Carole Kowalewicz, Michael Timmermans, David Fretin, Pierre Wattiau, Cécile Boland
Identifying antimicrobial resistance (AMR) genes and determining their occurrence in Gram-positive bacteria provide useful data to understand how resistance can be acquired and maintained in these bacteria. We describe an in-house bead array targeting AMR genes of Gram-positive bacteria and allowing their rapid detection all at once at a reduced cost. A total of 41 AMR probes were designed to target genes frequently associated with resistance to tetracycline, macrolides, lincosamides, streptogramins, pleuromutilins, phenicols, glycopeptides, aminoglycosides, diaminopyrimidines, oxazolidinones and particularly shared among Enterococcus and Staphylococcus spp. A collection of 124 enterococci and 62 staphylococci isolated from healthy livestock animals through the official Belgian AMR monitoring (2018–2020) was studied with this array from which a subsample was further investigated by whole-genome sequencing. The array detected AMR genes associated with phenotypic resistance for 93.0% and 89.2% of the individual resistant phenotypes in enterococci and staphylococci, respectively. Although linezolid is not used in veterinary medicine, linezolid-resistant isolates were detected. These were characterized by the presence of optrA and poxtA, providing cross-resistance to other antibiotics. Rarer, vancomycin resistance was conferred by the vanA or by the vanL cluster. Numerous resistance genes circulating among Enterococcus and Staphylococcus spp. were detected by this array allowing rapid screening of a large strain collection at an affordable cost. Our data stress the importance of interpreting AMR with caution and the complementarity of both phenotyping and genotyping methods. This array is now available to assess other One-Health AMR reservoirs.
鉴定抗微生物耐药性(AMR)基因并确定其在革兰氏阳性菌中的发生率,为了解这些细菌如何获得和维持耐药性提供了有用的数据。我们描述了一种针对革兰氏阳性菌AMR基因的内部珠阵列,并允许以降低的成本同时快速检测它们。共设计了41种AMR探针,靶向经常与四环素、大环内酯类、林可酰胺类、链菌素、胸膜菌素、氯霉素、糖肽、氨基糖苷类、二氨基嘧啶类、恶唑烷酮相关的基因,尤其是肠球菌和葡萄球菌共有的基因。使用该阵列研究了通过比利时官方AMR监测(2018-2020)从健康牲畜中分离的124株肠球菌和62株葡萄球菌,并通过全基因组测序进一步研究了其中的子样本。该阵列检测到与表型耐药性相关的AMR基因,分别占肠球菌和葡萄球菌个体耐药性表型的93.0%和89.2%。虽然利奈唑胺不用于兽医,但检测到了利奈唑啉耐药菌株。其特征是存在optrA和poxtA,提供对其他抗生素的交叉耐药性。更罕见的是,万古霉素耐药性是由vanA或vanL簇赋予的。通过该阵列检测到在肠球菌和葡萄球菌中循环的许多抗性基因,从而能够以负担得起的成本快速筛选大量菌株。我们的数据强调了谨慎解释AMR的重要性,以及表型和基因分型方法的互补性。该阵列现在可用于评估其他One Health AMR储层。
{"title":"An in-house 45-plex array for the detection of antimicrobial resistance genes in Gram-positive bacteria","authors":"Carole Kowalewicz, Michael Timmermans, David Fretin, Pierre Wattiau, Cécile Boland","doi":"10.1002/mbo3.1341","DOIUrl":"10.1002/mbo3.1341","url":null,"abstract":"<p>Identifying antimicrobial resistance (AMR) genes and determining their occurrence in Gram-positive bacteria provide useful data to understand how resistance can be acquired and maintained in these bacteria. We describe an in-house bead array targeting AMR genes of Gram-positive bacteria and allowing their rapid detection all at once at a reduced cost. A total of 41 AMR probes were designed to target genes frequently associated with resistance to tetracycline, macrolides, lincosamides, streptogramins, pleuromutilins, phenicols, glycopeptides, aminoglycosides, diaminopyrimidines, oxazolidinones and particularly shared among <i>Enterococcus</i> and <i>Staphylococcus</i> spp. A collection of 124 enterococci and 62 staphylococci isolated from healthy livestock animals through the official Belgian AMR monitoring (2018–2020) was studied with this array from which a subsample was further investigated by whole-genome sequencing. The array detected AMR genes associated with phenotypic resistance for 93.0% and 89.2% of the individual resistant phenotypes in enterococci and staphylococci, respectively. Although linezolid is not used in veterinary medicine, linezolid-resistant isolates were detected. These were characterized by the presence of <i>optrA</i> and <i>poxtA</i>, providing cross-resistance to other antibiotics. Rarer, vancomycin resistance was conferred by the <i>vanA</i> or by the <i>vanL</i> cluster. Numerous resistance genes circulating among <i>Enterococcus</i> and <i>Staphylococcus</i> spp. were detected by this array allowing rapid screening of a large strain collection at an affordable cost. Our data stress the importance of interpreting AMR with caution and the complementarity of both phenotyping and genotyping methods. This array is now available to assess other One-Health AMR reservoirs.</p>","PeriodicalId":18573,"journal":{"name":"MicrobiologyOpen","volume":"12 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2022-12-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/mbo3.1341","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9072646","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
L. Canini, Gabriela Modenesi, Aurélie Courcoul, M. Boschiroli, B. Durand, L. Michelet
