Pub Date : 2024-09-11DOI: 10.3390/microorganisms12091877
Litao Lin, Guixiang Li, Huiyi Yu, Keming Ma
Soil bacteria, the predominant microbiota in soil, are subject to the law of minimum and the law of tolerance, but the assembly patterns of soil bacteria in response to environmental factors remain far from clear. Here, we took advantage of an altitudinal gradient (1020–1770 asl) in oak-dominant forests and assessed whether soil bacteria linearly or nonlinearly respond to environmental properties through the changes in the community diversity and composition. We found that soil bacteria decreased with increasing altitude in terms of the species richness and phylogenetic structure, while they were unchanged with increasing altitude in terms of community composition. The species richness was nonlinearly affected by the soil pH (19.9%), C:N ratio (14.3%), SOC (11.4%), and silt+clay content (9.9%). Specifically, the species richness peaked at a pH of 5.5–6.5, and an SOC of 25–50 g kg−1, and it showed abrupt decreases and increases at a C:N ratio of 14.5 and a silt+clay content of 70%. The community composition was significantly affected by the soil pH (28.2%), then by the SOC (3.6%), available phosphorus (1.0%), and silt+clay content (0.5%), and it showed less turnovers at a pH of 6.0, SOC of 50 g kg−1, and available phosphorus > 3.0 g kg−1. These findings imply that environmental filtering processes nonlinearly shape bacterial communities.
{"title":"PH Nonlinearly Dominates Soil Bacterial Community Assembly along an Altitudinal Gradient in Oak-Dominant Forests","authors":"Litao Lin, Guixiang Li, Huiyi Yu, Keming Ma","doi":"10.3390/microorganisms12091877","DOIUrl":"https://doi.org/10.3390/microorganisms12091877","url":null,"abstract":"Soil bacteria, the predominant microbiota in soil, are subject to the law of minimum and the law of tolerance, but the assembly patterns of soil bacteria in response to environmental factors remain far from clear. Here, we took advantage of an altitudinal gradient (1020–1770 asl) in oak-dominant forests and assessed whether soil bacteria linearly or nonlinearly respond to environmental properties through the changes in the community diversity and composition. We found that soil bacteria decreased with increasing altitude in terms of the species richness and phylogenetic structure, while they were unchanged with increasing altitude in terms of community composition. The species richness was nonlinearly affected by the soil pH (19.9%), C:N ratio (14.3%), SOC (11.4%), and silt+clay content (9.9%). Specifically, the species richness peaked at a pH of 5.5–6.5, and an SOC of 25–50 g kg−1, and it showed abrupt decreases and increases at a C:N ratio of 14.5 and a silt+clay content of 70%. The community composition was significantly affected by the soil pH (28.2%), then by the SOC (3.6%), available phosphorus (1.0%), and silt+clay content (0.5%), and it showed less turnovers at a pH of 6.0, SOC of 50 g kg−1, and available phosphorus > 3.0 g kg−1. These findings imply that environmental filtering processes nonlinearly shape bacterial communities.","PeriodicalId":18667,"journal":{"name":"Microorganisms","volume":null,"pages":null},"PeriodicalIF":4.5,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142203410","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-11DOI: 10.3390/microorganisms12091873
Yingying Yang, Fangfang Ci, Ailing Xu, Xijian Zhang, Ning Ding, Nianxin Wan, Yuanyuan Lv, Zhiwen Song
Inter-basin water transfer projects, such as the Yellow River to Qingdao Water Diversion Project (YQWD), are essential for addressing water scarcity, but impact local aquatic ecosystems. This study investigates the seasonal characteristics of eukaryotic microbial communities in the Jihongtan Reservoir, the main water-receiving body of YQWD, over a one-year period using 18S rDNA amplicon sequencing. The results showed that the eukaryotic microbial diversity did not exhibit significant seasonal variation (p > 0.05), but there was a notable variance in the community structure (p < 0.05). Arthropoda and Paracyclopina, representing the most dominant phylum and the most dominant genus, respectively, both exhibited the lowest abundance during the winter. The Chlorophyta, as the second-dominant phylum, demonstrates its higher abundance in the spring and winter. The Mantel test and PLS-PM (Partial Least Squares Path Modeling) revealed that water temperature (WT), dissolved oxygen (DO), and pH influenced the seasonal dynamic of eukaryotic microbial communities significantly, of which WT was the primary driving factor. In addition to environmental factors, water diversion is likely to be an important influencing factor. The results of the co-occurrence network and robustness suggested that the spring network is the most complex and exhibits the highest stability. Moreover, keystone taxa within networks have been identified, revealing that these key groups encompass both abundant and rare species, with specificity to different seasons. These insights are vital for understanding the seasonal variation of microbial communities in the Jihongtan Reservoir during ongoing water diversions.
