cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.24329709.v1
title: Uncovering the hidden threat: The widespread presence of chromosome-borne accessory genetic elements and novel antibiotic resistance genetic environments in <i>Aeromonas</i>

description: The emergence of antibiotic-resistant <i>Aeromonas</i> strains in clinical settings has presented an escalating burden on human and public health. The dissemination of antibiotic resistance in <i>Aeromonas</i> is predominantly facilitated by chromosome-borne accessory genetic elements, although the existing literature on this subject remains limited. Hence, the primary objective of this study is to comprehensively investigate the genomic characteristics of chromosome-borne accessory genetic elements in <i>Aeromonas</i>. Moreover, the study aims to uncover novel genetic environments associated with antibiotic resistance on these elements. <i>Aeromonas</i> were screened from nonduplicated strains collected from two tertiary hospitals in China. Complete sequencing and population genetics analysis were performed. BLAST analysis was employed to identify related elements. All newly identified elements were subjected to detailed sequence annotation, dissection, and comparison. We identified and newly designated 19 chromosomal elements, including 18 integrative and mobilizable elements (IMEs) that could be classified into four categories: Tn<i>6737</i>-related, Tn<i>6836</i>-related, Tn<i>6840</i>-related, and Tn<i>6844a</i>-related IMEs. Each class exhibited a distinct pattern in the types of resistance genes carried by the IMEs. Several novel antibiotic resistance genetic environments were uncovered in these elements. Notably, we report the first identification of the <i>bla</i><sub>OXA-10</sub> gene and <i>bla</i><sub>VEB-1</sub> gene in clinical <i>A. veronii</i> genome, the first presence of a <i>tetA</i>(E)–<i>tetR</i>(E) resistance gene environment within the backbone region in IMEs, and a new <i>mcr-3.15</i> resistance gene environment. The implications of these findings are substantial, as they provide new insights into the evolution, structure, and dissemination of chromosomal-borne accessory elements.
DOI: 10.6084/m9.figshare.22040283
title: The major role of <i>sarA</i> in limiting <i>Staphylococcus aureus</i> extracellular protease production <i>in vitro</i> is correlated with decreased virulence in diverse clinical isolates in osteomyelitis

description: We previously demonstrated that MgrA, SarA, SarR, SarS, SarZ, and Rot bind at least three of the four promoters associated with genes encoding primary extracellular proteases in <i>Staphylococcus aureus</i> (Aur, ScpA, SspA/SspB, SplA-F). We also showed that mutation of <i>sarA</i> results in a greater increase in protease production, and decrease in biofilm formation, than mutation of the loci encoding any of these other proteins. However, these conclusions were based on <i>in vitro</i> studies. Thus, the goal of the experiments reported here was to determine the relative impact of the regulatory loci encoding these proteins <i>in vivo</i>. To this end, we compared the virulence of <i>mgrA</i>, <i>sarA</i>, <i>sarR</i>, <i>sarS</i>, <i>sarZ</i>, and <i>rot</i> mutants in a murine osteomyelitis model. Mutants were generated in the methicillin-resistant USA300 strain LAC and the methicillin-sensitive USA200 strain UAMS-1, which was isolated directly from the bone of an osteomyelitis patient during surgical debridement. Mutation of <i>mgrA</i> and <i>rot</i> limited virulence to a statistically significant extent in UAMS-1, but not in LAC, while the <i>sarA</i> mutant exhibited reduced virulence in both strains. The reduced virulence of the <i>sarA</i> mutant was correlated with reduced cytotoxicity for osteoblasts and osteoclasts, reduced biofilm formation, and reduced sensitivity to the antimicrobial peptide indolicidin, all of which were directly attributable to increased protease production in both LAC and UAMS-1. These results illustrate the importance of considering diverse clinical isolates when evaluating the impact of regulatory mutations on virulence and demonstrate the significance of SarA in limiting protease production <i>in vivo</i> in <i>S. aureus</i>.
DOI: 10.6084/m9.figshare.22040283.v1
title: The major role of <i>sarA</i> in limiting <i>Staphylococcus aureus</i> extracellular protease production <i>in vitro</i> is correlated with decreased virulence in diverse clinical isolates in osteomyelitis

