Juan Valdez-Baez, Francielly Morais Rodrigues da Costa, Anne Cybelle Pinto Gomide, Rodrigo Profeta, A. L. da Silva, T. Sousa, M. Viana, Rodrigo Bentes Kato, M. Americo, Andria dos Santos Freitas, R. Carvalho, B. Brenig, F. S. Martins, F. Aburjaile, V. Azevedo
Bifidobacterium breve is among the first microorganisms colonizing the intestinal tract in humans and is a predominant species in the gut microbiota of newborns and children. This bacterium is widely used in the probiotic industry due to its capacity to improve host health. The search for new targets with probiotic properties is an increasing trend with the help of next-generation sequencing as they facilitate the characterization of the bacterial features. B. breve 1101A was isolated from the faeces of healthy children in Brazil and therefore could play a protective role in the gut. To investigate the beneficial properties of this strain, the present study performed a comprehensive characterization of the genetic features involved in the bacterium resistance and adaptation to gastrointestinal conditions, production of nutrients, and immunomodulatory compounds. Furthermore, this study carried out the prediction of genomic elements (plasmids, prophages, CRISPR-Cas systems, insertion sequences, genomic islands, antibiotic resistance genes) to evaluate the safety of B. breve 1101A. A comparative genomics approach using 45 B. breve complete genomes based on pangenome and phylogenomic analysis was also performed to identify specific genes in B. breve 1101A. The prediction of genetic elements, possibly safety-related, did not detect plasmids, but only one incomplete prophage, two non-functional CRISPR systems, and seven genomic islands. Additionally, three antibiotic resistance genes were identified: ileS (resistance to mupirocin), rpoB, and erm(X). In the comparative genomic analysis, the pangenome was revealed to be open, and B. breve 1101A presented 63 unique genes associated with several processes, such as transmembrane transport, membrane components, DNA processes, and carbohydrate metabolism. In conclusion, B. breve 1101A is potentially safe and well-adapted for intestinal disorder therapeutics, although the role of its unique genetic repertoire needs further investigation.
{"title":"Comparative Genomics and In Silico Evaluation of Genes Related to the Probiotic Potential of Bifidobacterium breve 1101A","authors":"Juan Valdez-Baez, Francielly Morais Rodrigues da Costa, Anne Cybelle Pinto Gomide, Rodrigo Profeta, A. L. da Silva, T. Sousa, M. Viana, Rodrigo Bentes Kato, M. Americo, Andria dos Santos Freitas, R. Carvalho, B. Brenig, F. S. Martins, F. Aburjaile, V. Azevedo","doi":"10.3390/bacteria1030013","DOIUrl":"https://doi.org/10.3390/bacteria1030013","url":null,"abstract":"Bifidobacterium breve is among the first microorganisms colonizing the intestinal tract in humans and is a predominant species in the gut microbiota of newborns and children. This bacterium is widely used in the probiotic industry due to its capacity to improve host health. The search for new targets with probiotic properties is an increasing trend with the help of next-generation sequencing as they facilitate the characterization of the bacterial features. B. breve 1101A was isolated from the faeces of healthy children in Brazil and therefore could play a protective role in the gut. To investigate the beneficial properties of this strain, the present study performed a comprehensive characterization of the genetic features involved in the bacterium resistance and adaptation to gastrointestinal conditions, production of nutrients, and immunomodulatory compounds. Furthermore, this study carried out the prediction of genomic elements (plasmids, prophages, CRISPR-Cas systems, insertion sequences, genomic islands, antibiotic resistance genes) to evaluate the safety of B. breve 1101A. A comparative genomics approach using 45 B. breve complete genomes based on pangenome and phylogenomic analysis was also performed to identify specific genes in B. breve 1101A. The prediction of genetic elements, possibly safety-related, did not detect plasmids, but only one incomplete prophage, two non-functional CRISPR systems, and seven genomic islands. Additionally, three antibiotic resistance genes were identified: ileS (resistance to