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Lane Starr NM, Al-Rayyan N, Smith JM, Sandstrom S, Swaney MH, Salamzade R, Steidl O, Kalan LR, Singh AM. Combined metagenomic- and culture-based approaches to investigate bacterial strain-level associations with medication-controlled mild-moderate atopic dermatitis. THE JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY. GLOBAL 2024; 3:100259. [PMID: 38779310 PMCID: PMC11109885 DOI: 10.1016/j.jacig.2024.100259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 01/05/2024] [Accepted: 01/27/2024] [Indexed: 05/25/2024]
Abstract
Background The skin microbiome is disrupted in atopic dermatitis (AD). Existing research focuses on moderate to severe, unmedicated disease. Objective We sought to investigate metagenomic- and culture-based bacterial strain-level differences in mild, medicated AD and the effects these have on human keratinocytes (HKs). Methods Skin swabs from anterior forearms were collected from 20 pediatric participants (11 participants with AD sampled at lesional and nonlesional sites and 9 age- and sex-matched controls). Participants had primarily mild to moderate AD and maintained medication use. Samples were processed for microbial metagenomic sequencing and bacterial isolation. Isolates identified as Staphylococcus aureus were tested for enterotoxin production. HK cultures were treated with cell-free conditioned media from representative Staphylococcus species to measure barrier effects. Results Metagenomic sequencing identified significant differences in microbiome composition between AD and control groups. Differences were seen at the species and strain levels for Staphylococci, with S aureus found only in participants with AD and differences in Staphylococcus epidermidis strains between control and AD swabs. These strains showed differences in toxin gene presence, which was confirmed in vitro for S aureus enterotoxins. The strain from the participant with the most severe AD produced enterotoxin B levels more than 100-fold higher than the other strains (P < .001). Strains also displayed differential effects on HK metabolism and barrier function. Conclusions Strain-level differences in toxin genes from Staphylococcus strains may explain varying effects on HK, with S aureus and non-aureus strains negatively affecting viability and barrier function. These differences are likely important in AD pathogenesis.
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Affiliation(s)
- Nicole M. Lane Starr
- Department of Pediatrics, School of Medicine and Public Health, University of Wisconsin, Madison, Wis
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin, Madison, Wis
| | - Numan Al-Rayyan
- Department of Pediatrics, School of Medicine and Public Health, University of Wisconsin, Madison, Wis
| | - Jennifer M. Smith
- Department of Pediatrics, School of Medicine and Public Health, University of Wisconsin, Madison, Wis
| | - Shelby Sandstrom
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin, Madison, Wis
| | - Mary Hannah Swaney
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin, Madison, Wis
| | - Rauf Salamzade
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin, Madison, Wis
| | - Olivia Steidl
- Department of Pediatrics, School of Medicine and Public Health, University of Wisconsin, Madison, Wis
| | - Lindsay R. Kalan
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin, Madison, Wis
- Division of Infectious Disease, Department of Medicine, School of Medicine and Public Health, University of Wisconsin, Madison, Wis
- Department of Biochemistry and Biomedical Sciences, M.G. DeGroote Institute for Infectious Disease Research, David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada
| | - Anne Marie Singh
- Department of Pediatrics, School of Medicine and Public Health, University of Wisconsin, Madison, Wis
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin, Madison, Wis
- Department of Dermatology, School of Medicine and Public Health, University of Wisconsin, Madison, Wis
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Kellgren T, Dwibedi C, Widerström M, Sundell D, Öhrman C, Sjödin A, Monsen T, Rydén P, Johansson A. Completed genome and emergence scenario of the multidrug-resistant nosocomial pathogen Staphylococcus epidermidis ST215. BMC Microbiol 2024; 24:215. [PMID: 38890594 PMCID: PMC11186124 DOI: 10.1186/s12866-024-03367-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Accepted: 06/10/2024] [Indexed: 06/20/2024] Open
Abstract
BACKGROUND A multidrug-resistant lineage of Staphylococcus epidermidis named ST215 is a common cause of prosthetic joint infections and other deep surgical site infections in Northern Europe, but is not present elsewhere. The increasing resistance among S. epidermidis strains is a global concern. We used whole-genome sequencing to characterize ST215 from healthcare settings. RESULTS We completed the genome of a ST215 isolate from a Swedish hospital using short and long reads, resulting in a circular 2,676,787 bp chromosome and a 2,326 bp plasmid. The new ST215 genome was placed in phylogenetic context using 1,361 finished public S. epidermidis reference genomes. We generated 10 additional short-read ST215 genomes and 11 short-read genomes of ST2, which is another common multidrug-resistant lineage at the same hospital. We studied recombination's role in the evolution of ST2 and ST215, and found multiple recombination events averaging 30-50 kb. By comparing the results of antimicrobial susceptibility testing for 31 antimicrobial drugs with the genome content encoding antimicrobial resistance in the ST215 and ST2 isolates, we found highly similar resistance traits between the isolates, with 22 resistance genes being shared between all the ST215 and ST2 genomes. The ST215 genome contained 29 genes that were historically identified as virulence genes of S. epidermidis ST2. We established that in the nucleotide sequence stretches identified as recombination events, virulence genes were overrepresented in ST215, while antibiotic resistance genes were overrepresented in ST2. CONCLUSIONS This study features the extensive antibiotic resistance and virulence gene content in ST215 genomes. ST215 and ST2 lineages have similarly evolved, acquiring resistance and virulence through genomic recombination. The results highlight the threat of new multidrug-resistant S. epidermidis lineages emerging in healthcare settings.
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Affiliation(s)
- Therese Kellgren
- Department of Mathematics and Mathematical Statistics, Umeå University, Umeå, SE, 90187, Sweden
| | - Chinmay Dwibedi
- Department of Clinical Microbiology and Molecular Infection Medicine Sweden (MIMS), Umeå University, 90185, Umeå, Sweden
| | - Micael Widerström
- Department of Clinical Microbiology, Umeå University, 90185, Umeå, Sweden.
