Research in microbiology最新文献

{"title":"Assessment of calcium hypochlorite for Bacillus anthracis spore surface's decontamination","authors":"Noémie Verguet ,&nbsp;Lou Mondange ,&nbsp;Flora Nolent ,&nbsp;Anne Depeille ,&nbsp;Annabelle Garnier ,&nbsp;Fabienne Neulat-Ripoll ,&nbsp;Olivier Gorgé ,&nbsp;Jean-Nicolas Tournier","doi":"10.1016/j.resmic.2023.104053","DOIUrl":"10.1016/j.resmic.2023.104053","url":null,"abstract":"<div><p><span>Contamination with microorganisms occurs in laboratories but is also of high concern in the context of bioterrorism. Decontamination is a cornerstone that promotes good laboratory practices and occupational health and safety. Among the most resistant structures formed by microorganisms are spores, produced notably by </span><em>Clostridium</em> and <em>Bacillus</em> species. Here, we compared six products containing four different molecules (hydrogen peroxide, peracetic acid, sodium and calcium hypochlorite) on <em>B</em><em>. anthracis</em> Sterne spores. We first selected the most efficient product based on its activity against spore suspensions using French and European standards. Four products showed sporicidal activity, of which only two did so in a time frame consistent with good laboratory practices. Then, we tested one of these two products under laboratory conditions on fully virulent <em>B. anthracis</em><span> spores, during common use and after contamination through a spill of a highly concentrated spore suspension. We, thus, robustly validated a decontaminant based on calcium hypochlorite not only on its ability to kill spores but also on its effectiveness under laboratory conditions. At the end, we were able to assure a complete disinfection in 1 min after spillover and in 2 min for common use.</span></p></div>","PeriodicalId":21098,"journal":{"name":"Research in microbiology","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2023-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10053604","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Core genome multilocus sequence typing scheme for Bacillus cereus group bacteria","authors":"Nicolas J. Tourasse ,&nbsp;Keith A. Jolley ,&nbsp;Anne-Brit Kolstø ,&nbsp;Ole Andreas Økstad","doi":"10.1016/j.resmic.2023.104050","DOIUrl":"10.1016/j.resmic.2023.104050","url":null,"abstract":"<div><p>Core genome multilocus sequence typing (cgMLST) employs a strategy where the set of orthologous genes common to all members of a group of organisms are used for phylogenetic analysis of the group members. The <em>Bacillus cereus</em> group consists of species with pathogenicity towards insect species as well as warm-blooded animals including humans. While <em>B. cereus</em> is an opportunistic pathogen linked to a range of human disease conditions, including emesis and diarrhoea, <em>Bacillus thuringiensis</em> is an entomopathogenic species with toxicity toward insect larvae, and therefore used as a biological pesticide worldwide. <em>Bacillus anthracis</em> is a classical obligate pathogen causing anthrax, an acute lethal condition in herbivores as well as humans, and which is endemic in many parts of the world. The group also includes a range of additional species, and <em>B. cereus</em> group bacteria have been subject to analysis with a wide variety of phylogenetic typing systems. Here we present, based on analyses of 173 complete genomes from <em>B. cereus</em> group species available in public databases, the identification of a set of 1568 core genes which were used to create a core genome multilocus typing scheme for the group which is implemented in the PubMLST system as an open online database freely available to the community. The new cgMLST system provides unprecedented resolution over existing phylogenetic analysis schemes covering the <em>B. cereus</em> group.</p></div>","PeriodicalId":21098,"journal":{"name":"Research in microbiology","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2023-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10418673","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Biofilm formation and antibiotic resistance profiles of water-borne pathogens","authors":"Kursat Koskeroglu,&nbsp;Mukaddes Barel,&nbsp;Harun Hizlisoy,&nbsp;Yeliz Yildirim","doi":"10.1016/j.resmic.2023.104056","DOIUrl":"10.1016/j.resmic.2023.104056","url":null,"abstract":"<div><p><span><span>Water sources (surface water, drinking water, rivers, and ponds) are significant reservoirs for transmitting antibiotic-resistant bacteria. In addition, these waters are an important public health problem because they are suitable environments for transferring antibiotic resistance genes between bacterial species. Our study aimed to assess the prevalence of Extended-spectrum beta-lactamase (ESBL) producing isolates in water samples, the susceptibility of the isolates to the specified antibiotics, the determination of biofilm ability, antibiotic resistance genes, and the molecular typing of the isolates. For this purpose, </span>Polymerase chain reaction (PCR) and Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) analyses were used. Out of 70 isolates, 15 (21%) were ESBL producing, and sent for the MALDI-TOF analysis, where </span><span><span><em>Escherichia coli, </em><em>Acinetobacter calcoaceticus</em><em>, </em></span><em>Enterobacter</em><span><span><em> bugandensis, Acinetobacter pittii, </em><em>Pseudomonas aeruginosa</em><em>, </em></span><em>Acinetobacter junii</em><span><em>, </em><em>Pseudomonas oleovorans</em><em>,</em></span></span></span> and <em>Enterobacter ludwigigii</em><span> were identified. Moreover, colistin resistance genes (</span><em>mcr 1/2/6, mcr 4, mcr 5, mcr 3/7</em>, and <em>mcr 8</em>), ESBL-encoding genes (<em>bla</em>_SHV<em>, bla</em>_TEM, and <em>bla</em>_CTX-M) and carbapenemase genes (<em>bla</em>_NDM, <em>bla</em>_OXA-48, and <em>bla</em>_KPC) using molecular analysis (PCR) were confirmed. The colistin resistance gene was detected at 80% (12/15) in the isolates obtained. The distribution of these isolates according to resistance genes was found as <em>mcr 1/2/6</em> 4 (20%), <em>mcr 3/7</em> 3 (13%), and <em>mcr 5</em> (40%). Additionally, the isolates harbored <em>bla</em>_SHV(6.6%) and <em>bla</em>_TEM (6.6%) genes. However, <em>bla</em>_NDM, <em>bla</em>_OXA-48, <em>bla</em>_KPC, and <em>bla</em>_CTX-M genes were not detected in any isolates. According to the Congo red agar method, seven (46.6%) isolates showed negative biofilm ability, and eight (53.3%) showed moderate biofilm ability. However, the microplate method detected weak biofilm in 53.3% of the isolates. In conclusion, this study provides evidence for the existence of multidrug-resistant bacteria that co-exist with <em>mcr</em> and ESBL genes in water sources. These bacteria can migrate to other environments and pose increasing threats to public health.</p></div>","PeriodicalId":21098,"journal":{"name":"Research in microbiology","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9787088","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phylogenomics and molecular marker-based analyses of the order Nevskiales: proposal for the creation of Steroidobacterales ord. nov. and Peristeroidobacter gen. nov","authors":"Jake Adolf V. Montecillo","doi":"10.1016/j.resmic.2023.104057","DOIUrl":"10.1016/j.resmic.2023.104057","url":null,"abstract":"<div><p>The order <em>Nevskiales</em>, class <span><em>Gammaproteobacteria</em></span>, encompasses four families <em>Algiphilaceae</em>, <em>Salinisphaeraceae</em>, <em>Nevskiaceae,</em> and <em>Steroidobacteraceae.</em><span><span> The taxonomy of this order is structured from the inferences derived from the 16S rRNA gene and genome-based </span>phylogenetic tree analyses. However, previous taxonomic studies of the order failed to incorporate most of the representatives from other established orders within the class </span><em>Gammaproteobacteria</em>. Other divergent members within the class <em>Gammaproteobacteria</em> were therefore overlooked. In this study, the taxonomy of the order <em>Nevskiales</em> was revisited using genome-based analyses with an expanded scope of outgroups representing the vast majority of the diversity within the class <em>Gammaproteobacteria</em><span>. Results from the phylogenetic analyses strongly supported the exclusion of the family </span><em>Steroidobacteraceae</em> from the order <em>Nevskiales</em> and further implied the assignment of the family into a novel order. In addition, the analyses also supported the reclassification of <em>Steroidobacter gossypii</em>, <em>Steroidobacter soli</em>, <em>Steroidobacter agariperforans</em>, and <em>Steroidobacter agaridevorans</em><span> into a novel genus. The identified conserved signature indels in 33 protein sequences further reinforced the new taxonomic assignments. Furthermore, the results of the average nucleotide identity and average amino acid identity analyses, together with the phenotypic and genomic characteristics among the members of the genus </span><em>Steroidobacter</em> also provided evidence supporting the reclassification of the four <em>Steroidobacter</em> species. Based on these results, the family <em>Steroidobacteraceae</em> is proposed to be assigned to a novel order <em>Steroidobacterales</em> ord. nov., and the species <em>S. gossypii</em>, <em>S. soli</em>, <em>S. agariperforans</em>, and <em>S. agaridevorans</em> are proposed to be moved to a novel genus <em>Peristeroidobacter</em> gen. nov. within the family <em>Steroidobacteraceae</em>.