Bovine tuberculosis is a common disease affecting cattle and wildlife worldwide. Mycobacterium bovis circulation in wildlife decreases the efficacy of surveillance and control programs in cattle. Strains of the European 3 clonal complex are the most frequent in France. The aim of our work was hence to investigate the role played by cattle and wildlife species in the circulation of two M. bovis European 3 strains circulation. WGS of M. bovis strains collected between 2010 and 2017 in two distinct areas (Nouvelle‐Aquitaine region, NAq, and Côte‐d'Or département, CdO), from badgers, wild boars, and cattle were used in an evolutionary model to infer the transition between the three species. We computed host species transition and persistence between two consecutive nodes and the average number of transitions per tree. In total, 144 and 218 samples were collected respectively in CdO and NAq. In CdO, three between‐species transition rates stood out: from cattle to badgers, from badgers to wild boars, and from wild boars to cattle. In NAq an additional fourth transition rate was identified: from badgers to cattle. However, host transition remained a rare event. Our results suggest that wild boars could be an intermediary host between badgers and cattle in the circulation of the studied strains in CdO and NAq. Our results also highlight the differences between these two areas, suggesting that the transition pattern does not only depend on the host species and other ecological, landscape and anthropic factors are important.
{"title":"Deciphering the role of host species for two Mycobacterium bovis genotypes from the European 3 clonal complex circulation within a cattle‐badger‐wild boar multihost system","authors":"L. Canini, Gabriela Modenesi, Aurélie Courcoul, M. Boschiroli, B. Durand, L. Michelet","doi":"10.1002/mbo3.1331","DOIUrl":"https://doi.org/10.1002/mbo3.1331","url":null,"abstract":"Bovine tuberculosis is a common disease affecting cattle and wildlife worldwide. Mycobacterium bovis circulation in wildlife decreases the efficacy of surveillance and control programs in cattle. Strains of the European 3 clonal complex are the most frequent in France. The aim of our work was hence to investigate the role played by cattle and wildlife species in the circulation of two M. bovis European 3 strains circulation. WGS of M. bovis strains collected between 2010 and 2017 in two distinct areas (Nouvelle‐Aquitaine region, NAq, and Côte‐d'Or département, CdO), from badgers, wild boars, and cattle were used in an evolutionary model to infer the transition between the three species. We computed host species transition and persistence between two consecutive nodes and the average number of transitions per tree. In total, 144 and 218 samples were collected respectively in CdO and NAq. In CdO, three between‐species transition rates stood out: from cattle to badgers, from badgers to wild boars, and from wild boars to cattle. In NAq an additional fourth transition rate was identified: from badgers to cattle. However, host transition remained a rare event. Our results suggest that wild boars could be an intermediary host between badgers and cattle in the circulation of the studied strains in CdO and NAq. Our results also highlight the differences between these two areas, suggesting that the transition pattern does not only depend on the host species and other ecological, landscape and anthropic factors are important.","PeriodicalId":18573,"journal":{"name":"MicrobiologyOpen","volume":"12 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2022-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"51226578","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Bovine tuberculosis is a common disease affecting cattle and wildlife worldwide. Mycobacterium bovis circulation in wildlife decreases the efficacy of surveillance and control programs in cattle. Strains of the European 3 clonal complex are the most frequent in France. The aim of our work was hence to investigate the role played by cattle and wildlife species in the circulation of two M. bovis European 3 strains circulation. WGS of M. bovis strains collected between 2010 and 2017 in two distinct areas (Nouvelle-Aquitaine region, NAq, and Côte-d'Or département, CdO), from badgers, wild boars, and cattle were used in an evolutionary model to infer the transition between the three species. We computed host species transition and persistence between two consecutive nodes and the average number of transitions per tree. In total, 144 and 218 samples were collected respectively in CdO and NAq. In CdO, three between-species transition rates stood out: from cattle to badgers, from badgers to wild boars, and from wild boars to cattle. In NAq an additional fourth transition rate was identified: from badgers to cattle. However, host transition remained a rare event. Our results suggest that wild boars could be an intermediary host between badgers and cattle in the circulation of the studied strains in CdO and NAq. Our results also highlight the differences between these two areas, suggesting that the transition pattern does not only depend on the host species and other ecological, landscape and anthropic factors are important.