| | - David Sundell
- Division of CBRN Defence and Security, Swedish Defense Research Agency, 90182, Umeå, SE, Sweden
| | - Caroline Öhrman
- Division of CBRN Defence and Security, Swedish Defense Research Agency, 90182, Umeå, SE, Sweden
| | - Andreas Sjödin
- Division of CBRN Defence and Security, Swedish Defense Research Agency, 90182, Umeå, SE, Sweden
| | - Tor Monsen
- Department of Clinical Microbiology, Umeå University, 90185, Umeå, Sweden
| | - Patrik Rydén
- Department of Mathematics and Mathematical Statistics, Umeå University, Umeå, SE, 90187, Sweden
| | - Anders Johansson
- Department of Clinical Microbiology and Molecular Infection Medicine Sweden (MIMS), Umeå University, 90185, Umeå, Sweden
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Lee DH, Lee K, Kim YS, Cha CJ. Comprehensive genomic landscape of antibiotic resistance in Staphylococcus epidermidis. mSystems 2024; 9:e0022624. [PMID: 38727238 PMCID: PMC11237394 DOI: 10.1128/msystems.00226-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 04/04/2024] [Indexed: 06/19/2024] Open
Abstract
Staphylococcus epidermidis, a common commensal bacterium found on human skin, can cause infections in clinical settings, and the presence of antibiotic resistance genes (ARGs) impedes the treatment of S. epidermidis infections. However, studies characterizing the ARGs in S. epidermidis with regard to genomic and ecological diversities are limited. Thus, we performed a comprehensive and comparative analysis of 405 high-quality S. epidermidis genomes, including those of 35 environmental isolates from the Han River, to investigate the genomic diversity of antibiotic resistance in this pathogen. Comparative genomic analysis revealed the prevalence of ARGs in S. epidermidis genomes associated with multi-locus sequence types. The genes encoding dihydrofolate reductase (dfrC) and multidrug efflux pump (norA) were genome-wide core ARGs. β-Lactam class ARGs were also highly prevalent in the S. epidermidis genomes, which was consistent with the resistance phenotype observed in river isolates. Furthermore, we identified chloramphenicol acetyltransferase genes (cat) in the plasmid-like sequences of the six river isolates, which have not been reported previously in S. epidermidis genomes. These genes were identical to those harbored by the Enterococcus faecium plasmids and associated with the insertion sequence 6 family transposases, homologous to those found in Staphylococcus aureus plasmids, suggesting the possibility of horizontal gene transfer between these Gram-positive pathogens. Comparison of the ARG and virulence factor profiles between S. epidermidis and S. aureus genomes revealed that these two species were clearly distinguished, suggesting genomic demarcation despite ecological overlap. Our findings provide a comprehensive understanding of the genomic diversity of antibiotic resistance in S. epidermidis. IMPORTANCE A comprehensive understanding of the antibiotic resistance gene (ARG) profiles of the skin commensal bacterium and opportunistic pathogen Staphylococcus epidermidis needs to be documented from a genomic point of view. Our study encompasses a comparative analysis of entire S. epidermidis genomes from various habitats, including those of 35 environmental isolates from the Han River sequenced in this study. Our results shed light on the distribution and diversity of ARGs within different S. epidermidis multi-locus sequence types, providing valuable insights into the ecological and genetic factors associated with antibiotic resistance. A comparison between S. epidermidis and Staphylococcus aureus revealed marked differences in ARG and virulence factor profiles, despite their overlapping ecological niches.
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Affiliation(s)
- Do-Hoon Lee
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, South Korea
| | - Kihyun Lee
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, South Korea
| | - Yong-Seok Kim
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, South Korea
| | - Chang-Jun Cha
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, South Korea
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Wang Y, Liu C, Xia W, Cui Y, Yu L, Zhao D, Guan X, Wang Y, Wang Y, Li Y, Hu J, Liu J. Association of coagulase-negative staphylococci with orthopedic infections detected by in-house multiplex real-time PCR. Front Microbiol 2024; 15:1400096. [PMID: 38912353 PMCID: PMC11193334 DOI: 10.3389/fmicb.2024.1400096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 05/10/2024] [Indexed: 06/25/2024] Open
Abstract
Introduction Clinical significance of coagulase-negative staphylococci (CoNS) has been gradually acknowledged in both healthcare and clinical research, but approaches for their precise discrimination at the species level remain scarce. The current study aimed to evaluate the association of CoNS with orthopedic infections, where accurate and prompt identification of etiology is crucial for appropriate diagnosis and treatment decision-making. Methods A 16S rRNA-based quantitative PCR (qPCR) assay was developed for the detection of Staphylococcus genus and two panels of 3-plex qPCR assays for further differentiation of six CoNS species with remarkable clinical significance, including S. epidermidis, S. haemolyticus, S. simulans, S. hominis, S. capitis, and S. caprae. All the assays exhibited excellent analytical performance. ΔCq (quantification cycle) between 16S rRNA and CoNS species-specific targets was established to determine the primary CoNS. These methods were applied to detect CoNS in wound samples from orthopedic patients with and without infection. Results and discussion Overall, CoNS were detected in 17.8% (21/118) of patients with clinically suspected infection and in 9.8% (12/123) of patients without any infection symptom (p < 0.05). Moreover, the association with infection was found to be bacterial quantity dependent. S. epidermidis was identified as the predominant species, followed by S. simulans, S. haemolyticus, and S. hominis. Male sex, open injury, trauma, and lower extremity were determined as risk factors for CoNS infections. CoNS-positive patients had significantly longer hospitalization duration (20 days (15, 33) versus 13 days (7, 22) for Staphylococcus-negative patients, p = 0.003), which could be a considerable burden for healthcare and individual patients. Considering the complex characteristics and devastating consequences of orthopedic infections, further expanding the detection scope for CoNS may be pursued to better understand the etiology of orthopedic infections and to improve therapeutic strategies.
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Affiliation(s)
- Ying Wang
- School of Public Health, Qingdao University, Qingdao, Shandong, China
| | - Chao Liu
- School of Public Health, Qingdao University, Qingdao, Shandong, China
| | - Wenbo Xia
- Department of Orthopedics, Qingdao Huangdao Traditional Chinese Medicine Hospital, Qingdao, Shandong, China
| | - Yanxiang Cui
- Department of Clinical Laboratory, Qingdao Huangdao Traditional Chinese Medicine Hospital, Qingdao, Shandong, China
| | - Linhong Yu
- Qingdao Medical College, Qingdao University, Qingdao, Shandong, China
| | - Dan Zhao
- School of Public Health, Qingdao University, Qingdao, Shandong, China
| | - Xiaoxuan Guan
- Department of Clinical Laboratory, Qingdao Huangdao Traditional Chinese Medicine Hospital, Qingdao, Shandong, China
| | - Yingdi Wang
- School of Public Health, Qingdao University, Qingdao, Shandong, China
| | - Yani Wang
- School of Public Health, Qingdao University, Qingdao, Shandong, China
| | - Yisong Li
- School of Public Health, Qingdao University, Qingdao, Shandong, China
| | - Jianqiang Hu
- Department of Orthopedics, Qingdao Huangdao Traditional Chinese Medicine Hospital, Qingdao, Shandong, China
| | - Jie Liu
- School of Public Health, Qingdao University, Qingdao, Shandong, China
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Wang W, Qiu Z, Li H, Wu X, Cui Y, Xie L, Chang B, Li P, Zeng H, Ding T. Patient-derived pathogenic microbe deposition enhances exposure risk in pediatric clinics. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 924:171703. [PMID: 38490424 DOI: 10.1016/j.scitotenv.2024.171703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 03/11/2024] [Accepted: 03/12/2024] [Indexed: 03/17/2024]
Abstract
Healthcare-associated infections (HAIs) pose significant risks to pediatric patients in outpatient settings. To prevent HAIs, understanding the sources and transmission routes of pathogenic microorganisms is crucial. This study aimed to identify the sources of opportunistic bacterial pathogens (OBPs) in pediatric outpatient settings and determine their transmission routes. Furthermore, assessing the public health risks associated with the core OBPs is important. We collected 310 samples from various sites in pediatric outpatient areas and quantified the bacteria using qPCR and CFU counting. We also performed 16S rRNA gene and single-bacterial whole-genome sequencing to profile the transmission routes and antibiotic resistance characteristics of OBPs. We observed significant variations in microbial diversity and composition among sampling sites in pediatric outpatient settings, with active communication of the microbiota between linked areas. We found that the primary source of OBPs in multi-person contact areas was the hand surface, particularly in pediatric patients. Five core OBPs, Staphylococcus epidermidis, Acinetobacter baumannii, Pseudomonas aeruginosa, Streptococcus mitis, and Streptococcus oralis, were mainly derived from pediatric patients and spread into the environment. These OBPs accumulated at multi-person contact sites, resulting in high microbial diversity in these areas. Transmission tests confirmed the challenging spread of these pathogens, with S. epidermidis transferring from the patient's hand to the environment, leading to an increased abundance and emergence of related strains. More importantly, S. epidermidis isolated from pediatric patients carried more antibiotic-resistance genes. In addition, two strains of multidrug-resistant A. baumannii were isolated from both a child and a parent, confirming the transmission of the five core OBPs centered around pediatric patients and multi-person contact areas. Our results demonstrate that pediatric patients serve as a significant source of OBPs in pediatric outpatient settings. OBPs carried by pediatric patients pose a high public health risk. To effectively control HAIs, increasing hand hygiene measures in pediatric patients and enhancing the frequency of disinfection in multi-person contact areas remains crucial. By targeting these preventive measures, the spread of OBPs can be reduced, thereby mitigating the risk of HAIs in pediatric outpatient settings.