</p></div>","PeriodicalId":21098,"journal":{"name":"Research in microbiology","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9790852","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Physiological consequences of inactivation of lgmB and lpxL1, two genes involved in lipid A synthesis in Bordetella bronchiseptica","authors":"Jesús Pérez-Ortega ,&nbsp;Roel M. van Harten ,&nbsp;Henk P. Haagsman ,&nbsp;Jan Tommassen","doi":"10.1016/j.resmic.2023.104049","DOIUrl":"10.1016/j.resmic.2023.104049","url":null,"abstract":"<div><p>To develop a <em>Bordetella bronchiseptica</em> vaccine with reduced endotoxicity, we previously inactivated <em>lpxL1</em>, the gene encoding the enzyme that incorporates a secondary 2-hydroxy-laurate in lipid A. The mutant showed a myriad of phenotypes. Structural analysis showed the expected loss of the acyl chain but also of glucosamine (GlcN) substituents, which decorate the phosphates in lipid A. To determine which structural change causes the various phenotypes, we inactivated here <em>lgmB</em>, which encodes the GlcN transferase, and <em>lpxL1</em> in an isogenic background and compared the phenotypes. Like the <em>lpxL1</em> mutation, the <em>lgmB</em> mutation resulted in reduced potency to activate human TLR4 and to infect macrophages and in increased susceptibility to polymyxin B. These phenotypes are therefore related to the loss of GlcN decorations. The <em>lpxL1</em> mutation had a stronger effect on hTLR4 activation and additionally resulted in reduced murine TLR4 activation, surface hydrophobicity, and biofilm formation, and in a fortified outer membrane as evidenced by increased resistance to several antimicrobials. These phenotypes, therefore, appear to be related to the loss of the acyl chain. Moreover, we determined the virulence of the mutants in the <em>Galleria mellonella</em> infection model and observed reduced virulence of the <em>lpxL1</em> mutant but not of the <em>lgmB</em> mutant.</p></div>","PeriodicalId":21098,"journal":{"name":"Research in microbiology","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10271504","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Experimental evolution forcing Oenococcus oeni acid tolerance highlights critical role of the citrate locus","authors":"Frédérique Julliat ,&nbsp;Camille Eicher ,&nbsp;Nezha Tourti ,&nbsp;Philippe Glaser ,&nbsp;Nicolas Cabanel ,&nbsp;Joana Coulon ,&nbsp;Marion Favier ,&nbsp;Hervé Alexandre ,&nbsp;Cristina Reguant ,&nbsp;Stéphane Guyot ,&nbsp;Cosette Grandvalet","doi":"10.1016/j.resmic.2023.104048","DOIUrl":"10.1016/j.resmic.2023.104048","url":null,"abstract":"<div><p><em>Oenococcus oeni</em> is the main lactic acid bacterium associated with malolactic fermentation (MLF) of wines. MLF plays an important role in determining the final quality of wines. Nevertheless, due to the stressful conditions inherent to wine and especially acidity, MLF may be delayed. This study aimed to explore by adaptive evolution improvements in the acid tolerance of starters but also to gain a better understanding of the mechanisms involved in adaptation toward acidity. Four independent populations of the <em>O. oeni</em> ATCC BAA-1163 strain were propagated (approximately 560 generations) in a temporally varying environment, consisting in a gradual pH decrease from pH 5.3 to pH 2.9. Whole genome sequence comparison of these populations revealed that more than 45% of the substituted mutations occurred in only five loci for the evolved populations. One of these five fixed mutations affects <em>mae</em>, the first gene of the citrate operon. When grown in an acidic medium supplemented with citrate, a significantly higher bacterial biomass was produced with the evolved populations compared to the parental strain. Furthermore, the evolved populations slowed down their citrate consumption at low pH without impacting malolactic performance.</p></div>","PeriodicalId":21098,"journal":{"name":"Research in microbiology","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9789370","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Involvement of RNA chaperone hfq in the regulation of antibiotic resistance and virulence in Shigella sonnei","authors":"Ya Wang ,&nbsp;Yanli Teng ,&nbsp;Juan Geng ,&nbsp;Jinzhao Long ,&nbsp;Haiyan Yang ,&nbsp;Guangcai Duan ,&nbsp;Shuaiyin Chen","doi":"10.1016/j.resmic.2023.104047","DOIUrl":"10.1016/j.resmic.2023.104047","url":null,"abstract":"<div><p><span>The host factor for RNA phage<span> Qβ replicase (Hfq) is a crucial post-transcriptional regulator in many bacterial pathogens, facilitating the interaction between small non-coding RNAs (sRNAs) and their target mRNAs. Studies have suggested that Hfq plays a role in antibiotic resistance and virulence in bacteria, although its functions in </span></span><span><em>Shigella</em></span> are not fully understood. In this study, we investigated the functional roles of Hfq in <span><em>Shigella sonnei</em></span> (<em>S. sonnei</em>) by constructing an <em>hfq</em><span> deletion mutant. Our phenotypic assays showed that the </span><em>hfq</em><span> deletion mutant was more sensitivity to antibiotics and had impaired virulence. Transcriptome analyses supported the results concerning the phenotype of the </span><em>hfq</em> mutant and showed that differentially expressed genes were mainly enriched in the KEGG pathways two-component system, ABC transporters, ribosome, and <em>Escherichia coli</em> biofilm formation. Additionally, we predicted eleven novel Hfq-dependent sRNAs, which were potentially involved in the regulation of antibiotic resistance and/or virulence in <em>S. sonnei</em>. Our findings suggest that Hfq plays a post-transcriptional role in regulating antibiotic resistance and virulence in <em>S. sonnei</em>, and could provide a basis for future studies on Hfq-sRNA-mRNA regulatory networks in this important pathogen.