description: We previously demonstrated that MgrA, SarA, SarR, SarS, SarZ, and Rot bind at least three of the four promoters associated with genes encoding primary extracellular proteases in <i>Staphylococcus aureus</i> (Aur, ScpA, SspA/SspB, SplA-F). We also showed that mutation of <i>sarA</i> results in a greater increase in protease production, and decrease in biofilm formation, than mutation of the loci encoding any of these other proteins. However, these conclusions were based on <i>in vitro</i> studies. Thus, the goal of the experiments reported here was to determine the relative impact of the regulatory loci encoding these proteins <i>in vivo</i>. To this end, we compared the virulence of <i>mgrA</i>, <i>sarA</i>, <i>sarR</i>, <i>sarS</i>, <i>sarZ</i>, and <i>rot</i> mutants in a murine osteomyelitis model. Mutants were generated in the methicillin-resistant USA300 strain LAC and the methicillin-sensitive USA200 strain UAMS-1, which was isolated directly from the bone of an osteomyelitis patient during surgical debridement. Mutation of <i>mgrA</i> and <i>rot</i> limited virulence to a statistically significant extent in UAMS-1, but not in LAC, while the <i>sarA</i> mutant exhibited reduced virulence in both strains. The reduced virulence of the <i>sarA</i> mutant was correlated with reduced cytotoxicity for osteoblasts and osteoclasts, reduced biofilm formation, and reduced sensitivity to the antimicrobial peptide indolicidin, all of which were directly attributable to increased protease production in both LAC and UAMS-1. These results illustrate the importance of considering diverse clinical isolates when evaluating the impact of regulatory mutations on virulence and demonstrate the significance of SarA in limiting protease production <i>in vivo</i> in <i>S. aureus</i>.
DOI: 10.6084/m9.figshare.23122888.v2
title: Evolution of <i>Mycobacterium abscessus</i> in the human lung: Cumulative mutations and genomic rearrangement of porin genes in patient isolates

description: <i>Mycobacterium abscessus</i> subspecies <i>massiliense</i> (<i>M.</i> <i>massiliense</i>) is increasingly recognized as an emerging bacterial pathogen, particularly in cystic fibrosis (CF) patients and CF centres’ respiratory outbreaks. We characterized genomic and phenotypic changes in 15 serial isolates from two CF patients (1S and 2B) with chronic pulmonary M. massiliense infection leading to death, as well as four isolates from a CF centre outbreak in which patient 2B was the index case. Comparative genomic analysis revealed the mutations affecting growth rate, metabolism, transport, lipids (loss of glycopeptidolipids), antibiotic susceptibility (macrolides and aminoglycosides resistance), and virulence factors. Mutations in 23S rRNA, <i>mmpL</i>4, porin locus and <i>tet</i>R genes occurred in isolates from both CF patients. Interestingly, we identified two different spontaneous mutation events at the mycobacterial porin locus: a fusion of two tandem porin paralogs in patient 1S and a partial deletion of the first porin paralog in patient 2B. These genomic changes correlated with reduced porin protein expression, diminished <sup>14</sup>C-glucose uptake, slower bacterial growth rates, and enhanced TNF-α induction in mycobacteria-infected THP-1 human cells. Porin gene complementation of porin mutants partly restored <sup>14</sup>C-glucose uptake, growth rate and TNF-α levels to those of intact porin strains. We hypothesize that specific mutations accumulated and maintained over time in <i>M.</i> <i>massiliense</i>, including mutations shared among transmissible strains, collectively lead to more virulent, host adapted lineages in CF patients and other susceptible hosts.
DOI: 10.6084/m9.figshare.23122888
title: Evolution of <i>Mycobacterium abscessus</i> in the human lung: Cumulative mutations and genomic rearrangement of porin genes in patient isolates