{"title":"Seasonal Dynamics of Eukaryotic Microbial Communities in the Water-Receiving Reservoir of the Long-Distance Water Diversion Project, China","authors":"Yingying Yang, Fangfang Ci, Ailing Xu, Xijian Zhang, Ning Ding, Nianxin Wan, Yuanyuan Lv, Zhiwen Song","doi":"10.3390/microorganisms12091873","DOIUrl":"https://doi.org/10.3390/microorganisms12091873","url":null,"abstract":"Inter-basin water transfer projects, such as the Yellow River to Qingdao Water Diversion Project (YQWD), are essential for addressing water scarcity, but impact local aquatic ecosystems. This study investigates the seasonal characteristics of eukaryotic microbial communities in the Jihongtan Reservoir, the main water-receiving body of YQWD, over a one-year period using 18S rDNA amplicon sequencing. The results showed that the eukaryotic microbial diversity did not exhibit significant seasonal variation (p > 0.05), but there was a notable variance in the community structure (p < 0.05). Arthropoda and Paracyclopina, representing the most dominant phylum and the most dominant genus, respectively, both exhibited the lowest abundance during the winter. The Chlorophyta, as the second-dominant phylum, demonstrates its higher abundance in the spring and winter. The Mantel test and PLS-PM (Partial Least Squares Path Modeling) revealed that water temperature (WT), dissolved oxygen (DO), and pH influenced the seasonal dynamic of eukaryotic microbial communities significantly, of which WT was the primary driving factor. In addition to environmental factors, water diversion is likely to be an important influencing factor. The results of the co-occurrence network and robustness suggested that the spring network is the most complex and exhibits the highest stability. Moreover, keystone taxa within networks have been identified, revealing that these key groups encompass both abundant and rare species, with specificity to different seasons. These insights are vital for understanding the seasonal variation of microbial communities in the Jihongtan Reservoir during ongoing water diversions.","PeriodicalId":18667,"journal":{"name":"Microorganisms","volume":null,"pages":null},"PeriodicalIF":4.5,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142203409","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-11DOI: 10.3390/microorganisms12091875
Milagros Muñoz-Chimeno, Nazaret Díaz-Sánchez, Lucía Morago, Vanessa Rodríguez-Paredes, Silvia Barturen, Álvaro Rodríguez-Recio, Maira Alejandra García-Lugo, Maria Isabel Zamora, María Mateo, Mónica Sánchez-Martínez, Ana Avellón
HEV antibody detection constitutes the main screening test for HEV infection. The aim of this study is to compare the sensitivity and specificity of four techniques: LIAISON® MUREX DiaSorin anti-HEV IgG and anti-HEV IgM assays, Hepatitis E VIRCLIA® IgM and IgG monotests, WANTAI HEV-IgM and IgG ELISA and VIDAS® anti-HEV IgM and IgG tests in five panels of samples configurated according to the immunoblot (RecomLine, Mikrogen, Neuss, Germany). Anti-HEV IgM sensitivity in the acute phase was 100% in all techniques, while sensitivity, including the immediate convalescence phase, was 96.74% for LIAISON®, 83.14% for VIRCLIA®, 84.78% for WANTAI and 88.04% for VIDAS®. Anti-HEV IgM specificity was 100% for both LIAISON® and VIRCLIA®. Anti-HEV IgM WANTAI agreed with VIRCLIA® with a good Kappa coefficient (κ = 0.71). Anti-HEV IgG post-infection sensitivity was 100% for LIAISON®, VIDAS® and VIRCLIA® and 99% for WANTAI. Anti-HEV IgG specificity reached 97.17% for LIAISON and 88.68% for VIRCLIA®. Our results demonstrated a better capacity of LIAISON® MUREX anti-HEV IgM than that of competitors for detecting acute infections as well as accurate anti-HEV IgG results and in how to resolve them.