mupirocin), rpoB, and erm(X). In the comparative genomic analysis, the pangenome was revealed to be open, and B. breve 1101A presented 63 unique genes associated with several processes, such as transmembrane transport, membrane components, DNA processes, and carbohydrate metabolism. In conclusion, B. breve 1101A is potentially safe and well-adapted for intestinal disorder therapeutics, although the role of its unique genetic repertoire needs further investigation.","PeriodicalId":18020,"journal":{"name":"Lactic Acid Bacteria","volume":"15 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-07-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82411975","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
L. Albarracín, Fernanda Raya Tonetti, K. Fukuyama, Y. Suda, B. Zhou, Ayelén A. Baillo, S. Fadda, L. Saavedra, S. Kurata, E. Hebert, H. Kitazawa, J. Villena
Lactiplantibacillus plantarum strains are used in the food industry for their probiotic properties. Some of these bacteria have immunomodulatory effects on the host and are able to improve resistance against different pathogens, including viruses. However, to date, the bacterial genes involved in the immunomodulatory effect are not known. In this work, the complete genomes of L. plantarum MPL16, CRL1506, CRL681 and TL2766 were used to perform comparative genomics with the aim of identifying the genes involved in their differential immunomodulatory effects. L. plantarum WCFS1, a strain with proven probiotic activity, was also used for comparisons. The analysis of the genes involved in the metabolic pathways of the five strains did not reveal differences in the metabolism of amino acids, lipids, nucleotides, cofactors and vitamins, nor in the genes associated with energy metabolism or the biosynthesis of lipoproteins and teichoic acids. However, differences were found between the five strains when considering carbohydrate metabolism pathways, particularly in the presence/absence of glycosylhydrolases and glycosyltransferases. In addition, a great variability was detected in the predicted surface proteins of each L. plantarum strain. These results suggest that the surface molecules expressed in the different strains of L. plantarum could be involved in their differential ability to modulate the innate antiviral immune response.
植物乳杆菌菌株因其益生菌特性而被用于食品工业。其中一些细菌对宿主具有免疫调节作用，能够提高对不同病原体(包括病毒)的抵抗力。然而，迄今为止，参与免疫调节作用的细菌基因尚不清楚。本研究利用L. plantarum MPL16、CRL1506、CRL681和TL2766的全基因组进行比较基因组学研究，旨在鉴定其差异免疫调节作用的相关基因。植物乳杆菌WCFS1是一种已证实具有益生菌活性的菌株，也用于比较。对5株菌株代谢途径相关基因的分析没有发现氨基酸、脂质、核苷酸、辅助因子和维生素代谢的差异，也没有发现与能量代谢或脂蛋白和磷壁酸生物合成相关的基因的差异。然而，考虑到碳水化合物代谢途径，特别是糖基水解酶和糖基转移酶的存在/缺失，五种菌株之间存在差异。此外，各植物乳杆菌菌株的预测表面蛋白存在较大差异。这些结果表明，不同植物乳杆菌菌株中表达的表面分子可能参与了它们调节先天抗病毒免疫反应的不同能力。
{"title":"Genomic Characterization of Lactiplantibacillus plantarum Strains Possessing Differential Antiviral Immunomodulatory Activities","authors":"L. Albarracín, Fernanda Raya Tonetti, K. Fukuyama, Y. Suda, B. Zhou, Ayelén A. Baillo, S. Fadda, L. Saavedra, S. Kurata, E. Hebert, H. Kitazawa, J. Villena","doi":"10.3390/bacteria1030012","DOIUrl":"https://doi.org/10.3390/bacteria1030012","url":null,"abstract":"Lactiplantibacillus plantarum strains are used in the food industry for their probiotic properties. Some of these bacteria have immunomodulatory effects on the host and are able to improve resistance against different pathogens, including viruses. However, to date, the bacterial genes involved in the immunomodulatory effect are not known. In this work, the complete genomes of L. plantarum MPL16, CRL1506, CRL681 and TL2766 were used to perform comparative genomics with the aim of identifying the genes involved in their differential immunomodulatory effects. L. plantarum WCFS1, a strain with proven probiotic activity, was also used for comparisons. The analysis of the genes involved in the metabolic pathways of the five strains did not reveal differences in the metabolism of amino acids, lipids, nucleotides, cofactors and vitamins, nor in the genes associated with energy metabolism or the biosynthesis of lipoproteins and teichoic acids. However, differences were found between the five strains when considering carbohydrate metabolism pathways, particularly in the presence/absence of glycosylhydrolases and glycosyltransferases. In addition, a great variability was detected in the predicted surface proteins of each L. plantarum strain. These results suggest that the surface molecules expressed in the different strains of L. plantarum could be involved in their differential ability to modulate the innate antiviral immune response.","PeriodicalId":18020,"journal":{"name":"Lactic Acid Bacteria","volume":"55 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-07-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82102348","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