description: <i>Mycobacterium abscessus</i> subspecies <i>massiliense</i> (<i>M.</i> <i>massiliense</i>) is increasingly recognized as an emerging bacterial pathogen, particularly in cystic fibrosis (CF) patients and CF centres’ respiratory outbreaks. We characterized genomic and phenotypic changes in 15 serial isolates from two CF patients (1S and 2B) with chronic pulmonary M. massiliense infection leading to death, as well as four isolates from a CF centre outbreak in which patient 2B was the index case. Comparative genomic analysis revealed the mutations affecting growth rate, metabolism, transport, lipids (loss of glycopeptidolipids), antibiotic susceptibility (macrolides and aminoglycosides resistance), and virulence factors. Mutations in 23S rRNA, <i>mmpL</i>4, porin locus and <i>tet</i>R genes occurred in isolates from both CF patients. Interestingly, we identified two different spontaneous mutation events at the mycobacterial porin locus: a fusion of two tandem porin paralogs in patient 1S and a partial deletion of the first porin paralog in patient 2B. These genomic changes correlated with reduced porin protein expression, diminished <sup>14</sup>C-glucose uptake, slower bacterial growth rates, and enhanced TNF-α induction in mycobacteria-infected THP-1 human cells. Porin gene complementation of porin mutants partly restored <sup>14</sup>C-glucose uptake, growth rate and TNF-α levels to those of intact porin strains. We hypothesize that specific mutations accumulated and maintained over time in <i>M.</i> <i>massiliense</i>, including mutations shared among transmissible strains, collectively lead to more virulent, host adapted lineages in CF patients and other susceptible hosts.
DOI: 10.6084/m9.figshare.23122888.v1
title: Evolution of <i>Mycobacterium abscessus</i> in the human lung: Cumulative mutations and genomic rearrangement of porin genes in patient isolates

description: <i>Mycobacterium abscessus</i> subspecies <i>massiliense</i> (<i>M.</i> <i>massiliense</i>) is increasingly recognized as an emerging bacterial pathogen, particularly in cystic fibrosis (CF) patients and CF centres’ respiratory outbreaks. We characterized genomic and phenotypic changes in 15 serial isolates from two CF patients (1S and 2B) with chronic pulmonary M. massiliense infection leading to death, as well as four isolates from a CF centre outbreak in which patient 2B was the index case. Comparative genomic analysis revealed the mutations affecting growth rate, metabolism, transport, lipids (loss of glycopeptidolipids), antibiotic susceptibility (macrolides and aminoglycosides resistance), and virulence factors. Mutations in 23S rRNA, <i>mmpL</i>4, porin locus and <i>tet</i>R genes occurred in isolates from both CF patients. Interestingly, we identified two different spontaneous mutation events at the mycobacterial porin locus: a fusion of two tandem porin paralogs in patient 1S and a partial deletion of the first porin paralog in patient 2B. These genomic changes correlated with reduced porin protein expression, diminished <sup>14</sup>C-glucose uptake, slower bacterial growth rates, and enhanced TNF-α induction in mycobacteria-infected THP-1 human cells. Porin gene complementation of porin mutants partly restored <sup>14</sup>C-glucose uptake, growth rate and TNF-α levels to those of intact porin strains. We hypothesize that specific mutations accumulated and maintained over time in <i>M.</i> <i>massiliense</i>, including mutations shared among transmissible strains, collectively lead to more virulent, host adapted lineages in CF patients and other susceptible hosts.
DOI: 10.6084/m9.figshare.22203091
title: Establishing <i>Galleria mellonella</i> as an invertebrate model for the emerging multi-host pathogen <i>Helcococcus ovis</i>