HEV 抗体检测是 HEV 感染的主要筛查试验。本研究旨在比较四种技术的灵敏度和特异性：LIAISON® MUREX DiaSorin 抗 HEV IgG 和抗 HEV IgM 检测、戊型肝炎 VIRCLIA® IgM 和 IgG 单项检测、WANTAI HEV-IgM 和 IgG ELISA 以及 VIDAS® 抗 HEV IgM 和 IgG 检测。所有技术在急性期的抗-HEV IgM灵敏度均为100%，而LIAISON®的灵敏度（包括恢复期）为96.74%，VIRCLIA®为83.14%，WANTAI为84.78%，VIDAS®为88.04%。LIAISON® 和 VIRCLIA® 的抗-HEV IgM 特异性均为 100%。抗艾滋病毒 IgM WANTAI 与 VIRCLIA® 的卡帕系数（κ = 0.71）吻合。LIAISON® 、VIDAS® 和 VIRCLIA® 的感染后抗 HEV IgG 敏感性为 100%，WANTAI 为 99%。LIAISON® 和 VIRCLIA® 的抗 HEV IgG 特异性分别为 97.17% 和 88.68%。我们的结果表明，LIAISON® MUREX 抗 HEV IgM 检测急性感染的能力优于同类产品，抗 HEV IgG 检测结果也很准确，并能解决这些问题。
{"title":"Performance Comparison of Four Hepatitis E Antibodies Detection Methods","authors":"Milagros Muñoz-Chimeno, Nazaret Díaz-Sánchez, Lucía Morago, Vanessa Rodríguez-Paredes, Silvia Barturen, Álvaro Rodríguez-Recio, Maira Alejandra García-Lugo, Maria Isabel Zamora, María Mateo, Mónica Sánchez-Martínez, Ana Avellón","doi":"10.3390/microorganisms12091875","DOIUrl":"https://doi.org/10.3390/microorganisms12091875","url":null,"abstract":"HEV antibody detection constitutes the main screening test for HEV infection. The aim of this study is to compare the sensitivity and specificity of four techniques: LIAISON® MUREX DiaSorin anti-HEV IgG and anti-HEV IgM assays, Hepatitis E VIRCLIA® IgM and IgG monotests, WANTAI HEV-IgM and IgG ELISA and VIDAS® anti-HEV IgM and IgG tests in five panels of samples configurated according to the immunoblot (RecomLine, Mikrogen, Neuss, Germany). Anti-HEV IgM sensitivity in the acute phase was 100% in all techniques, while sensitivity, including the immediate convalescence phase, was 96.74% for LIAISON®, 83.14% for VIRCLIA®, 84.78% for WANTAI and 88.04% for VIDAS®. Anti-HEV IgM specificity was 100% for both LIAISON® and VIRCLIA®. Anti-HEV IgM WANTAI agreed with VIRCLIA® with a good Kappa coefficient (κ = 0.71). Anti-HEV IgG post-infection sensitivity was 100% for LIAISON®, VIDAS® and VIRCLIA® and 99% for WANTAI. Anti-HEV IgG specificity reached 97.17% for LIAISON and 88.68% for VIRCLIA®. Our results demonstrated a better capacity of LIAISON® MUREX anti-HEV IgM than that of competitors for detecting acute infections as well as accurate anti-HEV IgG results and in how to resolve them.","PeriodicalId":18667,"journal":{"name":"Microorganisms","volume":null,"pages":null},"PeriodicalIF":4.5,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142203431","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-11DOI: 10.3390/microorganisms12091874
Fabio Scarpa, Ilenia Azzena, Alessandra Ciccozzi, Francesco Branda, Chiara Locci, Maria Perra, Noemi Pascale, Chiara Romano, Giancarlo Ceccarelli, Giuseppe Terrazzano, Pier Luigi Fiori, Massimo Ciccozzi, Marco Casu, Daria Sanna
From 1 January 2022 to 31 May 2024, the World Health Organization (WHO) reported 97,745 laboratory-confirmed Mpox cases, including 203 deaths, across 116 countries. Despite a 2.3% decrease in new cases in May 2024 compared to April 2024, significant regional variations persist. The African Region reported the highest proportion of new cases, while other regions experienced mixed trends. Phylogenomic analyses of the Mpox virus Clade IIb lineage B.1 reveal stable genetic variability with minimal diversification. The Bayesian Skyline Plot indicates a generally stable viral population size with a modest peak in late 2023, followed by a decline. In general, the data indicate that the MPXV outbreak is primarily localized within a few consistent geographic clusters. The virus’s evolution is relatively slow, as indicated by its stable genetic variability, and Clade IIb lineage B.1 does not currently show signs of rapid genetic changes or population growth. The current low level of genetic diversity should not lead to complacency. Ongoing genomic surveillance is essential for effective outbreak management and understanding. This monitoring is crucial for identifying any shifts in the virus’s behavior or transmission, allowing for prompt public health responses and adjustments. In addition, continued vigilance is necessary to detect any new variants that might influence the outbreak’s trajectory.