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Affiliation(s)
- Wan Wang
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China
| | - Zongyao Qiu
- Center for Disease Control and Prevention of Nanhai District, Foshan 528200, China
| | - Hui Li
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China
| | - Xiaorong Wu
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China
| | - Ying Cui
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China
| | - Lixiang Xie
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China
| | - Bozhen Chang
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China
| | - Peipei Li
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China
| | - Hong Zeng
- Center for Disease Control and Prevention of Nanhai District, Foshan 528200, China.
| | - Tao Ding
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China.
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6
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Chen Z, Zhao Z. Study on the microbial diversity of ear canal secretions from patients with otomycosis. Front Surg 2024; 11:1277799. [PMID: 38450054 PMCID: PMC10916698 DOI: 10.3389/fsurg.2024.1277799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 01/30/2024] [Indexed: 03/08/2024] Open
Abstract
Otomycosis is caused by fungi, which usually cause discharge and additional discomfort. The highest incidence of otomycosis occurs in summer. To better treat this disease, it is necessary to study the microbial diversity of otomycosis secretions. In this regard, this study used high-throughput sequencing technology to determine the microbial diversity of the ear canal secretions of six typical patients with otomycosis in Wuhan via internal transcribed spacer (ITS) and 16S rRNA analyses and proposed a reasonable clinical treatment plan. Six patients with otomycosis in the Department of Otorhinolaryngology, Hubei Third People's Hospital Affiliated with Jianghan University, were selected from June 2022 to August 2022. The results showed that Staphylococcus spp. (average abundance 29.05%) was the dominant bacteria and Aspergillus spp. (average abundance 90.68%) was the dominant fungus involved in otomycosis secretion. Aspergillus spp. can cause inflammation of the external auditory canal combined with bacterial infections such as Staphylococcus spp., which can cause discharge in the ear canal. High-throughput sequencing provides comprehensive information on the microbial community involved in otomycosis discharge and will aid in evaluating the efficacy of clinical treatment and medication.
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Affiliation(s)
| | - Zhang Zhao
- Department of Otorhinolaryngology, Hubei NO.3 People's Hospital of Jianghan University, Wuhan, China
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7
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Yang S, Chen J, Fu J, Huang J, Li T, Yao Z, Ye X. Disease-Associated Streptococcus pneumoniae Genetic Variation. Emerg Infect Dis 2024; 30:39-49. [PMID: 38146979 PMCID: PMC10756394 DOI: 10.3201/eid3001.221927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2023] Open
Abstract
Streptococcus pneumoniae is an opportunistic pathogen that causes substantial illness and death among children worldwide. The genetic backgrounds of pneumococci that cause infection versus asymptomatic carriage vary substantially. To determine the evolutionary mechanisms of opportunistic pathogenicity, we conducted a genomic surveillance study in China. We collected 783 S. pneumoniae isolates from infected and asymptomatic children. By using a 2-stage genomewide association study process, we compared genomic differences between infection and carriage isolates to address genomic variation associated with pathogenicity. We identified 8 consensus k-mers associated with adherence, antimicrobial resistance, and immune modulation, which were unevenly distributed in the infection isolates. Classification accuracy of the best k-mer predictor for S. pneumoniae infection was good, giving a simple target for predicting pathogenic isolates. Our findings suggest that S. pneumoniae pathogenicity is complex and multifactorial, and we provide genetic evidence for precise targeted interventions.
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8
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Guo Y, Du X, Krusche J, Beck C, Ali S, Walter A, Winstel V, Mayer C, Codée JD, Peschel A, Stehle T. Invasive Staphylococcus epidermidis uses a unique processive wall teichoic acid glycosyltransferase to evade immune recognition. SCIENCE ADVANCES 2023; 9:eadj2641. [PMID: 38000019 PMCID: PMC10672168 DOI: 10.1126/sciadv.adj2641] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 10/26/2023] [Indexed: 11/26/2023]
Abstract
Staphylococcus epidermidis expresses glycerol phosphate wall teichoic acid (WTA), but some health care-associated methicillin-resistant S. epidermidis (HA-MRSE) clones produce a second, ribitol phosphate (RboP) WTA, resembling that of the aggressive pathogen Staphylococcus aureus. RboP-WTA promotes HA-MRSE persistence and virulence in bloodstream infections. We report here that the TarM enzyme of HA-MRSE [TarM(Se)] glycosylates RboP-WTA with glucose, instead of N-acetylglucosamine (GlcNAc) by TarM(Sa) in S. aureus. Replacement of GlcNAc with glucose in RboP-WTA impairs HA-MRSE detection by human immunoglobulin G, which may contribute to the immune-evasion capacities of many invasive S. epidermidis. Crystal structures of complexes with uridine diphosphate glucose (UDP-glucose), and with UDP and glycosylated poly(RboP), reveal the binding mode and glycosylation mechanism of this enzyme and explain why TarM(Se) and TarM(Sa) link different sugars to poly(RboP). These structural data provide evidence that TarM(Se) is a processive WTA glycosyltransferase. Our study will support the targeted inhibition of TarM enzymes, and the development of RboP-WTA targeting vaccines and phage therapies.