description: <i>Helcococcus ovis</i> (<i>H. ovis</i>) can cause disease in a broad range of animal hosts, including humans, and has been described as an emerging bacterial pathogen in bovine metritis, mastitis, and endocarditis. In this study, we developed an infection model that showed <i>H. ovis</i> can proliferate in the hemolymph and induce dose-dependent mortality in the invertebrate model organism <i>Galleria mellonella</i> (<i>G. mellonella</i>). We applied the model and identified <i>H. ovis</i> isolates with attenuated virulence originating from the uterus of a healthy post-partum dairy cow (KG38) and hypervirulent isolates (KG37, KG106) originating from the uterus of cows with metritis. Medium virulence isolates were also isolated (KG36, KG104) from the uterus of cows with metritis. A major advantage of this model is that a clear differentiation in induced mortality between <i>H. ovis</i> isolates was detected in just 48 h, resulting in an effective infection model able to identify virulence differences between <i>H. ovis</i> isolates with a short turnaround time. Histopathology showed <i>G. mellonella</i> employs hemocyte-mediated immune responses to <i>H. ovis</i> infection, which are analogous to the innate immune response in cows. In summary, <i>G. mellonella</i> can be used as an invertebrate infection model for the emerging multi-host pathogen <i>Helcococcus ovis.</i>
DOI: 10.6084/m9.figshare.22203091.v1
title: Establishing <i>Galleria mellonella</i> as an invertebrate model for the emerging multi-host pathogen <i>Helcococcus ovis</i>

description: <i>Helcococcus ovis</i> (<i>H. ovis</i>) can cause disease in a broad range of animal hosts, including humans, and has been described as an emerging bacterial pathogen in bovine metritis, mastitis, and endocarditis. In this study, we developed an infection model that showed <i>H. ovis</i> can proliferate in the hemolymph and induce dose-dependent mortality in the invertebrate model organism <i>Galleria mellonella</i> (<i>G. mellonella</i>). We applied the model and identified <i>H. ovis</i> isolates with attenuated virulence originating from the uterus of a healthy post-partum dairy cow (KG38) and hypervirulent isolates (KG37, KG106) originating from the uterus of cows with metritis. Medium virulence isolates were also isolated (KG36, KG104) from the uterus of cows with metritis. A major advantage of this model is that a clear differentiation in induced mortality between <i>H. ovis</i> isolates was detected in just 48 h, resulting in an effective infection model able to identify virulence differences between <i>H. ovis</i> isolates with a short turnaround time. Histopathology showed <i>G. mellonella</i> employs hemocyte-mediated immune responses to <i>H. ovis</i> infection, which are analogous to the innate immune response in cows. In summary, <i>G. mellonella</i> can be used as an invertebrate infection model for the emerging multi-host pathogen <i>Helcococcus ovis.</i>
DOI: 10.6084/m9.figshare.23834559
title: Comparative analysis of genomic characteristics, virulence and fitness of community-associated <i>Staphylococcus aureus</i> ST121 clone causing fatal diseases in China and other CA-MRSA clones