{"title":"Deciphering the role of host species for two Mycobacterium bovis genotypes from the European 3 clonal complex circulation within a cattle-badger-wild boar multihost system","authors":"Laetitia Canini, Gabriela Modenesi, Aurélie Courcoul, Maria-Laura Boschiroli, Benoit Durand, Lorraine Michelet","doi":"10.1002/mbo3.1331","DOIUrl":"https://doi.org/10.1002/mbo3.1331","url":null,"abstract":"<p>Bovine tuberculosis is a common disease affecting cattle and wildlife worldwide. <i>Mycobacterium bovis</i> circulation in wildlife decreases the efficacy of surveillance and control programs in cattle. Strains of the European 3 clonal complex are the most frequent in France. The aim of our work was hence to investigate the role played by cattle and wildlife species in the circulation of two <i>M. bovis</i> European 3 strains circulation. WGS of <i>M. bovis</i> strains collected between 2010 and 2017 in two distinct areas (Nouvelle-Aquitaine region, NAq, and Côte-d'Or département, CdO), from badgers, wild boars, and cattle were used in an evolutionary model to infer the transition between the three species. We computed host species transition and persistence between two consecutive nodes and the average number of transitions per tree. In total, 144 and 218 samples were collected respectively in CdO and NAq. In CdO, three between-species transition rates stood out: from cattle to badgers, from badgers to wild boars, and from wild boars to cattle. In NAq an additional fourth transition rate was identified: from badgers to cattle. However, host transition remained a rare event. Our results suggest that wild boars could be an intermediary host between badgers and cattle in the circulation of the studied strains in CdO and NAq. Our results also highlight the differences between these two areas, suggesting that the transition pattern does not only depend on the host species and other ecological, landscape and anthropic factors are important.</p>","PeriodicalId":18573,"journal":{"name":"MicrobiologyOpen","volume":"12 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2022-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/mbo3.1331","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"50133196","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Maria D. Barbuti, Ine S. Myrbråten, Danae Morales Angeles, Morten Kjos
As bacteria proliferate, DNA replication, chromosome segregation, cell wall synthesis, and cytokinesis occur concomitantly and need to be tightly regulated and coordinated. Although these cell cycle processes have been studied for decades, several mechanisms remain elusive, specifically in coccus-shaped cells such as Staphylococcus aureus. In recent years, major progress has been made in our understanding of how staphylococci divide, including new, fundamental insights into the mechanisms of cell wall synthesis and division site selection. Furthermore, several novel proteins and mechanisms involved in the regulation of replication initiation or progression of the cell cycle have been identified and partially characterized. In this review, we will summarize our current understanding of the cell cycle processes in the spheroid model bacterium S. aureus, with a focus on recent advances in the understanding of how these processes are regulated.