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Affiliation(s)
- Yinglan Guo
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
- Cluster of Excellence “Controlling Microbes to Fight Infections (CMFI)”, University of Tübingen, Tübingen, Germany
| | - Xin Du
- Cluster of Excellence “Controlling Microbes to Fight Infections (CMFI)”, University of Tübingen, Tübingen, Germany
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Infection Biology, University of Tübingen, Tübingen, Germany
- German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Janes Krusche
- Cluster of Excellence “Controlling Microbes to Fight Infections (CMFI)”, University of Tübingen, Tübingen, Germany
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Infection Biology, University of Tübingen, Tübingen, Germany
- German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Christian Beck
- Cluster of Excellence “Controlling Microbes to Fight Infections (CMFI)”, University of Tübingen, Tübingen, Germany
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Infection Biology, University of Tübingen, Tübingen, Germany
- German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Sara Ali
- Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands
| | - Axel Walter
- Cluster of Excellence “Controlling Microbes to Fight Infections (CMFI)”, University of Tübingen, Tübingen, Germany
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Organismic Interactions/Glycobiology, University of Tübingen, Tübingen, Germany
| | - Volker Winstel
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Infection Biology, University of Tübingen, Tübingen, Germany
- German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Christoph Mayer
- Cluster of Excellence “Controlling Microbes to Fight Infections (CMFI)”, University of Tübingen, Tübingen, Germany
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Organismic Interactions/Glycobiology, University of Tübingen, Tübingen, Germany
| | | | - Andreas Peschel
- Cluster of Excellence “Controlling Microbes to Fight Infections (CMFI)”, University of Tübingen, Tübingen, Germany
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Infection Biology, University of Tübingen, Tübingen, Germany
- German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Thilo Stehle
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
- Cluster of Excellence “Controlling Microbes to Fight Infections (CMFI)”, University of Tübingen, Tübingen, Germany
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Ruis C, Weimann A, Tonkin-Hill G, Pandurangan AP, Matuszewska M, Murray GGR, Lévesque RC, Blundell TL, Floto RA, Parkhill J. Mutational spectra are associated with bacterial niche. Nat Commun 2023; 14:7091. [PMID: 37925514 PMCID: PMC10625568 DOI: 10.1038/s41467-023-42916-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 10/25/2023] [Indexed: 11/06/2023] Open
Abstract
As observed in cancers, individual mutagens and defects in DNA repair create distinctive mutational signatures that combine to form context-specific spectra within cells. We reasoned that similar processes must occur in bacterial lineages, potentially allowing decomposition analysis to detect both disruption of DNA repair processes and exposure to niche-specific mutagens. Here we reconstruct mutational spectra for 84 clades from 31 diverse bacterial species and find distinct mutational patterns. We extract signatures driven by specific DNA repair defects using hypermutator lineages, and further deconvolute the spectra into multiple signatures operating within different clades. We show that these signatures are explained by both bacterial phylogeny and replication niche. By comparing mutational spectra of clades from different environmental and biological locations, we identify niche-associated mutational signatures, and then employ these signatures to infer the predominant replication niches for several clades where this was previously obscure. Our results show that mutational spectra may be associated with sites of bacterial replication when mutagen exposures differ, and can be used in these cases to infer transmission routes for established and emergent human bacterial pathogens.
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Affiliation(s)
- Christopher Ruis
- Molecular Immunity Unit, University of Cambridge Department of Medicine, MRC-Laboratory of Molecular Biology, Cambridge, UK
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
- Cambridge Centre for AI in Medicine, University of Cambridge, Cambridge, UK
| | - Aaron Weimann
- Molecular Immunity Unit, University of Cambridge Department of Medicine, MRC-Laboratory of Molecular Biology, Cambridge, UK
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
- Cambridge Centre for AI in Medicine, University of Cambridge, Cambridge, UK
| | | | | | - Marta Matuszewska
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Gemma G R Murray
- Parasites and Microbes Programme, Wellcome Sanger Institute; Wellcome Genome Campus, Cambridge, UK
| | - Roger C Lévesque
- Institut de biologie intégrative et des systèmes (IBIS), Université Laval, Québec City, Québec, Canada
| | - Tom L Blundell
- Department of Biochemistry, Sanger Building, University of Cambridge, Cambridge, UK
| | - R Andres Floto
- Molecular Immunity Unit, University of Cambridge Department of Medicine, MRC-Laboratory of Molecular Biology, Cambridge, UK.
- Cambridge Centre for AI in Medicine, University of Cambridge, Cambridge, UK.
- Cambridge Centre for Lung Infection, Papworth Hospital, Cambridge, UK.
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK.
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10
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Dutta A, McDonald BA, Croll D. Combined reference-free and multi-reference based GWAS uncover cryptic variation underlying rapid adaptation in a fungal plant pathogen. PLoS Pathog 2023; 19:e1011801. [PMID: 37972199 PMCID: PMC10688896 DOI: 10.1371/journal.ppat.1011801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 11/30/2023] [Accepted: 11/06/2023] [Indexed: 11/19/2023] Open
Abstract
Microbial pathogens often harbor substantial functional diversity driven by structural genetic variation. Rapid adaptation from such standing variation threatens global food security and human health. Genome-wide association studies (GWAS) provide a powerful approach to identify genetic variants underlying recent pathogen adaptation. However, the reliance on single reference genomes and single nucleotide polymorphisms (SNPs) obscures the true extent of adaptive genetic variation. Here, we show quantitatively how a combination of multiple reference genomes and reference-free approaches captures substantially more relevant genetic variation compared to single reference mapping. We performed reference-genome based association mapping across 19 reference-quality genomes covering the diversity of the species. We contrasted the results with a reference-free (i.e., k-mer) approach using raw whole-genome sequencing data in a panel of 145 strains collected across the global distribution range of the fungal wheat pathogen Zymoseptoria tritici. We mapped the genetic architecture of 49 life history traits including virulence, reproduction and growth in multiple stressful environments. The inclusion of additional reference genome SNP datasets provides a nearly linear increase in additional loci mapped through GWAS. Variants detected through the k-mer approach explained a higher proportion of phenotypic variation than a reference genome-based approach and revealed functionally confirmed loci that classic GWAS approaches failed to map. The power of GWAS in microbial pathogens can be significantly enhanced by comprehensively capturing structural genetic variation. Our approach is generalizable to a large number of species and will uncover novel mechanisms driving rapid adaptation of pathogens.
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Affiliation(s)
- Anik Dutta
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Bruce A. McDonald
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
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11
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Wolska-Gębarzewska M, Międzobrodzki J, Kosecka-Strojek M. Current types of staphylococcal cassette chromosome mec (SCC mec) in clinically relevant coagulase-negative staphylococcal (CoNS) species. Crit Rev Microbiol 2023:1-17. [PMID: 37882662 DOI: 10.1080/1040841x.2023.2274841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 10/17/2023] [Indexed: 10/27/2023]
Abstract
Coagulase-negative staphylococci (CoNS) colonize human skin and mucosal membranes, which is why they are considered harmless commensal bacteria. Two species, Staphylococcus epidermidis and Staphylococcus haemolyticus belong to the group of CoNS species and are most frequently isolated from nosocomial infections, including device-associated healthcare-associated infections (DA-HAIs) and local or systemic body-related infections (FBRIs). Methicillin resistance, initially described in Staphylococcus aureus, has also been reported in CoNS species. It is mediated by the mecA gene within the staphylococcal cassette chromosome (SCCmec). SCCmec typing, primarily using PCR-based methods, has been employed as a molecular epidemiological tool. However, the introduction of whole genome sequencing (WGS) and next-generation sequencing (NGS) has enabled the identification and verification of new SCCmec types. This review describes the current distribution of SCCmec types, subtypes, and variants among CoNS species, including S. epidermidis, S. haemolyticus, and S. capitis. The literature review focuses on recent research articles from the past decade that discuss new combinations of SCCmec in coagulase-negative Staphylococcus. The high genetic diversity and gaps in CoNS SCCmec annotation rules underscore the need for an efficient typing system. Typing SCCmec cassettes in CoNS strains is crucial to continuously updating databases and developing a unified classification system.