description: The increasing rate of community-associated <i>Staphylococcus aureus</i> (CA-SA) worldwide has aroused global public concern for decades. Although ST121 clone is one of the prevalent CA-SA in China, there is still limited knowledge about it. In this study, we conducted a genomic analysis of 28 CA-SA ST121 isolates from severe bloodstream infection cases and 175 ST121 isolates from the public database. Phylogenetic analysis revealed the consistency and the complexity of global ST121 lineages, and suggested potential cross-country even cross-continental transmission of ST121 isolates. By investigating the virulence and fitness between ST121-CA-methicillin-resistant SA (CA-MRSA) and other CA-MRSA clones, we found that ST121-MRSA exhibits virulence comparable to the highly virulent USA300 clone, exceeding that of the predominant CA-MRSA lineage ST59 in China and the other American CA-MRSA clone MW2. Notably, based on analyses of virulence genes, <i>eta</i>, <i>etb</i>, <i>edin-C</i> and egc were only found in ST121, suggesting that the high virulence of ST121 may be attributed to the combination of these virulence factors encoded by mobile genetic elements. However, results of experiments in mice nasal and human alveolar epithelial cells showed that the colonization capacity of ST121 is much lower than that of other clones. Moreover, ST121-MRSA displayed much lower acid tolerance, suggesting that ST121-MRSA may not have such capacity to achieve the epidemiological success of other CA-MRSA clones and become the dominant lineage. Our findings expand current understanding of the epidemiology and pathogenicity of the hypervirulent ST121 clone, and highlight the importance of colonization capacity and environmental adaption in MRSA epidemiological success.
DOI: 10.6084/m9.figshare.23834559.v1
title: Comparative analysis of genomic characteristics, virulence and fitness of community-associated <i>Staphylococcus aureus</i> ST121 clone causing fatal diseases in China and other CA-MRSA clones

description: The increasing rate of community-associated <i>Staphylococcus aureus</i> (CA-SA) worldwide has aroused global public concern for decades. Although ST121 clone is one of the prevalent CA-SA in China, there is still limited knowledge about it. In this study, we conducted a genomic analysis of 28 CA-SA ST121 isolates from severe bloodstream infection cases and 175 ST121 isolates from the public database. Phylogenetic analysis revealed the consistency and the complexity of global ST121 lineages, and suggested potential cross-country even cross-continental transmission of ST121 isolates. By investigating the virulence and fitness between ST121-CA-methicillin-resistant SA (CA-MRSA) and other CA-MRSA clones, we found that ST121-MRSA exhibits virulence comparable to the highly virulent USA300 clone, exceeding that of the predominant CA-MRSA lineage ST59 in China and the other American CA-MRSA clone MW2. Notably, based on analyses of virulence genes, <i>eta</i>, <i>etb</i>, <i>edin-C</i> and egc were only found in ST121, suggesting that the high virulence of ST121 may be attributed to the combination of these virulence factors encoded by mobile genetic elements. However, results of experiments in mice nasal and human alveolar epithelial cells showed that the colonization capacity of ST121 is much lower than that of other clones. Moreover, ST121-MRSA displayed much lower acid tolerance, suggesting that ST121-MRSA may not have such capacity to achieve the epidemiological success of other CA-MRSA clones and become the dominant lineage. Our findings expand current understanding of the epidemiology and pathogenicity of the hypervirulent ST121 clone, and highlight the importance of colonization capacity and environmental adaption in MRSA epidemiological success.
DOI: 10.6084/m9.figshare.21952541
title: The crosstalk between microbial sensors ELMO1 and NOD2 shape intestinal immune responses

description: Microbial sensors play an essential role in maintaining cellular homoeostasis. Our knowledge is limited on how microbial sensing helps in differential immune response and its link to inflammatory diseases. Recently we have confirmed that ELMO1 (Engulfment and Cell Motility Protein-1) present in cytosol is involved in pathogen sensing, engulfment, and intestinal inflammation. Here, we show that ELMO1 interacts with another sensor, NOD2 (Nucleotide-binding oligomerization domain-containing protein 2), that recognizes bacterial cell wall component muramyl dipeptide (MDP). The polymorphism of NOD2 is linked to Crohn’s disease (CD) pathogenesis. Interestingly, we found that overexpression of ELMO1 and mutant NOD2 (L1007fs) were not able to clear the CD-associated adherent invasive <i>E. coli (AIEC</i>-LF82). The functional implications of ELMO1-NOD2 interaction in epithelial cells were evaluated by using enteroid-derived monolayers (EDMs) from ELMO1 and NOD2 KO mice. Subsequently we also assessed the immune response in J774 macrophages depleted of either ELMO1 or NOD2 or both. The infection of murine EDMs with <i>AIEC</i>-LF82 showed higher bacterial load in ELMO1-KO, NOD2 KO EDMs, and ELMO1 KO EDMs treated with NOD2 inhibitors. The murine macrophage cells showed that the downregulation of ELMO1 and NOD2 is associated with impaired bacterial clearance that is linked to reduce pro-inflammatory cytokines and reactive oxygen species. Our results indicated that the crosstalk between microbial sensors in enteric infection and inflammatory diseases impacts the fate of the bacterial load and disease pathogenesis.
DOI: 10.6084/m9.figshare.21952541.v1
title: The crosstalk between microbial sensors ELMO1 and NOD2 shape intestinal immune responses