{"title":"The cell cycle of Staphylococcus aureus: An updated review","authors":"Maria D. Barbuti, Ine S. Myrbråten, Danae Morales Angeles, Morten Kjos","doi":"10.1002/mbo3.1338","DOIUrl":"10.1002/mbo3.1338","url":null,"abstract":"<p>As bacteria proliferate, DNA replication, chromosome segregation, cell wall synthesis, and cytokinesis occur concomitantly and need to be tightly regulated and coordinated. Although these cell cycle processes have been studied for decades, several mechanisms remain elusive, specifically in coccus-shaped cells such as <i>Staphylococcus aureus</i>. In recent years, major progress has been made in our understanding of how staphylococci divide, including new, fundamental insights into the mechanisms of cell wall synthesis and division site selection. Furthermore, several novel proteins and mechanisms involved in the regulation of replication initiation or progression of the cell cycle have been identified and partially characterized. In this review, we will summarize our current understanding of the cell cycle processes in the spheroid model bacterium <i>S. aureus</i>, with a focus on recent advances in the understanding of how these processes are regulated.</p>","PeriodicalId":18573,"journal":{"name":"MicrobiologyOpen","volume":"12 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2022-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/mbo3.1338","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9072651","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Andrew O'Connor, Irene Jurado-Martín, Margaritha M. Mysior, Anotidaishe L. Manzira, Joanna Drabinska, Jeremy C. Simpson, Mary Lucey, Kirsten Schaffer, Rita Berisio, Siobhán McClean
Universal stress proteins (USPs) are ubiquitously expressed in bacteria, archaea, and eukaryotes and play a lead role in adaptation to environmental conditions. They enable adaptation of bacterial pathogens to the conditions encountered in the human niche, including hypoxia, oxidative stress, osmotic stress, nutrient deficiency, or acid stress, thereby facilitating colonization. We previously reported that all six USP proteins encoded within a low-oxygen activated (lxa) locus in Burkholderia cenocepacia showed increased abundance during chronic colonization of the cystic fibrosis (CF) lung. However, the role of USPs in chronic cystic fibrosis infection is not well understood. Structural modeling identified surface arginines on one lxa-encoded USP, USP76, which suggested it mediated interactions with heparan sulfate. Using mutants derived from the B. cenocepacia strain, K56-2, we show that USP76 is involved in host cell attachment. Pretreatment of lung epithelial cells with heparanase reduced the binding of the wild-type and complement strains but not the Δusp76 mutant strain, indicating that USP76 is directly or indirectly involved in receptor recognition on the surface of epithelial cells. We also show that USP76 is required for growth and survival in many conditions associated with the CF lung, including acidic conditions and oxidative stress. Moreover, USP76 also has a role in survival in macrophages isolated from people with CF. Overall, while further elucidation of the exact mechanism(s) is required, we can conclude that USP76, which is upregulated during chronic infection, is involved in bacterial survival within CF macrophages, a hallmark of Burkholderia infection.
{"title":"A universal stress protein upregulated by hypoxia has a role in Burkholderia cenocepacia intramacrophage survival: Implications for chronic infection in cystic fibrosis","authors":"Andrew O'Connor, Irene Jurado-Martín, Margaritha M. Mysior, Anotidaishe L. Manzira, Joanna Drabinska, Jeremy C. Simpson, Mary Lucey, Kirsten Schaffer, Rita Berisio, Siobhán McClean","doi":"10.1002/mbo3.1311","DOIUrl":"10.1002/mbo3.1311","url":null,"abstract":"<p>Universal stress proteins (USPs) are ubiquitously expressed in bacteria, archaea, and eukaryotes and play a lead role in adaptation to environmental conditions. They enable adaptation of bacterial pathogens to the conditions encountered in the human niche, including hypoxia, oxidative stress, osmotic stress, nutrient deficiency, or acid stress, thereby facilitating colonization. We previously reported that all six USP proteins encoded within a low-oxygen activated (<i>lxa</i>) locus in <i>Burkholderia cenocepacia</i> showed increased abundance during chronic colonization of the cystic fibrosis (CF) lung. However, the role of USPs in chronic cystic fibrosis infection is not well understood. Structural modeling identified surface arginines on one <i>lxa</i>-encoded USP, USP76, which suggested it mediated interactions with heparan sulfate. Using mutants derived from the <i>B. cenocepacia</i> strain, K56-2, we show that USP76 is involved in host cell attachment. Pretreatment of lung epithelial cells with heparanase reduced the binding of the wild-type and complement strains but not the Δ<i>usp76</i> mutant strain, indicating that USP76 is directly or indirectly involved in receptor recognition on the surface of epithelial cells. We also show that USP76 is required for growth and survival in many conditions associated with the CF lung, including acidic conditions and oxidative stress. Moreover, USP76 also has a role in survival in macrophages isolated from people with CF. Overall, while further elucidation of the exact mechanism(s) is required, we can conclude that USP76, which is upregulated during chronic infection, is involved in bacterial survival within CF macrophages, a hallmark of <i>Burkholderia</i> infection.