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Affiliation(s)
- Mariola Wolska-Gębarzewska
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Krakow, Poland
| | - Jacek Międzobrodzki
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Maja Kosecka-Strojek
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
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12
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Landemaine L, Da Costa G, Fissier E, Francis C, Morand S, Verbeke J, Michel ML, Briandet R, Sokol H, Gueniche A, Bernard D, Chatel JM, Aguilar L, Langella P, Clavaud C, Richard ML. Staphylococcus epidermidis isolates from atopic or healthy skin have opposite effect on skin cells: potential implication of the AHR pathway modulation. Front Immunol 2023; 14:1098160. [PMID: 37304256 PMCID: PMC10250813 DOI: 10.3389/fimmu.2023.1098160] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 05/04/2023] [Indexed: 06/13/2023] Open
Abstract
Introduction Staphylococcus epidermidis is a commensal bacterium ubiquitously present on human skin. This species is considered as a key member of the healthy skin microbiota, involved in the defense against pathogens, modulating the immune system, and involved in wound repair. Simultaneously, S. epidermidis is the second cause of nosocomial infections and an overgrowth of S. epidermidis has been described in skin disorders such as atopic dermatitis. Diverse isolates of S. epidermidis co-exist on the skin. Elucidating the genetic and phenotypic specificities of these species in skin health and disease is key to better understand their role in various skin conditions. Additionally, the exact mechanisms by which commensals interact with host cells is partially understood. We hypothesized that S. epidermidis isolates identified from different skin origins could play distinct roles on skin differentiation and that these effects could be mediated by the aryl hydrocarbon receptor (AhR) pathway. Methods For this purpose, a library of 12 strains originated from healthy skin (non-hyperseborrheic (NH) and hyperseborrheic (H) skin types) and disease skin (atopic (AD) skin type) was characterized at the genomic and phenotypic levels. Results and discussion Here we showed that strains from atopic lesional skin alter the epidermis structure of a 3D reconstructed skin model whereas strains from NH healthy skin do not. All strains from NH healthy skin induced AhR/OVOL1 path and produced high quantities of indole metabolites in co-culture with NHEK; especially indole-3-aldehyde (IAld) and indole-3-lactic acid (ILA); while AD strains did not induce AhR/OVOL1 path but its inhibitor STAT6 and produced the lowest levels of indoles as compared to the other strains. As a consequence, strains from AD skin altered the differentiation markers FLG and DSG1. The results presented here, on a library of 12 strains, showed that S. epidermidis originated from NH healthy skin and atopic skin have opposite effects on the epidermal cohesion and structure and that these differences could be linked to their capacity to produce metabolites, which in turn could activate AHR pathway. Our results on a specific library of strains provide new insights into how S. epidermidis may interact with the skin to promote health or disease.
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Affiliation(s)
- Leslie Landemaine
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
- L’Oréal Research and Innovation, Aulnay-sous-Bois, France
| | - Gregory Da Costa
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
- Paris Center for Microbiome Medicine (PaCeMM), Fédération Hospitalo-Universitaire, Paris, France
| | - Elsa Fissier
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
- Paris Center for Microbiome Medicine (PaCeMM), Fédération Hospitalo-Universitaire, Paris, France
| | - Carine Francis
- L’Oréal Research and Innovation, Aulnay-sous-Bois, France
| | | | | | - Marie-Laure Michel
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
- Paris Center for Microbiome Medicine (PaCeMM), Fédération Hospitalo-Universitaire, Paris, France
| | - Romain Briandet
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Harry Sokol
- Paris Center for Microbiome Medicine (PaCeMM), Fédération Hospitalo-Universitaire, Paris, France
- Sorbonne Université, INSERM UMRS-938, Centre de Recherche Saint-Antoine, Assistance Publique - Hôpitaux de Paris (AP-HP), Paris, France
| | | | | | - Jean-Marc Chatel
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
- Paris Center for Microbiome Medicine (PaCeMM), Fédération Hospitalo-Universitaire, Paris, France
| | - Luc Aguilar
- L’Oréal Research and Innovation, Aulnay-sous-Bois, France
| | - Philippe Langella
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
- Paris Center for Microbiome Medicine (PaCeMM), Fédération Hospitalo-Universitaire, Paris, France
| | - Cecile Clavaud
- L’Oréal Research and Innovation, Aulnay-sous-Bois, France
| | - Mathias L. Richard
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
- Paris Center for Microbiome Medicine (PaCeMM), Fédération Hospitalo-Universitaire, Paris, France
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13
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Saber MM, Donner J, Levade I, Acosta N, Parkins MD, Boyle B, Levesque RC, Nguyen D, Shapiro BJ. Single nucleotide variants in Pseudomonas aeruginosa populations from sputum correlate with baseline lung function and predict disease progression in individuals with cystic fibrosis. Microb Genom 2023; 9. [PMID: 37052589 DOI: 10.1099/mgen.0.000981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023] Open
Abstract
The severity and progression of lung disease are highly variable across individuals with cystic fibrosis (CF) and are imperfectly predicted by mutations in the human gene CFTR, lung microbiome variation or other clinical factors. The opportunistic pathogen Pseudomonas aeruginosa (Pa) dominates airway infections in most CF adults. Here we hypothesized that within-host genetic variation of Pa populations would be associated with lung disease severity. To quantify Pa genetic variation within CF sputum samples, we used deep amplicon sequencing (AmpliSeq) of 209 Pa genes previously associated with pathogenesis or adaptation to the CF lung. We trained machine learning models using Pa single nucleotide variants (SNVs), microbiome diversity data and clinical factors to classify lung disease severity at the time of sputum sampling, and to predict lung function decline after 5 years in a cohort of 54 adult CF patients with chronic Pa infection. Models using Pa SNVs alone classified lung disease severity with good sensitivity and specificity (area under the receiver operating characteristic curve: AUROC=0.87). Models were less predictive of lung function decline after 5 years (AUROC=0.74) but still significantly better than random. The addition of clinical data, but not sputum microbiome diversity data, yielded only modest improvements in classifying baseline lung function (AUROC=0.92) and predicting lung function decline (AUROC=0.79), suggesting that Pa AmpliSeq data account for most of the predictive value. Our work provides a proof of principle that Pa genetic variation in sputum tracks lung disease severity, moderately predicts lung function decline and could serve as a disease biomarker among CF patients with chronic Pa infections.
