibacillus larvae (17%), Bacillus pumilus (13%), Bacillus licheniformis (13%), Bacillus amyloliquefaciens (10%), Lysinibacillus sphaericus (7%), Bacillus coagulans (7%), Rummelliibacillus stabekisii (7%), Bacillus thuringiensis (7%), Bacillus clausii (3%), Paenibacillus alvei (3%), Bacillus simplex (3%), and Paenibacillus amylolyticus (3%) were also found. Our results showed that Argentinean bee pollen could transmit honey bee diseases due to the presence of viable spores of P. larvae and also spores of toxicogenic B. cereus s.s. and B. megaterium strains.

Molecular characterisation of carbapenem-resistant Pseudomonas aeruginosa clinical isolates in Nepal

The emergence of carbapenem-resistant Pseudomonas aeruginosa has become a serious worldwide medical problem. The aim of this study was to determine the genetic and epidemiological properties of carbapenem-resistant P. aeruginosa strains isolated from hospitals in Nepal. A total of 43 carbapenem-resistant P. aeruginosa isolates obtained from patients in two hospitals in Nepal between 2018 and 2020 were analysed. Their whole genomes were sequenced by next-generation sequencing. A phylogenetic tree was constructed from single nucleotide polymorphism (SNP) concatemers. Multilocus sequence typing (MLST) was performed and antimicrobial resistance genes were identified. Of the 43 isolates, 17 harboured genes encoding carbapenemases, including IMP-1, IMP-26, KPC-2, NDM-1, VIM-2 and VIM-5, and 12 harboured genes encoding 16S rRNA methylases, including RmtB4 and RmtF2. The carbapenem-resistant P. aeruginosa isolated in Nepal belonged to various sequence types (STs), including ST235 (5 isolates), ST244 (7 isolates), ST274 (1 isolate), ST357 (10 isolates), ST654 (3 isolates), ST664 (1 isolate), ST773 (1 isolate), ST823 (3 isolates), ST1047 (8 isolates), ST1203 (2 isolates) and ST3453 (2 isolates). To the best of our knowledge, this is the first molecular epidemiological analysis of carbapenem-resistant P. aeruginosa clinical isolates from Nepal. The findings strongly suggest that P. aeruginosa isolates producing carbapenemases and 16S rRNA methylases have spread throughout medical settings in Nepal.

Limited Bacterial Removal in Full-Scale Stormwater Biofilters as Evidenced by Community Sequencing Analysis.

In urban areas, untreated stormwater runoff can pollute downstream surface waters. To intercept and treat runoff, low-impact or "green infrastructure" approaches such as using biofilters are adopted. Yet, actual biofilter pollutant removal is poorly understood; removal is often studied in laboratory columns, with variable removal of viable and culturable microbial cell numbers including pathogens. Here, to assess bacterial pollutant removal in full-scale planted biofilters, stormwater was applied, unspiked or spiked with untreated sewage, in simulated storm events under transient flow conditions, during which biofilter influents versus effluents were compared. Based on microbial biomass, sequences of bacterial community genes encoding 16S rRNA, and gene copies of the human fecal marker HF183 and of the Enterococcus spp. marker Entero1A, removal of bacterial pollutants in biofilters was limited. Dominant bacterial taxa were similar for influent versus effluent aqueous samples within each inflow treatment of either spiked or unspiked stormwater. Bacterial pollutants in soil were gradually washed out, albeit incompletely, during simulated storm flushing events. In post-storm biofilter soil cores, retained influent bacteria were concentrated in the top layers (0-10 cm), indicating that the removal of bacterial pollutants was spatially limited to surface soils. To the extent that plant-associated processes are responsible for this spatial pattern, treatment performance might be enhanced by biofilter designs that maximize influent contact with the rhizosphere.

Molecular identification of crude oil-degrading bacteria isolated from polluted sites in Algeria

The petroleum industry in Algeria takes a predominant place in the econo-my. This industry amplifies the environmental contamination and affects microbial diversity of soils. Bioremediation is a cost-effective and efficient process for removing hydrocarbon pollutants. The aim of the study was to isolate cultivable telluric bacteria and to assess their potential as bioremedi-ation agents against the contamination of petroleum hydrocarbons. Crude oil polluted soil samples were taken from different oil refinery in Algeria. Elemental analysis was determined by inductively coupled plasma optical emission spectrometry (ECP-OES). The screening of bacteria degrading hy-drocarbons was studied with oil spreading technique on mineral salt medium (MSM agar) supplemented with crude oil as the only carbon source and en-ergy for direct visualization of clear zones on agar plates. Among the isolates, ten were selected for their degradation potential based on their large clear zone (from 0.5 to 3.2 Cm) for phenotypic and genotypic characterization. Molecular identification was performed by sequencing the gene encoding 16s rRNA. The comparison of sequences with GenBank database showed similarity with different strains Aeromonas hydrophila, Stenotrophomonas maltophilia, Enterobacter xiangfangensis, Pseudomonas aeruginosa, Serratia marcescens, and Raoultella sp. These results are significant for the applica-tion of these isolates at the environmental scale in bioremediation of pollut-ed soils.

Newly discovered Asgard archaea Hermodarchaeota potentially degrade alkanes and aromatics via alkyl/benzyl-succinate synthase and benzoyl-CoA pathway

Asgard archaea are widely distributed in anaerobic environments. Previous studies revealed the potential capability of Asgard archaea to utilize various organic substrates including proteins, carbohydrates, fatty acids, amino acids and hydrocarbons, suggesting that Asgard archaea play an important role in sediment carbon cycling. Here, we describe a previously unrecognized archaeal phylum, Hermodarchaeota, affiliated with the Asgard superphylum. The genomes of these archaea were recovered from metagenomes generated from mangrove sediments, and were found to encode alkyl/benzyl-succinate synthases and their activating enzymes that are similar to those identified in alkane-degrading sulfate-reducing bacteria. Hermodarchaeota also encode enzymes potentially involved in alkyl-coenzyme A and benzoyl-coenzyme A oxidation, the Wood–Ljungdahl pathway and nitrate reduction. These results indicate that members of this phylum have the potential to strictly anaerobically degrade alkanes and aromatic compounds, coupling the reduction of nitrate. By screening Sequence Read Archive, additional genes encoding 16S rRNA and alkyl/benzyl-succinate synthases analogous to those in Hermodarchaeota were identified in metagenomic datasets from a wide range of marine and freshwater sediments. These findings suggest that Asgard archaea capable of degrading alkanes and aromatics via formation of alkyl/benzyl-substituted succinates are ubiquitous in sediments.