J. Valgardson, Sarah A. Struyvenberg, Zachary R. Sailer, I. Piper, Justin E. Svendsen, D. A. Johnson, Brandon A. Vogel, John M. Antos, M. Harms, J. Amacher
Gram-positive bacteria are some of the earliest known life forms, diverging from gram-negative bacteria 2 billion years ago. These organisms utilize sortase enzymes to attach proteins to their peptidoglycan cell wall, a structural feature that distinguishes the two types of bacteria. The transpeptidase activity of sortases make them an important tool in protein engineering applications, e.g., in sortase-mediated ligations or sortagging. However, due to relatively low catalytic efficiency, there are ongoing efforts to create better sortase variants for these uses. Here, we use bioinformatics tools, principal component analysis and ancestral sequence reconstruction, in combination with protein biochemistry, to analyze natural sequence variation in these enzymes. Principal component analysis on the sortase superfamily distinguishes previously described classes and identifies regions of relatively high sequence variation in structurally-conserved loops within each sortase family, including those near the active site. Using ancestral sequence reconstruction, we determined sequences of ancestral Staphylococcus and Streptococcus Class A sortase proteins. Enzyme assays revealed that the ancestral Streptococcus enzyme is relatively active and shares similar sequence variation with other Class A Streptococcus sortases. Taken together, we highlight how natural sequence variation can be utilized to investigate this important protein family, arguing that these and similar techniques may be used to discover or design sortases with increased catalytic efficiency and/or selectivity for sortase-mediated ligation experiments.
{"title":"Comparative Analysis and Ancestral Sequence Reconstruction of Bacterial Sortase Family Proteins Generates Functional Ancestral Mutants with Different Sequence Specificities","authors":"J. Valgardson, Sarah A. Struyvenberg, Zachary R. Sailer, I. Piper, Justin E. Svendsen, D. A. Johnson, Brandon A. Vogel, John M. Antos, M. Harms, J. Amacher","doi":"10.3390/bacteria1020011","DOIUrl":"https://doi.org/10.3390/bacteria1020011","url":null,"abstract":"Gram-positive bacteria are some of the earliest known life forms, diverging from gram-negative bacteria 2 billion years ago. These organisms utilize sortase enzymes to attach proteins to their peptidoglycan cell wall, a structural feature that distinguishes the two types of bacteria. The transpeptidase activity of sortases make them an important tool in protein engineering applications, e.g., in sortase-mediated ligations or sortagging. However, due to relatively low catalytic efficiency, there are ongoing efforts to create better sortase variants for these uses. Here, we use bioinformatics tools, principal component analysis and ancestral sequence reconstruction, in combination with protein biochemistry, to analyze natural sequence variation in these enzymes. Principal component analysis on the sortase superfamily distinguishes previously described classes and identifies regions of relatively high sequence variation in structurally-conserved loops within each sortase family, including those near the active site. Using ancestral sequence reconstruction, we determined sequences of ancestral Staphylococcus and Streptococcus Class A sortase proteins. Enzyme assays revealed that the ancestral Streptococcus enzyme is relatively active and shares similar sequence variation with other Class A Streptococcus sortases. Taken together, we highlight how natural sequence variation can be utilized to investigate this important protein family, arguing that these and similar techniques may be used to discover or design sortases with increased catalytic efficiency and/or selectivity for sortase-mediated ligation experiments.","PeriodicalId":18020,"journal":{"name":"Lactic Acid Bacteria","volume":"3 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83441183","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