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Affiliation(s)
- Morteza M Saber
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
| | - Jannik Donner
- Department of Medicine, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Inès Levade
- Department of Medicine, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Nicole Acosta
- Department of Microbiology, Immunology and Infectious Disease, University of Calgary, Calgary, AB, Canada
| | - Michael D Parkins
- Department of Microbiology, Immunology and Infectious Disease, University of Calgary, Calgary, AB, Canada
- Department of Medicine, University of Calgary, Calgary, AB, Canada
| | - Brian Boyle
- Integrative Systems Biology Institute, University of Laval, Québec, QC, Canada
| | - Roger C Levesque
- Integrative Systems Biology Institute, University of Laval, Québec, QC, Canada
| | - Dao Nguyen
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
- Department of Medicine, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- Meakins Christie Laboratories, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - B Jesse Shapiro
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
- McGill Genome Centre, Montreal, QC, Canada
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14
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Hellmann KT, Challagundla L, Gray BM, Robinson DA. Improved Genomic Prediction of Staphylococcus epidermidis Isolation Sources with a Novel Polygenic Score. J Clin Microbiol 2023; 61:e0141222. [PMID: 36840569 PMCID: PMC10035303 DOI: 10.1128/jcm.01412-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 01/22/2023] [Indexed: 02/25/2023] Open
Abstract
Staphylococcus epidermidis infections can be challenging to diagnose due to the species frequent contamination of clinical specimens and indolent course of infection. Nevertheless, S. epidermidis is the major cause of late-onset sepsis among premature infants and of intravascular infection in all age groups. Prior work has shown that bacterial virulence factors, antimicrobial resistances, and strains have up to 80% in-sample accuracy to distinguish hospital from community sources, but are unable to distinguish true bacteremia from blood culture contamination. Here, a phylogeny-informed genome-wide association study of 88 isolates was used to estimate effect sizes of particular genomic variants for isolation sources. A "polygenic score" was calculated for each isolate as the summed effect sizes of its repertoire of genomic variants. Predictive models of isolation sources based on polygenic scores were tested with in-samples and out-samples from prior studies of different patient populations. Polygenic scores from accessory genes (AGs) distinguished hospital from community sources with the highest accuracy to date, up to 98% for in-samples and 65% to 91% for various out-samples, whereas scores from single nucleotide polymorphisms (SNPs) had lower accuracy. Scores from AGs and SNPs achieved the highest in-sample accuracy to date, up to 76%, in distinguishing infection from contaminant sources within a hospital. Model training and testing data sets with more similar population structures resulted in more accurate predictions. This study reports the first use of a polygenic score for predicting a complex bacterial phenotype and shows the potential of this approach for enhancing S. epidermidis diagnosis.
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Affiliation(s)
- K. Taylor Hellmann
- Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - Lavanya Challagundla
- Department of Pharmacology and Toxicology, University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - Barry M. Gray
- Department of Pediatrics, University of Illinois College of Medicine at Peoria, Peoria, Illinois, USA
| | - D. Ashley Robinson
- Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, Mississippi, USA
- Center for Immunology and Microbial Research, University of Mississippi Medical Center, Jackson, Mississippi, USA
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15
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Newberry EA, Minsavage GV, Holland A, Jones JB, Potnis N. Genome-Wide Association to Study the Host-Specificity Determinants of Xanthomonas perforans. PHYTOPATHOLOGY 2023; 113:400-412. [PMID: 36318253 DOI: 10.1094/phyto-08-22-0294-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Xanthomonas perforans and X. euvesicatoria are the causal agents of bacterial spot disease of tomato and pepper, endemic to the Southeastern United States. Although very closely related, the two bacterial species differ in host specificity, where X. perforans is the dominant pathogen of tomato and X. euvesicatoria that of pepper. This is in part due to the activity of avirulence proteins that are secreted by X. perforans strains and elicit effector-triggered immunity in pepper leaves, thereby restricting pathogen growth. In recent years, the emergence of several pepper-pathogenic X. perforans lineages has revealed variability within the bacterial species to multiply and cause disease in pepper, even in the absence of avirulence gene activity. Here, we investigated the basal evolutionary processes underlying the host range of this species using multiple genome-wide association analyses. Surprisingly, we identified two novel gene candidates that were significantly associated with pepper-pathogenic X. perforans and X. euvesicatoria. Both candidates were predicted to be involved in the transport/acquisition of nutrients common to the plant cell wall or apoplast and included a TonB-dependent receptor, which was disrupted through independent mutations within the X. perforans lineage. The other included a symporter of protons/glutamate, gltP, enriched with pepper-associated mutations near the promoter and start codon of the gene. Functional analysis of these candidates revealed that only the TonB-dependent receptor had a minor effect on the symptom development and growth of X. perforans in pepper leaves, indicating that pathogenicity to this host might have evolved independently within the bacterial species and is likely a complex, multigenic trait.
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Affiliation(s)
- Eric A Newberry
- Department of Entomology and Plant Pathology, Auburn University, AL 36849
| | | | - Auston Holland
- Department of Entomology and Plant Pathology, Auburn University, AL 36849
| | - Jeffrey B Jones
- Department of Plant Pathology, University of Florida, FL 32611
| | - Neha Potnis
- Department of Entomology and Plant Pathology, Auburn University, AL 36849
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16
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Dinic M, Verpile R, Meng J, Marjanovic J, Burgess JL, Plano L, Hower S, Thaller SR, Banerjee S, Lev-Tov H, Tomic-Canic M, Pastar I. Chronic wound microenvironment mediates selection of biofilm-forming multi drug resistant Staphylococcus epidermidis with capability to impair healing. RESEARCH SQUARE 2023:rs.3.rs-2562300. [PMID: 36824891 PMCID: PMC9949177 DOI: 10.21203/rs.3.rs-2562300/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
Venous leg ulcers (VLU) are the most common chronic wounds characterized by bacterial biofilms and perturbed microbiome. Staphylococcus epidermidis is primarily known as skin commensal beneficial for the host, however, some strains can form biofilms and cause infections. By employing shotgun metagenomic sequencing we show that genetic signatures of antimicrobial resistance, adhesion and biofilm formation in VLU isolates correlate with in vitro bacterial traits. We demonstrate that the capability of chronic wound isolates to form biofilms and elicit IL-8 and IL-1β expression in human ex vivo wounds, correlates with the non-healing outcomes in patients with VLU. In contrast, commensal strains were incapable of surviving in the human ex vivo wounds. We show that major fitness traits of S. epidermis from VLU involve genes for resistance to methicillin and mupirocin, while the biofilm formation relied on the minimal number of genetic elements responsible for bacterial binding to fibronectin and fibrinogen. This underscores the importance of the emergence of treatment resistant virulent lineages in patients with non-healing wounds.
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Affiliation(s)
- Miroslav Dinic
- Wound Healing and Regenerative Medicine Research Program, Dr. Phillip Frost Department of Dermatology and Cutaneous Surgery, University of Miami Miller School of Medicine, Miami, FL, USA
- Group for Probiotics and Microbiota-Host Interaction, Laboratory for Molecular Microbiology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Rebecca Verpile
- Wound Healing and Regenerative Medicine Research Program, Dr. Phillip Frost Department of Dermatology and Cutaneous Surgery, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Jingjing Meng
- Wound Healing and Regenerative Medicine Research Program, Dr. Phillip Frost Department of Dermatology and Cutaneous Surgery, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Jelena Marjanovic
- Wound Healing and Regenerative Medicine Research Program, Dr. Phillip Frost Department of Dermatology and Cutaneous Surgery, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Jamie L Burgess
- Wound Healing and Regenerative Medicine Research Program, Dr. Phillip Frost Department of Dermatology and Cutaneous Surgery, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Lisa Plano
- Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Suzanne Hower
- Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Seth R Thaller
- Department of Surgery, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Santanu Banerjee
- Department of Surgery, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Hadar Lev-Tov
- Wound Healing and Regenerative Medicine Research Program, Dr. Phillip Frost Department of Dermatology and Cutaneous Surgery, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Marjana Tomic-Canic
- Wound Healing and Regenerative Medicine Research Program, Dr. Phillip Frost Department of Dermatology and Cutaneous Surgery, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Irena Pastar
- Wound Healing and Regenerative Medicine Research Program, Dr. Phillip Frost Department of Dermatology and Cutaneous Surgery, University of Miami Miller School of Medicine, Miami, FL, USA
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17
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Smythe P, Wilkinson HN. The Skin Microbiome: Current Landscape and Future Opportunities. Int J Mol Sci 2023; 24:ijms24043950. [PMID: 36835363 PMCID: PMC9963692 DOI: 10.3390/ijms24043950] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/11/2023] [Accepted: 02/12/2023] [Indexed: 02/18/2023] Open
Abstract
Our skin is the largest organ of the body, serving as an important barrier against the harsh extrinsic environment. Alongside preventing desiccation, chemical damage and hypothermia, this barrier protects the body from invading pathogens through a sophisticated innate immune response and co-adapted consortium of commensal microorganisms, collectively termed the microbiota. These microorganisms inhabit distinct biogeographical regions dictated by skin physiology. Thus, it follows that perturbations to normal skin homeostasis, as occurs with ageing, diabetes and skin disease, can cause microbial dysbiosis and increase infection risk. In this review, we discuss emerging concepts in skin microbiome research, highlighting pertinent links between skin ageing, the microbiome and cutaneous repair. Moreover, we address gaps in current knowledge and highlight key areas requiring further exploration. Future advances in this field could revolutionise the way we treat microbial dysbiosis associated with skin ageing and other pathologies.