</p></div>","PeriodicalId":21098,"journal":{"name":"Research in microbiology","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9785464","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Does environmental replication contribute to Bacillus anthracis spore persistence and infectivity in soil?","authors":"Hsin-Yeh Hsieh,&nbsp;George C. Stewart","doi":"10.1016/j.resmic.2023.104052","DOIUrl":"10.1016/j.resmic.2023.104052","url":null,"abstract":"<div><p><span><em>Bacillus anthracis</em></span><span> is the zoonotic<span> causal agent of anthrax. Its infectious form is the spore, which can persist in soil. Herbivores usually acquire the disease from grazing in spore-contaminated sites. There are two schools of thought regarding </span></span><em>B. anthracis</em> activities in soil. One contends the bacteria are obligate animal parasites and soil-based spores remain inert until taken up by another animal host. Others contend that spores can germinate in soil and the bacteria replicate and re-sporulate to maintain and/or increase spore numbers. This review discusses whether soil replication of <em>B. anthracis</em> is an important part of its life cycle.</p></div>","PeriodicalId":21098,"journal":{"name":"Research in microbiology","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10146996","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcriptome analysis reveals a common adaptive transcriptional response of Candida glabrata to diverse environmental stresses","authors":"Maruti Nandan Rai ,&nbsp;Rikky Rai ,&nbsp;Pooja Sethiya ,&nbsp;Chirag Parsania","doi":"10.1016/j.resmic.2023.104073","DOIUrl":"10.1016/j.resmic.2023.104073","url":null,"abstract":"<div><p><span><em>Candida glabrata</em></span>, an opportunistic fungal pathogen, causes superficial and life-threatening infections in humans. In the host microenvironment, <em>C. glabrata</em> encounters a variety of stresses, and its ability to cope with these stresses is crucial for its pathogenesis. To gain insights into how <em>C. glabrata</em><span> adapts to adverse environmental conditions, we examined its transcriptional landscape under heat, osmotic, cell wall, oxidative, and genotoxic stresses using RNA sequencing and reveal that </span><em>C. glabrata</em> displays a diverse transcriptional response involving ∼75% of its genome for adaptation to different environmental stresses. <em>C. glabrata</em><span> mounts a central common adaptation response wherein ∼25% of all genes (n = 1370) are regulated in a similar fashion at different environmental stresses. Elevated cellular translation and diminished mitochondrial activity-associated transcriptional signature characterize the common adaptation response. Transcriptional regulatory association networks of common adaptation response genes revealed a set of 29 transcription factors acting as potential activators and repressors of associated adaptive response genes. Overall, the current work delineates the adaptive responses of </span><em>C. glabrata</em> to diverse environmental stresses and reports the existence of a common adaptive transcriptional response upon prolonged exposure to environmental stresses.</p></div>","PeriodicalId":21098,"journal":{"name":"Research in microbiology","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9791082","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Skin microbiome of people living at the Dead Sea area – The lowest place on earth","authors":"Nurit Harel ,&nbsp;Leah Reshef ,&nbsp;Dvora Biran ,&nbsp;Eliora Z. Ron ,&nbsp;Uri Gophna","doi":"10.1016/j.resmic.2023.104059","DOIUrl":"10.1016/j.resmic.2023.104059","url":null,"abstract":"<div><p>The Dead Sea is a salt lake with surface water at about 430 m below sea level and considered the lowest place on Earth. The Dead Sea basin is characterized by relatively high temperatures, attenuated UV radiation and the air above it has a relatively high-salt aerosol content. When we compared the skin microbiome of individuals from the hot, salty and arid Dead Sea area with that of individuals from the humid Mediterranean regions we observed a significantly lower bacterial diversity in the Dead Sea group as well as distinct differences in the composition of bacterial species. Our results suggest that these factors have a profound effect on the skin microbiome. Further study is required to understand how the local environment influences the skin microbiome, as well as the functional implications of these effects.</p></div>","PeriodicalId":21098,"journal":{"name":"Research in microbiology","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9788144","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}