D. L. Rodrigues, F. M. Costa, W. M. Silva, F. Aburjaile, V. Azevedo
Infections by antibiotic-resistant bacteria are a significant and complex global health issue. In this context, Acinetobacter baumannii is particularly important because of its ability to withstand treatments by β-lactams, such as carbapenem. The objective of this work was to investigate, through systematic analysis and meta-analysis, the chance of resistance to carbapenem in A. baumannii strains. For this, a search was conducted for the PubMed and Cochrane databases based on the keywords: “Acinetobacter baumannii” AND “beta-lactam” OR “penicillin” OR “cephalosporin” OR “cephamycin” OR “carbapenem” OR “monobactam”. The initial search resulted in a total of 90,475 articles. It was filtered based on eligibility criteria, and eight articles were selected for analysis. An odds ratio value equivalent to 3.55 was obtained, indicating a high chance of resistance to the carbapenem of strains of the species. Therefore, it is supposed that A. baumannii infection cases have a high probability of not responding adequately to treatments based on carbapenem.
{"title":"Acinetobacter baumannii and Its Relationship to Carbapenem Resistance: A Meta-Analysis","authors":"D. L. Rodrigues, F. M. Costa, W. M. Silva, F. Aburjaile, V. Azevedo","doi":"10.3390/bacteria1020010","DOIUrl":"https://doi.org/10.3390/bacteria1020010","url":null,"abstract":"Infections by antibiotic-resistant bacteria are a significant and complex global health issue. In this context, Acinetobacter baumannii is particularly important because of its ability to withstand treatments by β-lactams, such as carbapenem. The objective of this work was to investigate, through systematic analysis and meta-analysis, the chance of resistance to carbapenem in A. baumannii strains. For this, a search was conducted for the PubMed and Cochrane databases based on the keywords: “Acinetobacter baumannii” AND “beta-lactam” OR “penicillin” OR “cephalosporin” OR “cephamycin” OR “carbapenem” OR “monobactam”. The initial search resulted in a total of 90,475 articles. It was filtered based on eligibility criteria, and eight articles were selected for analysis. An odds ratio value equivalent to 3.55 was obtained, indicating a high chance of resistance to the carbapenem of strains of the species. Therefore, it is supposed that A. baumannii infection cases have a high probability of not responding adequately to treatments based on carbapenem.","PeriodicalId":18020,"journal":{"name":"Lactic Acid Bacteria","volume":"19 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88098606","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Neisseria gonorrhoeae has become a significant global public health problem due to growing infection rates and antibiotic resistance development. In 2012, N. gonorrhoeae positive samples isolated from Southeast Asia were reported to be the first strains showing resistance to all first-line antibiotics. To date, N. gonorrhoeae’s antimicrobial resistance has since been identified against a wide range of antimicrobial drugs globally. Hence, the World Health Organization (WHO) listed N. gonorrhoeae’s drug resistance as high-priority, necessitating novel therapy development. The persistence of N. gonorrhoeae infections globally underlines the need to better understand the molecular basis of N. gonorrhoeae infection, growing antibiotic resistance, and treatment difficulties in underdeveloped countries. Historically, Africa has had minimal or rudimentary N. gonorrhoeae monitoring systems, and while antimicrobial-resistant N. gonorrhoeae is known to exist, the degree of resistance is unknown. This review looks at the gender-related symptomatic gonorrhoeae disease and provides an overview of the essential bacterial factors for the different stages of pathogenesis, including transmission, immune evasion, and antibiotic resistance. Finally, we deliberate on how molecular epidemiological studies have informed our current understanding of sexual networks in the Sub-Saharan region.