</p>","PeriodicalId":18573,"journal":{"name":"MicrobiologyOpen","volume":"12 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2022-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/mbo3.1311","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10822471","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Margot W. J. Geerinck, Sara Van Hee, Gabriele Gloder, Sam Crauwels, Stefano Colazza, Hans Jacquemyn, Antonino Cusumano, Bart Lievens
Although microbial communities of insects from larval to adult stage have been increasingly investigated in recent years, little is still known about the diversity and composition of egg-associated microbiomes. In this study, we used high-throughput amplicon sequencing and quantitative PCR to get a better understanding of the microbiome of insect eggs and how they are established using the Southern green stinkbug Nezara viridula (L.) (Hemiptera: Pentatomidae) as a study object. First, to determine the bacterial community composition, egg masses from two natural populations in Belgium and Italy were examined. Subsequently, microbial community establishment was assessed by studying stinkbug eggs of different ages obtained from laboratory strains (unlaid eggs collected from the ovaries, eggs less than 24 h old, and eggs collected 4 days after oviposition). Both the external and internal egg-associated microbiomes were analyzed by investigating egg washes and surface-sterilized washed eggs, respectively. Eggs from the ovaries were completely devoid of bacteria, indicating that egg-associated bacteria were deposited on the eggs during or after oviposition. The bacterial diversity of deposited eggs was very low, with on average 6.1 zero-radius operational taxonomic units (zOTUs) in the external microbiome and 1.2 zOTUs in internal samples of egg masses collected from the field. Bacterial community composition and density did not change significantly over time, suggesting limited bacterial growth. A Pantoea-like symbiont previously found in the midgut of N. viridula was found in every sample and generally occurred at high relative and absolute densities, especially in the internal egg samples. Additionally, some eggs harbored a Sodalis symbiont, which has previously been found in the abdomen of several insects, but so far not in N. viridula populations. We conclude that the egg-associated bacterial microbiome of N. viridula is species-poor and dominated by a few symbionts, particularly the species-specific obligate Pantoea-like symbiont.
{"title":"Diversity and composition of the microbiome associated with eggs of the Southern green stinkbug, Nezara viridula (Hemiptera: Pentatomidae)","authors":"Margot W. J. Geerinck, Sara Van Hee, Gabriele Gloder, Sam Crauwels, Stefano Colazza, Hans Jacquemyn, Antonino Cusumano, Bart Lievens","doi":"10.1002/mbo3.1337","DOIUrl":"10.1002/mbo3.1337","url":null,"abstract":"<p>Although microbial communities of insects from larval to adult stage have been increasingly investigated in recent years, little is still known about the diversity and composition of egg-associated microbiomes. In this study, we used high-throughput amplicon sequencing and quantitative PCR to get a better understanding of the microbiome of insect eggs and how they are established using the Southern green stinkbug <i>Nezara viridula</i> (L.) (Hemiptera: Pentatomidae) as a study object. First, to determine the bacterial community composition, egg masses from two natural populations in Belgium and Italy were examined. Subsequently, microbial community establishment was assessed by studying stinkbug eggs of different ages obtained from laboratory strains (unlaid eggs collected from the ovaries, eggs less than 24 h old, and eggs collected 4 days after oviposition). Both the external and internal egg-associated microbiomes were analyzed by investigating egg washes and surface-sterilized washed eggs, respectively. Eggs from the ovaries were completely devoid of bacteria, indicating that egg-associated bacteria were deposited on the eggs during or after oviposition. The bacterial diversity of deposited eggs was very low, with on average 6.1 zero-radius operational taxonomic units (zOTUs) in the external microbiome and 1.2 zOTUs in internal samples of egg masses collected from the field. Bacterial community composition and density did not change significantly over time, suggesting limited bacterial growth. A <i>Pantoea</i>-like symbiont previously found in the midgut of <i>N. viridula</i> was found in every sample and generally occurred at high relative and absolute densities, especially in the internal egg samples. Additionally, some eggs harbored a <i>Sodalis</i> symbiont, which has previously been found in the abdomen of several insects, but so far not in <i>N. viridula</i> populations. We conclude that the egg-associated bacterial microbiome of <i>N. viridula</i> is species-poor and dominated by a few symbionts, particularly the species-specific obligate <i>Pantoea</i>-like symbiont.