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Affiliation(s)
- Paisleigh Smythe
- Centre for Biomedicine, Hull York Medical School, University of Hull, Hull HU6 7RX, UK
- Skin Research Centre, Hull York Medical School, University of York, York YO10 5DD, UK
| | - Holly N. Wilkinson
- Centre for Biomedicine, Hull York Medical School, University of Hull, Hull HU6 7RX, UK
- Skin Research Centre, Hull York Medical School, University of York, York YO10 5DD, UK
- Correspondence:
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18
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Kim J, Choi Y, Park J, Choi J. Gelatin-Gallic Acid Microcomplexes Release GO/Cu Nanomaterials to Eradicate Antibiotic-Resistant Microbes and Their Biofilm. ACS Infect Dis 2023; 9:296-307. [PMID: 36696596 DOI: 10.1021/acsinfecdis.2c00439] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Wound-infecting bacteria are typically Pseudomonas aeruginosa and Staphylococcus epidermidis, both of which form biofilms and become resistant to antibiotics. To solve this problem, copper nanoparticles (Cu) on graphene oxide (GO) nanosheets were used as antibacterial materials. Since the excessive use of antibacterial substances is fatal to normal tissues, GO/Cu was encapsulated with a gelatin complex to lower the cytotoxicity. Among the catechol-based substances, gallic acid (GA), which has anti-inflammatory and antibacterial properties, was used in this study to impart stability to the gelatin complex. Gelatin (GE) and gallic acid (GA) were combined by a crosslinking method using 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC)/N-hydroxysuccinimide (NHS) as a crosslinker, and the crosslinking was confirmed by Fourier transform infrared (FT-IR), 1H NMR, and the fluorescence property of GA. The GO/Cu@GE-GA microcomplexes exhibited more antibacterial effect against Gram-positive bacteria (S. epidermidis) and Gram-negative bacteria (P. aeruginosa) than when GO/Cu alone was used, and the antibiofilm effect was also confirmed. The cytotoxicity evaluation for human skin cells (human dermal fibroblast (HDF)) at the same concentration showed that it had low cytotoxicity and biocompatibility. This study shows the potential of antimicrobial gelatin microcomplex in prohibiting infectious bacteria and their biofilms and controlling the release of antimicrobial substances.
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Affiliation(s)
- Jiwon Kim
- School of Integrative Engineering, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Yonghyun Choi
- School of Integrative Engineering, Chung-Ang University, Seoul 06974, Republic of Korea.,Feynman Institute of Technology, Nanomedicine Corporation, Seoul 06974, Republic of Korea
| | - Jongjun Park
- School of Integrative Engineering, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Jonghoon Choi
- School of Integrative Engineering, Chung-Ang University, Seoul 06974, Republic of Korea.,Feynman Institute of Technology, Nanomedicine Corporation, Seoul 06974, Republic of Korea
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19
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Staphylococcus epidermidis and its dual lifestyle in skin health and infection. Nat Rev Microbiol 2023; 21:97-111. [PMID: 36042296 PMCID: PMC9903335 DOI: 10.1038/s41579-022-00780-3] [Citation(s) in RCA: 66] [Impact Index Per Article: 66.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/19/2022] [Indexed: 01/20/2023]
Abstract
The coagulase-negative bacterium Staphylococcus epidermidis is a member of the human skin microbiota. S. epidermidis is not merely a passive resident on skin but actively primes the cutaneous immune response, maintains skin homeostasis and prevents opportunistic pathogens from causing disease via colonization resistance. However, it is now appreciated that S. epidermidis and its interactions with the host exist on a spectrum of potential pathogenicity derived from its high strain-level heterogeneity. S. epidermidis is the most common cause of implant-associated infections and is a canonical opportunistic biofilm former. Additional emerging evidence suggests that some strains of S. epidermidis may contribute to the pathogenesis of common skin diseases. Here, we highlight new developments in our understanding of S. epidermidis strain diversity, skin colonization dynamics and its multifaceted interactions with the host and other members of the skin microbiota.
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20
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Didelot X. Phylogenetic Analysis of Bacterial Pathogen Genomes. Methods Mol Biol 2023; 2674:87-99. [PMID: 37258962 DOI: 10.1007/978-1-0716-3243-7_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The development of high-throughput sequencing technology has led to a significant reduction in the time and cost of sequencing whole genomes of bacterial pathogens. Studies can sequence and compare hundreds or even thousands of genomes within a given bacterial population. A phylogenetic tree is the most frequently used method of depicting the relationships between these bacterial pathogen genomes. However, the presence of homologous recombination in most bacterial pathogen species can invalidate the application of standard phylogenetic tools. Here we describe a method to produce phylogenetic analyses that accounts for the disruptive effect of recombination. This allows users to investigate the recombination events that have occurred, as well as to produce more meaningful phylogenetic analyses which recover the clonal genealogy representing the clonal relationships between genomes.
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Affiliation(s)
- Xavier Didelot
- School of Life Sciences and Department of Statistics, University of Warwick, Coventry, UK.