{"title":"Antimicrobial Resistance of Neisseria gonorrhoeae in Sub-Saharan Populations","authors":"Sinethemba H. Yakobi, O. Pooe","doi":"10.3390/bacteria1020009","DOIUrl":"https://doi.org/10.3390/bacteria1020009","url":null,"abstract":"Neisseria gonorrhoeae has become a significant global public health problem due to growing infection rates and antibiotic resistance development. In 2012, N. gonorrhoeae positive samples isolated from Southeast Asia were reported to be the first strains showing resistance to all first-line antibiotics. To date, N. gonorrhoeae’s antimicrobial resistance has since been identified against a wide range of antimicrobial drugs globally. Hence, the World Health Organization (WHO) listed N. gonorrhoeae’s drug resistance as high-priority, necessitating novel therapy development. The persistence of N. gonorrhoeae infections globally underlines the need to better understand the molecular basis of N. gonorrhoeae infection, growing antibiotic resistance, and treatment difficulties in underdeveloped countries. Historically, Africa has had minimal or rudimentary N. gonorrhoeae monitoring systems, and while antimicrobial-resistant N. gonorrhoeae is known to exist, the degree of resistance is unknown. This review looks at the gender-related symptomatic gonorrhoeae disease and provides an overview of the essential bacterial factors for the different stages of pathogenesis, including transmission, immune evasion, and antibiotic resistance. Finally, we deliberate on how molecular epidemiological studies have informed our current understanding of sexual networks in the Sub-Saharan region.","PeriodicalId":18020,"journal":{"name":"Lactic Acid Bacteria","volume":"51 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-05-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88661554","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Bees’ and beehives’ health are strongly influenced by the honeybees’ gut microbiota which in turn is strongly dependent on many different factors, including environmental factors as well as anthropogenic pressure. In this study, in four locations in Bulgaria differing strongly in environmental conditions and anthropogenic pressure, an assessment was made using several obligatory core symbiont species and genera for reference, such as Lactobacillus sp., Bifidobacterium sp., Snodgrassiella alvi, Gilliamella apicola, Frishella perrara, and Commensalibacter sp., as well as an observation of the overall number of species. A snapshot of the relative abundances of the total number of species and the core species was made using a next-generation sequencing (NGS)-based metagenomic approach using the Illumina 2 × 250 bp paired-end platform. It was found that the two forms of anthropogenic pressure, the agricultural and the urban/industrial, have distinct effects, affecting different core genera and species. It was also demonstrated that both types of anthropogenic pressure cause a reduction in the overall number of bacterial species.
{"title":"Environmental and Anthropogenic Influence on the Core Beneficial Honeybee Gut Microbiota—A Short Communication from Bulgaria","authors":"S. Dimov","doi":"10.3390/bacteria1020008","DOIUrl":"https://doi.org/10.3390/bacteria1020008","url":null,"abstract":"Bees’ and beehives’ health are strongly influenced by the honeybees’ gut microbiota which in turn is strongly dependent on many different factors, including environmental factors as well as anthropogenic pressure. In this study, in four locations in Bulgaria differing strongly in environmental conditions and anthropogenic pressure, an assessment was made using several obligatory core symbiont species and genera for reference, such as Lactobacillus sp., Bifidobacterium sp., Snodgrassiella alvi, Gilliamella apicola, Frishella perrara, and Commensalibacter sp., as well as an observation of the overall number of species. A snapshot of the relative abundances of the total number of species and the core species was made using a next-generation sequencing (NGS)-based metagenomic approach using the Illumina 2 × 250 bp paired-end platform. It was found that the two forms of anthropogenic pressure, the agricultural and the urban/industrial, have distinct effects, affecting different core genera and species. It was also demonstrated that both types of anthropogenic pressure cause a reduction in the overall number of bacterial species.","PeriodicalId":18020,"journal":{"name":"Lactic Acid Bacteria","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83483243","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Ł. Wajda, A. Ostrowski, Ewelina Błasiak, Patrycja Godowska
Using Enterococcus faecium strains as probiotics raises several controversies related to their antibiotic resistance (AR). In the current study, we examined isolates of E. faecium obtained from human breast milk. Catalase-negative and γ-haemolytic isolates were identified by analyzing the sequences of 16S rRNA gene and their phenotypic resistance to antibiotics was investigated. We examined the expression of genes that were found on plasmids. The majority of isolates tested were resistant to erythromycin (96%), followed by trimethoprim (67%), tetracycline (57%), and gentamicin (55%). Ninety-seven percent of E. faecium isolates were resistant to at least two antibiotics. We detected the presence of the following genes on plasmids: ErmB (erythromycin), dfrA17 (trimethoprim), tetO, tetK (tetracycline), Aph(3′)-IIIa (neomycin), and marA (rifampicin). TetO was not expressed in all cases, dfrA14 was not expressed in CDCP1449, while tetK was only expressed in CDCP1128 and CDCP1331 isolates. In the majority of isolates, AR genes were located on chromosomes since they were not detected on plasmids. Our study shows that due to the spread of AR, human milk could be one of the first sources of the bacteria resistant to antimicrobials to infants.