</p>","PeriodicalId":18573,"journal":{"name":"MicrobiologyOpen","volume":"11 6","pages":""},"PeriodicalIF":3.4,"publicationDate":"2022-12-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9728049/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10568688","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Miad Boodaghidizaji, Shreya Milind Athalye, Sukirt Thakur, Ehsan Esmaili, Mohit S. Verma, Arezoo M. Ardekani
Machine learning methods can be used as robust techniques to provide invaluable information for analyzing biological samples in pharmaceutical industries, such as predicting the concentration of viral particles of interest in biological samples. Here, we utilized both convolutional neural networks (CNNs) and random forests (RFs) to predict the concentration of the samples containing measles, mumps, rubella, and varicella-zoster viruses (ProQuad®) based on Raman and absorption spectroscopy. We prepared Raman and absorption spectra data sets with known concentration values, then used the Raman and absorption signals individually and together to train RFs and CNNs. We demonstrated that both RFs and CNNs can make predictions with R2 values as high as 95%. We proposed two different networks to jointly use the Raman and absorption spectra, where our results demonstrated that concatenating the Raman and absorption data increases the prediction accuracy compared to using either Raman or absorption spectrum alone. Additionally, we further verified the advantage of using joint Raman-absorption with principal component analysis. Furthermore, our method can be extended to characterize properties other than concentration, such as the type of viral particles.
{"title":"Characterizing viral samples using machine learning for Raman and absorption spectroscopy","authors":"Miad Boodaghidizaji, Shreya Milind Athalye, Sukirt Thakur, Ehsan Esmaili, Mohit S. Verma, Arezoo M. Ardekani","doi":"10.1002/mbo3.1336","DOIUrl":"10.1002/mbo3.1336","url":null,"abstract":"<p>Machine learning methods can be used as robust techniques to provide invaluable information for analyzing biological samples in pharmaceutical industries, such as predicting the concentration of viral particles of interest in biological samples. Here, we utilized both convolutional neural networks (CNNs) and random forests (RFs) to predict the concentration of the samples containing measles, mumps, rubella, and varicella-zoster viruses (ProQuad®) based on Raman and absorption spectroscopy. We prepared Raman and absorption spectra data sets with known concentration values, then used the Raman and absorption signals individually and together to train RFs and CNNs. We demonstrated that both RFs and CNNs can make predictions with <i>R</i><sup>2</sup> values as high as 95%. We proposed two different networks to jointly use the Raman and absorption spectra, where our results demonstrated that concatenating the Raman and absorption data increases the prediction accuracy compared to using either Raman or absorption spectrum alone. Additionally, we further verified the advantage of using joint Raman-absorption with principal component analysis. Furthermore, our method can be extended to characterize properties other than concentration, such as the type of viral particles.</p>","PeriodicalId":18573,"journal":{"name":"MicrobiologyOpen","volume":"11 6","pages":""},"PeriodicalIF":3.4,"publicationDate":"2022-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9721089/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10863228","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Peter Gajdoš, Rodrigo Ledesma-Amaro, Jean-Marc Nicaud, Tristan Rossignol
Dysregulation of lipid metabolism is associated with obesity and metabolic diseases but there is also increasing evidence of a relationship between lipid body excess and cancer. Lipid body synthesis requires diacylglycerol acyltransferases (DGATs) which catalyze the last step of triacylglycerol synthesis from diacylglycerol and acyl-coenzyme A. The DGATs and in particular DGAT2, are therefore considered potential therapeutic targets for the control of these pathologies. Here, the murine and the human DGAT2 were overexpressed in the oleaginous yeast Yarrowia lipolytica deleted for all DGAT activities, to evaluate the functionality of the enzymes in this heterologous host and DGAT activity inhibitors. This work provides evidence that mammalian DGATs expressed in Y. lipolytica are a useful tool for screening chemical libraries to identify potential inhibitors or activators of these enzymes of therapeutic interest.