{"title":"Update of the Genetic Variability of Monkeypox Virus Clade IIb Lineage B.1","authors":"Fabio Scarpa, Ilenia Azzena, Alessandra Ciccozzi, Francesco Branda, Chiara Locci, Maria Perra, Noemi Pascale, Chiara Romano, Giancarlo Ceccarelli, Giuseppe Terrazzano, Pier Luigi Fiori, Massimo Ciccozzi, Marco Casu, Daria Sanna","doi":"10.3390/microorganisms12091874","DOIUrl":"https://doi.org/10.3390/microorganisms12091874","url":null,"abstract":"From 1 January 2022 to 31 May 2024, the World Health Organization (WHO) reported 97,745 laboratory-confirmed Mpox cases, including 203 deaths, across 116 countries. Despite a 2.3% decrease in new cases in May 2024 compared to April 2024, significant regional variations persist. The African Region reported the highest proportion of new cases, while other regions experienced mixed trends. Phylogenomic analyses of the Mpox virus Clade IIb lineage B.1 reveal stable genetic variability with minimal diversification. The Bayesian Skyline Plot indicates a generally stable viral population size with a modest peak in late 2023, followed by a decline. In general, the data indicate that the MPXV outbreak is primarily localized within a few consistent geographic clusters. The virus’s evolution is relatively slow, as indicated by its stable genetic variability, and Clade IIb lineage B.1 does not currently show signs of rapid genetic changes or population growth. The current low level of genetic diversity should not lead to complacency. Ongoing genomic surveillance is essential for effective outbreak management and understanding. This monitoring is crucial for identifying any shifts in the virus’s behavior or transmission, allowing for prompt public health responses and adjustments. In addition, continued vigilance is necessary to detect any new variants that might influence the outbreak’s trajectory.","PeriodicalId":18667,"journal":{"name":"Microorganisms","volume":null,"pages":null},"PeriodicalIF":4.5,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142203408","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-11DOI: 10.3390/microorganisms12091872
Liis Lutter, Aljona Kuzina, Helena Andreson
Sourdough bread production relies on metabolically active starters refreshed daily with flour and water. The stability of sourdough microbial strains is crucial for consistent bread quality. However, many bakeries lack information on the persistence of starter cultures in ongoing sourdough production. Consequently, there is growing interest in identifying microbial strains from regularly used sourdoughs that possess good functional properties and resist changes in the complex growth environment. This study aimed to evaluate the composition and stability of lactic acid bacteria (LAB) in industrial wheat (WS) and rye (RS) sourdoughs propagated over a long period. LAB isolates (n = 66) from both sourdoughs, sampled over four seasons, were identified using phenotypic methods and genotyped via ITS-PCR and ITS-PCR/TaqI restriction analysis. Eight LAB species were detected, with Lactiplantibacillus plantarum being the most dominant and stable. Nineteen distinct LAB genotypes were observed, highlighting significant diversity. The presence of identical LAB genotypes in both sourdoughs suggests microbial transfer through the environment and bakery workers. LAB in RS were found to be more stable than those in WS. These findings underscore the importance of monitoring microbial stability and diversity in industrial sourdough production to maintain consistent bread quality.