{"title":"Enterococcus faecium Isolates Present in Human Breast Milk Might Be Carriers of Multi-Antibiotic Resistance Genes","authors":"Ł. Wajda, A. Ostrowski, Ewelina Błasiak, Patrycja Godowska","doi":"10.3390/bacteria1020007","DOIUrl":"https://doi.org/10.3390/bacteria1020007","url":null,"abstract":"Using Enterococcus faecium strains as probiotics raises several controversies related to their antibiotic resistance (AR). In the current study, we examined isolates of E. faecium obtained from human breast milk. Catalase-negative and γ-haemolytic isolates were identified by analyzing the sequences of 16S rRNA gene and their phenotypic resistance to antibiotics was investigated. We examined the expression of genes that were found on plasmids. The majority of isolates tested were resistant to erythromycin (96%), followed by trimethoprim (67%), tetracycline (57%), and gentamicin (55%). Ninety-seven percent of E. faecium isolates were resistant to at least two antibiotics. We detected the presence of the following genes on plasmids: ErmB (erythromycin), dfrA17 (trimethoprim), tetO, tetK (tetracycline), Aph(3′)-IIIa (neomycin), and marA (rifampicin). TetO was not expressed in all cases, dfrA14 was not expressed in CDCP1449, while tetK was only expressed in CDCP1128 and CDCP1331 isolates. In the majority of isolates, AR genes were located on chromosomes since they were not detected on plasmids. Our study shows that due to the spread of AR, human milk could be one of the first sources of the bacteria resistant to antimicrobials to infants.","PeriodicalId":18020,"journal":{"name":"Lactic Acid Bacteria","volume":"48 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77057872","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Christian Stocks, R. Schlechter, Mitja N. P. Remus-Emsermann
A recent publication described the construction and utility of a comprehensive “Chromatic Bacteria” toolbox containing a set of genetic tools that allows for fluorescently tagging a variety of Proteobacteria. In an effort to expand the range of bacteria taggable with the Chromatic Bacteria toolbox, a series of Himar1 transposon vectors was constructed to mediate insertion of fluorescent protein and antibiotic resistant genes. The Himar1 transposon was chosen as it is known to function in a wide range of bacterial species. To test the suitability of the new Himar1 Chromatic Bacteria plasmid derivatives, conjugations were attempted on recently isolated non-model organisms. Although we were unsuccessful in delivering the plasmids into Gram-positive bacterial isolates, we successfully modified previously recalcitrant isolates to the first set of the Chromatic Bacteria toolbox, such as Sphingomonas sp. Leaf357 and Acidovorax sp. Leaf84. This manuscript reports on the currently available plasmids and transposition success in different bacteria.