{"title":"A yeast-based tool for screening mammalian diacylglycerol acyltransferase inhibitors","authors":"Peter Gajdoš, Rodrigo Ledesma-Amaro, Jean-Marc Nicaud, Tristan Rossignol","doi":"10.1002/mbo3.1334","DOIUrl":"10.1002/mbo3.1334","url":null,"abstract":"<p>Dysregulation of lipid metabolism is associated with obesity and metabolic diseases but there is also increasing evidence of a relationship between lipid body excess and cancer. Lipid body synthesis requires diacylglycerol acyltransferases (DGATs) which catalyze the last step of triacylglycerol synthesis from diacylglycerol and acyl-coenzyme A. The DGATs and in particular DGAT2, are therefore considered potential therapeutic targets for the control of these pathologies. Here, the murine and the human DGAT2 were overexpressed in the oleaginous yeast <i>Yarrowia lipolytica</i> deleted for all DGAT activities, to evaluate the functionality of the enzymes in this heterologous host and DGAT activity inhibitors. This work provides evidence that mammalian DGATs expressed in <i>Y. lipolytica</i> are a useful tool for screening chemical libraries to identify potential inhibitors or activators of these enzymes of therapeutic interest.</p>","PeriodicalId":18573,"journal":{"name":"MicrobiologyOpen","volume":"11 6","pages":""},"PeriodicalIF":3.4,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9716225/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10568690","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pseudomonas fluorescens, strains L124, L228, L321, and the positive control strain F113 used in this study, produce compounds associated with plant growth promotion, biocontrol, antimicrobial and antiviral activity, and adaptation to stresses. These bacterial strains were tested in vitro and in vivo in tomato plants, to determine their potential role in Meloidogyne javanica suppression. In laboratory experiments, only 2% of M. javanica eggs hatched when exposed to the metabolites of each bacterial strain. Additionally, 100% M. javanica J2 mortality was recorded when nematodes were exposed to the metabolites of F113 and L228. In greenhouse experiments, M. javanica infected tomato plants, which were also inoculated with the bacterial strains F113 and L124, displayed the highest biomass (height, number of leaves, fresh and dry weight) of all bacterial treatments tested. Results from the development and induced systemic resistance experiments indicated that the bacterial strains F113 and L321 had the most effective biocontrol capacity over nematode infection, delayed nematode development (J3/J4, adults and galls), and reduced nematode fecundity. In addition, these results indicated that the bacterial strain L124 is an effective plant growth promoter of tomato plants. Furthermore, it was determined that the bacterial strain L321 was capable of M. javanica biocontrol. P. fluorescens F113 was effective at both increasing tomato plant biomass and M. javanica biocontrol. In an agricultural context, applying successional drenches with these beneficial plant growth promoting rhizobacteria would ensure bacteria viability in the rhizosphere of the plants, encourage positive plant bacterial interactions and increase biocontrol against M. javanica.