description: Microbial sensors play an essential role in maintaining cellular homoeostasis. Our knowledge is limited on how microbial sensing helps in differential immune response and its link to inflammatory diseases. Recently we have confirmed that ELMO1 (Engulfment and Cell Motility Protein-1) present in cytosol is involved in pathogen sensing, engulfment, and intestinal inflammation. Here, we show that ELMO1 interacts with another sensor, NOD2 (Nucleotide-binding oligomerization domain-containing protein 2), that recognizes bacterial cell wall component muramyl dipeptide (MDP). The polymorphism of NOD2 is linked to Crohn’s disease (CD) pathogenesis. Interestingly, we found that overexpression of ELMO1 and mutant NOD2 (L1007fs) were not able to clear the CD-associated adherent invasive <i>E. coli (AIEC</i>-LF82). The functional implications of ELMO1-NOD2 interaction in epithelial cells were evaluated by using enteroid-derived monolayers (EDMs) from ELMO1 and NOD2 KO mice. Subsequently we also assessed the immune response in J774 macrophages depleted of either ELMO1 or NOD2 or both. The infection of murine EDMs with <i>AIEC</i>-LF82 showed higher bacterial load in ELMO1-KO, NOD2 KO EDMs, and ELMO1 KO EDMs treated with NOD2 inhibitors. The murine macrophage cells showed that the downregulation of ELMO1 and NOD2 is associated with impaired bacterial clearance that is linked to reduce pro-inflammatory cytokines and reactive oxygen species. Our results indicated that the crosstalk between microbial sensors in enteric infection and inflammatory diseases impacts the fate of the bacterial load and disease pathogenesis.
DOI: 10.6084/m9.figshare.23660550
title: Identification of <i>Staphylococcus aureus</i> virulence-modulating RNA from transcriptomics data with machine learning

description: The virulence factors of <i>Staphylococcus aureus</i> are tightly controlled by two-component systems (TCSs) and small RNA (sRNA). TCSs have been well studied over the past several decades, but our understanding of sRNA functions lags far behind that of TCS functions. Here, we studied the biological role of sRNA from 506 <i>S. aureus</i> RNA-seq datasets using independent component analysis (ICA). We found that a previously neglected sRNA, Sau-41, functions in the Agr system. Sau-41 is located within the PSMα operon and controlled by the Agr system. It was predicted to share 22-base complementarity with RNAIII, a major regulator of <i>S. aureus</i> virulence. The EMSA results demonstrated that Sau-41 directly binds to RNAIII. Furthermore, our results found that Sau-41 is capable of repressing <i>S. aureus</i> haemolysin activity by downregulating α-haemolysin and δ-toxin. The repression of α-haemolysin was attributed to the competition between the 5’ UTR of <i>hla</i> and Sau-41 for binding RNAIII. We observed that Sau-41 mitigated <i>S. aureus</i> virulence in an orthopaedic implant infection mouse model and alleviated osteolysis. Together, our results indicate that Sau-41 is a virulence-regulating RNA and suggest that Sau-41 might be involved in a negative feedback mechanism to control the Agr system. This work is a demonstration of using ICA in sRNA identification by mining high-throughput data and could be extended to other organisms as well.