{"title":"Chromatic Bacteria v.2-A Himar1 Transposon-Based Delivery Vector to Extend the Host Range of a Toolbox to Fluorescently Tag Bacteria","authors":"Christian Stocks, R. Schlechter, Mitja N. P. Remus-Emsermann","doi":"10.3390/bacteria1010006","DOIUrl":"https://doi.org/10.3390/bacteria1010006","url":null,"abstract":"A recent publication described the construction and utility of a comprehensive “Chromatic Bacteria” toolbox containing a set of genetic tools that allows for fluorescently tagging a variety of Proteobacteria. In an effort to expand the range of bacteria taggable with the Chromatic Bacteria toolbox, a series of Himar1 transposon vectors was constructed to mediate insertion of fluorescent protein and antibiotic resistant genes. The Himar1 transposon was chosen as it is known to function in a wide range of bacterial species. To test the suitability of the new Himar1 Chromatic Bacteria plasmid derivatives, conjugations were attempted on recently isolated non-model organisms. Although we were unsuccessful in delivering the plasmids into Gram-positive bacterial isolates, we successfully modified previously recalcitrant isolates to the first set of the Chromatic Bacteria toolbox, such as Sphingomonas sp. Leaf357 and Acidovorax sp. Leaf84. This manuscript reports on the currently available plasmids and transposition success in different bacteria.","PeriodicalId":18020,"journal":{"name":"Lactic Acid Bacteria","volume":"27 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76410232","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Asinibacterium spp. (Family Chitinophagaceae, Phylum Bacteroidota) are abundant in environments contaminated with heavy metals. We characterized the physiology and genome of two Asinibacterium species to elucidate their ability to survive and grow at ambient conditions in the uranium-contaminated environments. Both strains were able to grow at pH 4.5 or 50 mM nitrate under aerobic conditions and did not grow with alternative electron acceptors under anaerobic conditions. Asinibacterium sp. OR53 grew in medium with uranium concentrations up to 300 µM uranium while Asinibacterium sp. OR43 could not grow at uranium concentrations > 200 µM. Elemental mapping using energy dispersive X-ray spectroscopy indicate that uranium co-localized with phosphorus-containing compounds on the cell surface. Genes potentially encoding resistance mechanisms to a variety of heavy metals were detected in the genomes of both strains. The localization of uranium and missing acidic and alkaline phosphatase genes in the genome suggest that biosorption of uranium to the lipopolysaccharide layer might be the mechanism of uranium resistance. In summary, Asinibacterium spp. OR43 and OR53 are physiologically similar to closely related strains within the Chitinophagaceae family but are uniquely acclimated to the presence of uranium and other heavy metals prevalent in the subsurface at Oak Ridge, Tennessee.
{"title":"Physiological and Genomic Characterization of Two Novel Bacteroidota Strains Asinibacterium spp. OR43 and OR53","authors":"R. Brzoska, R. Edelmann, A. Bollmann","doi":"10.3390/bacteria1010004","DOIUrl":"https://doi.org/10.3390/bacteria1010004","url":null,"abstract":"Asinibacterium spp. (Family Chitinophagaceae, Phylum Bacteroidota) are abundant in environments contaminated with heavy metals. We characterized the physiology and genome of two Asinibacterium species to elucidate their ability to survive and grow at ambient conditions in the uranium-contaminated environments. Both strains were able to grow at pH 4.5 or 50 mM nitrate under aerobic conditions and did not grow with alternative electron acceptors under anaerobic conditions. Asinibacterium sp. OR53 grew in medium with uranium concentrations up to 300 µM uranium while Asinibacterium sp. OR43 could not grow at uranium concentrations > 200 µM. Elemental mapping using energy dispersive X-ray spectroscopy indicate that uranium co-localized with phosphorus-containing compounds on the cell surface. Genes potentially encoding resistance mechanisms to a variety of heavy metals were detected in the genomes of both strains. The localization of uranium and missing acidic and alkaline phosphatase genes in the genome suggest that biosorption of uranium to the lipopolysaccharide layer might be the mechanism of uranium resistance. In summary, Asinibacterium spp. OR43 and OR53 are physiologically similar to closely related strains within the Chitinophagaceae family but are uniquely acclimated to the presence of uranium and other heavy metals prevalent in the subsurface at Oak Ridge, Tennessee.","PeriodicalId":18020,"journal":{"name":"Lactic Acid Bacteria","volume":"31 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-02-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81097085","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