{"title":"Genotypic Stability of Lactic Acid Bacteria in Industrial Rye Bread Sourdoughs Assessed by ITS-PCR Analysis","authors":"Liis Lutter, Aljona Kuzina, Helena Andreson","doi":"10.3390/microorganisms12091872","DOIUrl":"https://doi.org/10.3390/microorganisms12091872","url":null,"abstract":"Sourdough bread production relies on metabolically active starters refreshed daily with flour and water. The stability of sourdough microbial strains is crucial for consistent bread quality. However, many bakeries lack information on the persistence of starter cultures in ongoing sourdough production. Consequently, there is growing interest in identifying microbial strains from regularly used sourdoughs that possess good functional properties and resist changes in the complex growth environment. This study aimed to evaluate the composition and stability of lactic acid bacteria (LAB) in industrial wheat (WS) and rye (RS) sourdoughs propagated over a long period. LAB isolates (n = 66) from both sourdoughs, sampled over four seasons, were identified using phenotypic methods and genotyped via ITS-PCR and ITS-PCR/TaqI restriction analysis. Eight LAB species were detected, with Lactiplantibacillus plantarum being the most dominant and stable. Nineteen distinct LAB genotypes were observed, highlighting significant diversity. The presence of identical LAB genotypes in both sourdoughs suggests microbial transfer through the environment and bakery workers. LAB in RS were found to be more stable than those in WS. These findings underscore the importance of monitoring microbial stability and diversity in industrial sourdough production to maintain consistent bread quality.","PeriodicalId":18667,"journal":{"name":"Microorganisms","volume":null,"pages":null},"PeriodicalIF":4.5,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142203406","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-11DOI: 10.3390/microorganisms12091876
Tereza Kodešová, Anna Mašlejová, Eva Vlková, Šárka Musilová, Kristýna Horváthová, Hana Šubrtová Salmonová
Listeria monocytognes is an emerging pathogen responsible for the serious foodborne disease, listeriosis. The commensal gut microbiota is the first line of defense against pathogen internalization. The gut microbiome can be modified by prebiotic substrates, which are frequently added to food products and dietary supplements. Prebiotics should selectively support the growth of beneficial microbes and thus improve host health. Nevertheless, little is known about their effect on the growth of L. monocytogenes. The aim of this study was to evaluate the growth ability of four L. monocytogenes strains, representing the most common serotypes, on prebiotic oligosaccharides (beta-(1,3)-D-glucan, inulin, fructooligosaccharides, galactooligosaccharides, lactulose, raffinose, stachyose and 2′-fucosyllactose and a mixture of human milk oligosaccharides) as a sole carbon source. The results showed that only beta-(1,3)-D-glucan was metabolized by L. monocytogenes. These cell culture data suggest that beta-(1,3)-D-glucan may not be selectively utilized by healthy commensal bacteria, and its role in intestinal pathogen growth warrants further exploration in vivo.
{"title":"In Vitro Utilization of Prebiotics by Listeria monocytogenes","authors":"Tereza Kodešová, Anna Mašlejová, Eva Vlková, Šárka Musilová, Kristýna Horváthová, Hana Šubrtová Salmonová","doi":"10.3390/microorganisms12091876","DOIUrl":"https://doi.org/10.3390/microorganisms12091876","url":null,"abstract":"Listeria monocytognes is an emerging pathogen responsible for the serious foodborne disease, listeriosis. The commensal gut microbiota is the first line of defense against pathogen internalization. The gut microbiome can be modified by prebiotic substrates, which are frequently added to food products and dietary supplements. Prebiotics should selectively support the growth of beneficial microbes and thus improve host health. Nevertheless, little is known about their effect on the growth of L. monocytogenes. The aim of this study was to evaluate the growth ability of four L. monocytogenes strains, representing the most common serotypes, on prebiotic oligosaccharides (beta-(1,3)-D-glucan, inulin, fructooligosaccharides, galactooligosaccharides, lactulose, raffinose, stachyose and 2′-fucosyllactose and a mixture of human milk oligosaccharides) as a sole carbon source. The results showed that only beta-(1,3)-D-glucan was metabolized by L. monocytogenes. These cell culture data suggest that beta-(1,3)-D-glucan may not be selectively utilized by healthy commensal bacteria, and its role in intestinal pathogen growth warrants further exploration in vivo.","PeriodicalId":18667,"journal":{"name":"Microorganisms","volume":null,"pages":null},"PeriodicalIF":4.5,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142203433","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-09DOI: 10.3390/microorganisms12091862
Themba Titus Sigudu, James Wabwire Oguttu, Daniel Nenene Qekwana
Antimicrobial resistance (AMR) poses a significant worldwide health challenge associated with prolonged illnesses, increased healthcare costs, and high mortality rates. The present study examined the patterns and predictors of AMR among human Staphylococcus isolates obtained from diagnostic laboratories in South Africa between 2012 and 2017. This study examined data from 404 217 isolates, assessing resistance rates across different characteristics such as age, sample origin, Staphylococcus species, and study period. The highest resistance was observed against cloxacillin (70.3%), while the lowest resistance was against Colistin (0.1%). A significant (p < 0.05) decreasing trend in AMR was observed over the study period, while a significant increasing temporal trend (p < 0.05) was observed for multidrug resistance (MDR) over the same period. A significant (p < 0.05) association was observed between specimen type, species of organism, and year of isolation with AMR outcome. Significant (p < 0.05) associations were observed between specimen type and season with MDR. The observed high levels of AMR and a growing trend in MDR are concerning for public health. Clinicians should take these findings into account when deciding on therapeutic options. Continued monitoring of AMR among Staphylococcus spp. and judicious use of antimicrobials in human medicine should be promoted.