{"title":"Observations on the interaction between plant growth-promoting bacteria and the root-knot nematode Meloidogyne javanica","authors":"Aoife Egan, Thomais Kakouli-Duarte","doi":"10.1002/mbo3.1319","DOIUrl":"10.1002/mbo3.1319","url":null,"abstract":"<p><i>Pseudomonas fluorescens</i>, strains L124, L228, L321, and the positive control strain F113 used in this study, produce compounds associated with plant growth promotion, biocontrol, antimicrobial and antiviral activity, and adaptation to stresses. These bacterial strains were tested in vitro and in vivo in tomato plants, to determine their potential role in <i>Meloidogyne javanica</i> suppression. In laboratory experiments, only 2% of <i>M. javanica</i> eggs hatched when exposed to the metabolites of each bacterial strain. Additionally, 100% <i>M. javanica</i> J2 mortality was recorded when nematodes were exposed to the metabolites of F113 and L228. In greenhouse experiments, <i>M. javanica</i> infected tomato plants, which were also inoculated with the bacterial strains F113 and L124, displayed the highest biomass (height, number of leaves, fresh and dry weight) of all bacterial treatments tested. Results from the development and induced systemic resistance experiments indicated that the bacterial strains F113 and L321 had the most effective biocontrol capacity over nematode infection, delayed nematode development (J3/J4, adults and galls), and reduced nematode fecundity. In addition, these results indicated that the bacterial strain L124 is an effective plant growth promoter of tomato plants. Furthermore, it was determined that the bacterial strain L321 was capable of <i>M. javanica</i> biocontrol. <i>P. fluorescens</i> F113 was effective at both increasing tomato plant biomass and <i>M. javanica</i> biocontrol. In an agricultural context, applying successional drenches with these beneficial plant growth promoting rhizobacteria would ensure bacteria viability in the rhizosphere of the plants, encourage positive plant bacterial interactions and increase biocontrol against <i>M. javanica</i>.</p>","PeriodicalId":18573,"journal":{"name":"MicrobiologyOpen","volume":"11 6","pages":""},"PeriodicalIF":3.4,"publicationDate":"2022-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9701088/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10863227","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Floyd G. Adsit Jr, Thomas A. Randall, Jacqueline Locklear, David M. Kurtz
Escherichia coli pathogenic variants (pathovars) are generally characterized by defined virulence traits and are susceptible to the evolution of hybridized identities due to the considerable plasticity of the E. coli genome. We have isolated a strain from a purified diet intended for research animals that further demonstrates the ability of E. coli to acquire novel genetic elements leading potentially to emergent new pathovars. Utilizing next generation sequencing to obtain a whole genome profile, we report an atypical strain of E. coli, EcoFA807-17, possessing a tetrathionate reductase (ttr) operon, which enables the utilization of tetrathionate as an electron acceptor, thus facilitating respiration in anaerobic environments such as the mammalian gut. The ttr operon is a potent virulence factor for several enteric pathogens, most prominently Salmonella enterica. However, the presence of chromosomally integrated tetrathionate reductase genes does not appear to have been previously reported in wild-type E. coli or Shigella. Accordingly, it is possible that the appearance of this virulence factor may signal the evolution of new mechanisms of pathogenicity in E. coli and Shigella and may potentially alter the effectiveness of existing assays using tetrathionate reductase as a unique marker for the detection of Salmonella enterica.
{"title":"The emergence of the tetrathionate reductase operon in the Escherichia coli/Shigella pan-genome","authors":"Floyd G. Adsit Jr, Thomas A. Randall, Jacqueline Locklear, David M. Kurtz","doi":"10.1002/mbo3.1333","DOIUrl":"10.1002/mbo3.1333","url":null,"abstract":"<p><i>Escherichia coli</i> pathogenic variants (pathovars) are generally characterized by defined virulence traits and are susceptible to the evolution of hybridized identities due to the considerable plasticity of the <i>E. coli</i> genome. We have isolated a strain from a purified diet intended for research animals that further demonstrates the ability of <i>E. coli</i> to acquire novel genetic elements leading potentially to emergent new pathovars. Utilizing next generation sequencing to obtain a whole genome profile, we report an atypical strain of <i>E. coli</i>, EcoFA807-17, possessing a tetrathionate reductase (<i>ttr</i>) operon, which enables the utilization of tetrathionate as an electron acceptor, thus facilitating respiration in anaerobic environments such as the mammalian gut. The <i>ttr</i> operon is a potent virulence factor for several enteric pathogens, most prominently <i>Salmonella enterica</i>. However, the presence of chromosomally integrated tetrathionate reductase genes does not appear to have been previously reported in wild-type <i>E. coli</i> or <i>Shigella</i>. Accordingly, it is possible that the appearance of this virulence factor may signal the evolution of new mechanisms of pathogenicity in <i>E. coli</i> and <i>Shigella</i> and may potentially alter the effectiveness of existing assays using tetrathionate reductase as a unique marker for the detection of <i>Salmonella enterica</i>.</p>","PeriodicalId":18573,"journal":{"name":"MicrobiologyOpen","volume":"11 6","pages":""},"PeriodicalIF":3.4,"publicationDate":"2022-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9638481/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10568689","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}