C. Vrettou, E. Drosos, Martha Nepka, G. Bouboulis, T. Kalamatianos, C. Liakopoulou, Grigorios Gkouvelos, A. Kotanidou, G. Stranjalis
There is little evidence on the role of prior infection in patients with external ventricular drains (EVDs) and lumbar drains (LDs). In this study, our aim is to investigate whether previous bacteremia is a risk factor for cerebrospinal fluid drain infection (CSFDI) in patients with EVDs and LDs and to describe the microorganisms implicated. We designed a retrospective, single-center cohort study. We recorded patients’ demographic and clinical characteristics, as well as microbiology laboratory data. We used non-parametric statistical methods to identify possible risk factors for CSFDI. We found 799 neurosurgical admissions during the study period, 70 of which fulfilled the inclusion criteria. Acinetobacter baumannii was the most frequent single pathogen isolated in the cerebrospinal fluid (CSF). Acinetobacter baumannii bacteremia was more common in patients with Acinetobacter baumannii CSFDI (p = 0.01). The distribution of the pathogens in the CSF differed from that of the pathogens isolated in blood (p = 0.001). In the univariate analysis, prior bacteremia was more common in patients with CSFDI (p = 0.027), but, in the multivariate model, prior bacteremia was not identified as an independent risk factor (OR = 0.456, CI: 0.138–1.512, p = 0.2). In an ICU population, the most frequently isolated pathogens were Gram-negative Enterobacteriaceae and Acinetobacter baumannii. Previous bacteremia was significantly more probable among patients with EVDs or LDs who developed a CSFDI, and its role warrants further investigation.
{"title":"Bacteremia Is a Risk Factor for Cerebrospinal Fluid Infection in Patients with Cerebrospinal Fluid Drains—A Retrospective Study","authors":"C. Vrettou, E. Drosos, Martha Nepka, G. Bouboulis, T. Kalamatianos, C. Liakopoulou, Grigorios Gkouvelos, A. Kotanidou, G. Stranjalis","doi":"10.3390/bacteria1010005","DOIUrl":"https://doi.org/10.3390/bacteria1010005","url":null,"abstract":"There is little evidence on the role of prior infection in patients with external ventricular drains (EVDs) and lumbar drains (LDs). In this study, our aim is to investigate whether previous bacteremia is a risk factor for cerebrospinal fluid drain infection (CSFDI) in patients with EVDs and LDs and to describe the microorganisms implicated. We designed a retrospective, single-center cohort study. We recorded patients’ demographic and clinical characteristics, as well as microbiology laboratory data. We used non-parametric statistical methods to identify possible risk factors for CSFDI. We found 799 neurosurgical admissions during the study period, 70 of which fulfilled the inclusion criteria. Acinetobacter baumannii was the most frequent single pathogen isolated in the cerebrospinal fluid (CSF). Acinetobacter baumannii bacteremia was more common in patients with Acinetobacter baumannii CSFDI (p = 0.01). The distribution of the pathogens in the CSF differed from that of the pathogens isolated in blood (p = 0.001). In the univariate analysis, prior bacteremia was more common in patients with CSFDI (p = 0.027), but, in the multivariate model, prior bacteremia was not identified as an independent risk factor (OR = 0.456, CI: 0.138–1.512, p = 0.2). In an ICU population, the most frequently isolated pathogens were Gram-negative Enterobacteriaceae and Acinetobacter baumannii. Previous bacteremia was significantly more probable among patients with EVDs or LDs who developed a CSFDI, and its role warrants further investigation.","PeriodicalId":18020,"journal":{"name":"Lactic Acid Bacteria","volume":"79 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-02-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82399164","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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