抗菌药耐药性（AMR）是一项重大的世界性健康挑战，它与病程延长、医疗成本增加和高死亡率有关。本研究考察了 2012 年至 2017 年间从南非诊断实验室获得的人类葡萄球菌分离物中的 AMR 模式和预测因素。本研究检查了来自 404 217 株分离物的数据，评估了不同特征（如年龄、样本来源、葡萄球菌种类和研究时期）的耐药率。对氯唑西林的耐药性最高（70.3%），而对可乐定的耐药性最低（0.1%）。在研究期间，AMR 呈明显下降趋势（p < 0.05），而在同一时期，耐多药（MDR）呈明显上升趋势（p < 0.05）。标本类型、生物种类和分离年份与 AMR 结果之间存在明显关联（p < 0.05）。标本类型和季节与 MDR 之间也存在明显的关联（p < 0.05）。所观察到的 AMR 高水平和 MDR 不断增长的趋势令人担忧公共卫生问题。临床医生在决定治疗方案时应考虑到这些发现。应继续监测葡萄球菌中的 AMR，并在人类医疗中合理使用抗菌药物。
{"title":"Antimicrobial Resistance of Staphylococcus spp. from Human Specimens Submitted to Diagnostic Laboratories in South Africa, 2012–2017","authors":"Themba Titus Sigudu, James Wabwire Oguttu, Daniel Nenene Qekwana","doi":"10.3390/microorganisms12091862","DOIUrl":"https://doi.org/10.3390/microorganisms12091862","url":null,"abstract":"Antimicrobial resistance (AMR) poses a significant worldwide health challenge associated with prolonged illnesses, increased healthcare costs, and high mortality rates. The present study examined the patterns and predictors of AMR among human Staphylococcus isolates obtained from diagnostic laboratories in South Africa between 2012 and 2017. This study examined data from 404 217 isolates, assessing resistance rates across different characteristics such as age, sample origin, Staphylococcus species, and study period. The highest resistance was observed against cloxacillin (70.3%), while the lowest resistance was against Colistin (0.1%). A significant (p < 0.05) decreasing trend in AMR was observed over the study period, while a significant increasing temporal trend (p < 0.05) was observed for multidrug resistance (MDR) over the same period. A significant (p < 0.05) association was observed between specimen type, species of organism, and year of isolation with AMR outcome. Significant (p < 0.05) associations were observed between specimen type and season with MDR. The observed high levels of AMR and a growing trend in MDR are concerning for public health. Clinicians should take these findings into account when deciding on therapeutic options. Continued monitoring of AMR among Staphylococcus spp. and judicious use of antimicrobials in human medicine should be promoted.","PeriodicalId":18667,"journal":{"name":"Microorganisms","volume":null,"pages":null},"PeriodicalIF":4.5,"publicationDate":"2024-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142203412","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-09DOI: 10.3390/microorganisms12091866
Meng Zhang, Xiang Li, Adelumola Oladeinde, Michael Rothrock, Anthony Pokoo-Aikins, Gregory Zock
Networks are widely used to represent relationships between objects, including microorganisms within ecosystems, based on high-throughput sequencing data. However, challenges arise with appropriate statistical algorithms, handling of rare taxa, excess zeros in compositional data, and interpretation. This work introduces a novel Slope-Matrix-Graph (SMG) algorithm to identify microbiome correlations primarily based on slope-based distance calculations. SMG effectively handles any proportion of zeros in compositional data and involves: (1) searching for correlated relationships (e.g., positive and negative directions of changes) based on a “target of interest” within a setting, and (2) quantifying graph changes via slope-based distances between objects. Evaluations on simulated datasets demonstrated SMG’s ability to accurately cluster microbes into distinct positive/negative correlation groups, outperforming methods like Bray–Curtis and SparCC in both sensitivity and specificity. Moreover, SMG demonstrated superior accuracy in detecting differential abundance (DA) compared to ZicoSeq and ANCOM-BC2, making it a robust tool for microbiome analysis. A key advantage is SMG’s natural capacity to analyze zero-inflated compositional data without transformations. Overall, this simple yet powerful algorithm holds promise for diverse microbiome analysis applications.
{"title":"A Novel Slope-Matrix-Graph Algorithm to Analyze Compositional Microbiome Data","authors":"Meng Zhang, Xiang Li, Adelumola Oladeinde, Michael Rothrock, Anthony Pokoo-Aikins, Gregory Zock","doi":"10.3390/microorganisms12091866","DOIUrl":"https://doi.org/10.3390/microorganisms12091866","url":null,"abstract":"Networks are widely used to represent relationships between objects, including microorganisms within ecosystems, based on high-throughput sequencing data. However, challenges arise with appropriate statistical algorithms, handling of rare taxa, excess zeros in compositional data, and interpretation. This work introduces a novel Slope-Matrix-Graph (SMG) algorithm to identify microbiome correlations primarily based on slope-based distance calculations. SMG effectively handles any proportion of zeros in compositional data and involves: (1) searching for correlated relationships (e.g., positive and negative directions of changes) based on a “target of interest” within a setting, and (2) quantifying graph changes via slope-based distances between objects. Evaluations on simulated datasets demonstrated SMG’s ability to accurately cluster microbes into distinct positive/negative correlation groups, outperforming methods like Bray–Curtis and SparCC in both sensitivity and specificity. Moreover, SMG demonstrated superior accuracy in detecting differential abundance (DA) compared to ZicoSeq and ANCOM-BC2, making it a robust tool for microbiome analysis. A key advantage is SMG’s natural capacity to analyze zero-inflated compositional data without transformations. Overall, this simple yet powerful algorithm holds promise for diverse microbiome analysis applications.","PeriodicalId":18667,"journal":{"name":"Microorganisms","volume":null,"pages":null},"PeriodicalIF":4.5,"publicationDate":"2024-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142203463","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-09DOI: 10.3390/microorganisms12091863
Jeremy W. Prokop, Sheryl Alberta, Martin Witteveen-Lane, Samantha Pell, Hosam A. Farag, Disha Bhargava, Robert M. Vaughan, Austin Frisch, Jacob Bauss, Humza Bhatti, Sanjana Arora, Charitha Subrahmanya, David Pearson, Austin Goodyke, Mason Westgate, Taylor W. Cook, Jackson T. Mitchell, Jacob Zieba, Matthew D. Sims, Adam Underwood, Habiba Hassouna, Surender Rajasekaran, Maximiliano A. Tamae Kakazu, Dave Chesla, Rosemary Olivero, Adam J. Caulfield
As of 2024, SARS-CoV-2 continues to propagate and drift as an endemic virus, impacting healthcare for years. The largest sequencing initiative for any species was initiated to combat the virus, tracking changes over time at a full virus base-pair resolution. The SARS-CoV-2 sequencing represents a unique opportunity to understand selective pressures and viral evolution but requires cross-disciplinary approaches from epidemiology to functional protein biology. Within this work, we integrate a two-year genotyping window with structural biology to explore the selective pressures of SARS-CoV-2 on protein insights. Although genotype and the Spike (Surface Glycoprotein) protein continue to drift, most SARS-CoV-2 proteins have had few amino acid alterations. Within Spike, the high drift rate of amino acids involved in antibody evasion also corresponds to changes within the ACE2 binding pocket that have undergone multiple changes that maintain functional binding. The genotyping suggests selective pressure for receptor specificity that could also confer changes in viral risk. Mapping of amino acid changes to the structures of the SARS-CoV-2 co-transcriptional complex (nsp7-nsp14), nsp3 (papain-like protease), and nsp5 (cysteine protease) proteins suggest they remain critical factors for drug development that will be sustainable, unlike those strategies targeting Spike.
{"title":"SARS-CoV-2 Genotyping Highlights the Challenges in Spike Protein Drift Independent of Other Essential Proteins","authors":"Jeremy W. Prokop, Sheryl Alberta, Martin Witteveen-Lane, Samantha Pell, Hosam A. Farag, Disha Bhargava, Robert M. Vaughan, Austin Frisch, Jacob Bauss, Humza Bhatti, Sanjana Arora, Charitha Subrahmanya, David Pearson, Austin Goodyke, Mason Westgate, Taylor W. Cook, Jackson T. Mitchell, Jacob Zieba, Matthew D. Sims, Adam Underwood, Habiba Hassouna, Surender Rajasekaran, Maximiliano A. Tamae Kakazu, Dave Chesla, Rosemary Olivero, Adam J. Caulfield","doi":"10.3390/microorganisms12091863","DOIUrl":"https://doi.org/10.3390/microorganisms12091863","url":null,"abstract":"As of 2024, SARS-CoV-2 continues to propagate and drift as an endemic virus, impacting healthcare for years. The largest sequencing initiative for any species was initiated to combat the virus, tracking changes over time at a full virus base-pair resolution. The SARS-CoV-2 sequencing represents a unique opportunity to understand selective pressures and viral evolution but requires cross-disciplinary approaches from epidemiology to functional protein biology. Within this work, we integrate a two-year genotyping window with structural biology to explore the selective pressures of SARS-CoV-2 on protein insights. Although genotype and the Spike (Surface Glycoprotein) protein continue to drift, most SARS-CoV-2 proteins have had few amino acid alterations. Within Spike, the high drift rate of amino acids involved in antibody evasion also corresponds to changes within the ACE2 binding pocket that have undergone multiple changes that maintain functional binding. The genotyping suggests selective pressure for receptor specificity that could also confer changes in viral risk. Mapping of amino acid changes to the structures of the SARS-CoV-2 co-transcriptional complex (nsp7-nsp14), nsp3 (papain-like protease), and nsp5 (cysteine protease) proteins suggest they remain critical factors for drug development that will be sustainable, unlike those strategies targeting Spike.","PeriodicalId":18667,"journal":{"name":"Microorganisms","volume":null,"pages":null},"PeriodicalIF":4.5,"publicationDate":"2024-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142203428","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-09DOI: 10.3390/microorganisms12091864
Diantong Li, Zhenjiang Liu, Xueni Fan, Tingting Zhao, Dongxu Wen, Xiaodan Huang, Bin Li
Inflammatory bowel disease (IBD), encompassing ulcerative colitis (UC) and Crohn’s disease (CD), arises from intricate interactions involving genetics, environment, and pharmaceuticals with an ambiguous pathogenic mechanism. Recently, there has been an increasing utilization of lactic acid bacteria (LAB) in managing IBD, attributed to their ability to enhance intestinal barrier function, mitigate inflammatory responses, and modulate gut microbiota. This review initiates by elucidating the pathogenesis of IBD and its determinants, followed by an exploration of the mechanisms underlying LAB therapy in UC and CD. Special attention is directed towards their influence on intestinal barrier function and homeostasis regulated by gut microbiota. Furthermore, the review investigates the complex interplay among pivotal gut microbiota, metabolites, and pathways associated with inflammation. Moreover, it underscores the limitations of LAB in treating IBD, particularly in light of their varying roles in UC and CD. This comprehensive analysis endeavors to offer insights for the optimized application of LAB in IBD therapy.
{"title":"Lactic Acid Bacteria–Gut-Microbiota-Mediated Intervention towards Inflammatory Bowel Disease","authors":"Diantong Li, Zhenjiang Liu, Xueni Fan, Tingting Zhao, Dongxu Wen, Xiaodan Huang, Bin Li","doi":"10.3390/microorganisms12091864","DOIUrl":"https://doi.org/10.3390/microorganisms12091864","url":null,"abstract":"Inflammatory bowel disease (IBD), encompassing ulcerative colitis (UC) and Crohn’s disease (CD), arises from intricate interactions involving genetics, environment, and pharmaceuticals with an ambiguous pathogenic mechanism. Recently, there has been an increasing utilization of lactic acid bacteria (LAB) in managing IBD, attributed to their ability to enhance intestinal barrier function, mitigate inflammatory responses, and modulate gut microbiota. This review initiates by elucidating the pathogenesis of IBD and its determinants, followed by an exploration of the mechanisms underlying LAB therapy in UC and CD. Special attention is directed towards their influence on intestinal barrier function and homeostasis regulated by gut microbiota. Furthermore, the review investigates the complex interplay among pivotal gut microbiota, metabolites, and pathways associated with inflammation. Moreover, it underscores the limitations of LAB in treating IBD, particularly in light of their varying roles in UC and CD. This comprehensive analysis endeavors to offer insights for the optimized application of LAB in IBD therapy.","PeriodicalId":18667,"journal":{"name":"Microorganisms","volume":null,"pages":null},"PeriodicalIF":4.5,"publicationDate":"2024-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142203415","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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