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21
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Shakeel M, Majeed MI, Nawaz H, Rashid N, Ali A, Haque A, Akbar MU, Tahir M, Munir S, Ali Z, Shahbaz M, Saleem M. Surface-enhanced Raman spectroscopy for the characterization of pellets of biofilm forming bacterial strains of Staphylococcus epidermidis. Photodiagnosis Photodyn Ther 2022; 40:103145. [PMID: 36210039 DOI: 10.1016/j.pdpdt.2022.103145] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 09/20/2022] [Accepted: 10/04/2022] [Indexed: 11/06/2022]
Abstract
BACKGROUND Surface-enhanced Raman spectroscopy (SERS) is an effective tool for identifying biofilm forming bacterial strains. Biofilm forming bacteria are considered a major issue in the health sector because they have strong resistance against antibiotics. Staphylococcus epidermidis is commonly present on intravascular devices and prosthetic joints, catheters and wounds. OBJECTIVES To identify and characterize biofilm forming and non-biofilm forming bacterial strains, surface- enhanced Raman spectroscopy with principal component analysis (PCA) and partial least square discriminant analysis (PLS-DA) were used. METHODS Surface-enhanced Raman spectroscopy (SERS) with silver nanoparticles were employed for the analysis and characterization of biofilm forming bacterial strains. SERS is used to differentiate between non biofilm forming (five samples), medium biofilm forming (five samples) and strong biofilm forming (five samples) bacterial strains by applying silver nanoparticles (AgNPs) as SERS substrate. Principal component analysis (PCA) and Partial least square discriminant analysis (PLS-DA) were used to discriminate between non, medium and strong biofilm ability of bacterial strains. RESULTS Principal component analysis (PCA) and Partial least square discriminant analysis (PLS-DA) have been used to identify the biochemical differences in the form of SERS features which can be used to differentiate between biofilm forming and non-biofilm forming bacterial strains. PLS-DA provides successful differentiation and classification of these different strains with 94.5% specificity, 96% sensitivity and 89% area under the curve (AUC). CONCLUSIONS Surface-enhanced Raman spectroscopy can be utilized to differentiate between non, medium and strong biofilm forming bacterial strains.
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Affiliation(s)
- Muhammad Shakeel
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
| | - Muhammad Irfan Majeed
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan.
| | - Haq Nawaz
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan.
| | - Nosheen Rashid
- Department of Chemistry, University of Education, Faisalabad Campus, Faisalabad 38000, Pakistan.
| | - Aamir Ali
- National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Jhang Road, Faisalabad 38000, Pakistan
| | - Asma Haque
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad 38000, Pakistan
| | - Muhammad Umair Akbar
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad 38000, Pakistan
| | - Muhammad Tahir
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
| | - Saania Munir
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
| | - Zain Ali
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
| | - Muhammad Shahbaz
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
| | - Mudassar Saleem
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
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22
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Caldwell R, Zhou W, Oh J. Strains to go: interactions of the skin microbiome beyond its species. Curr Opin Microbiol 2022; 70:102222. [PMID: 36242896 PMCID: PMC9701184 DOI: 10.1016/j.mib.2022.102222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 09/07/2022] [Accepted: 09/14/2022] [Indexed: 01/25/2023]
Abstract
An extraordinary biodiversity of bacteria, fungi, viruses, and even small multicellular eukaryota inhabit the human skin. Genomic innovations have accelerated characterization of this biodiversity both at a species as well as the subspecies, or strain level, which further imparts a tremendous genetic diversity to an individual's skin microbiome. In turn, these advances portend significant species- and strain-specificity in the skin microbiome's functional impact on cutaneous immunity, barrier integrity, aging, and other skin physiologic processes. Future advances in defining strain diversity, spatial distribution, and metabolic diversity for major skin species will be foundational for understanding the microbiome's essentiality to the skin ecosystem and for designing topical therapeutics that leverage or target the skin microbiome.
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Affiliation(s)
- Ryan Caldwell
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, United States
| | - Wei Zhou
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, United States
| | - Julia Oh
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, United States.
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23
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Zamora-Mendoza L, Guamba E, Miño K, Romero MP, Levoyer A, Alvarez-Barreto JF, Machado A, Alexis F. Antimicrobial Properties of Plant Fibers. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27227999. [PMID: 36432099 PMCID: PMC9699224 DOI: 10.3390/molecules27227999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/09/2022] [Accepted: 11/12/2022] [Indexed: 11/19/2022]
Abstract
Healthcare-associated infections (HAI), or nosocomial infections, are a global health and economic problem in developed and developing countries, particularly for immunocompromised patients in their intensive care units (ICUs) and surgical site hospital areas. Recurrent pathogens in HAIs prevail over antibiotic-resistant bacteria, such as methicillin-resistant Staphylococcus aureus (MRSA) and Pseudomonas aeruginosa. For this reason, natural antibacterial mechanisms are a viable alternative for HAI treatment. Natural fibers can inhibit bacterial growth, which can be considered a great advantage in these applications. Moreover, these fibers have been reported to be biocompatible and biodegradable, essential features for biomedical materials to avoid complications due to infections and significant immune responses. Consequently, tissue engineering, medical textiles, orthopedics, and dental implants, as well as cosmetics, are fields currently expanding the use of plant fibers. In this review, we will discuss the source of natural fibers with antimicrobial properties, antimicrobial mechanisms, and their biomedical applications.
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Affiliation(s)
- Lizbeth Zamora-Mendoza
- School of Biological Sciences & Engineering, Yachay Tech University, Urcuquí 100119, Ecuador
| | - Esteban Guamba
- School of Biological Sciences & Engineering, Yachay Tech University, Urcuquí 100119, Ecuador
| | - Karla Miño
- School of Biological Sciences & Engineering, Yachay Tech University, Urcuquí 100119, Ecuador
| | - Maria Paula Romero
- School of Biological Sciences & Engineering, Yachay Tech University, Urcuquí 100119, Ecuador
| | - Anghy Levoyer
- Colegio de Ciencias e Ingenierías, Universidad San Francisco de Quito (USFQ), Departamento de Ingeniería Química, Quito 170901, Ecuador
| | - José F. Alvarez-Barreto
- Colegio de Ciencias e Ingenierías, Universidad San Francisco de Quito (USFQ), Departamento de Ingeniería Química, Quito 170901, Ecuador
| | - António Machado
- Colegio de Ciencias Biológicas y Ambientales COCIBA, Instituto de Microbiología, Universidad San Francisco de Quito (USFQ), Laboratorio de Bacteriología, Quito 170901, Ecuador
| | - Frank Alexis
- Colegio de Ciencias e Ingenierías, Universidad San Francisco de Quito (USFQ), Departamento de Ingeniería Química, Quito 170901, Ecuador
- Correspondence:
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24
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Chaguza C, Smith JT, Bruce SA, Gibson R, Martin IW, Andam CP. Prophage-encoded immune evasion factors are critical for Staphylococcus aureus host infection, switching, and adaptation. CELL GENOMICS 2022; 2:100194. [PMID: 36465278 PMCID: PMC9718559 DOI: 10.1016/j.xgen.2022.100194] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Staphylococcus aureus is a multi-host pathogen that causes infections in animals and humans globally. The specific genetic loci-and the extent to which they drive cross-species switching, transmissibility, and adaptation-are not well understood. Here, we conducted a population genomic study of 437 S. aureus isolates to identify bacterial genetic variation that determines infection of human and animal hosts through a genome-wide association study (GWAS) using linear mixed models. We found genetic variants tagging φSa3 prophage-encoded immune evasion genes associated with human hosts, which contributed ~99.9% of the overall heritability (~88%), highlighting their key role in S. aureus human infection. Furthermore, GWAS of pairs of phylogenetically matched human and animal isolates confirmed and uncovered additional loci not implicated in GWAS of unmatched isolates. Our findings reveal the loci that are critical for S. aureus host transmissibility, infection, switching, and adaptation and how their spread alters the specificity of host-adapted clones.
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Affiliation(s)
- Chrispin Chaguza
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, Yale University, New Haven, CT, USA,Corresponding author
| | | | - Spencer A. Bruce
- Department of Biological Sciences, University at Albany, State University of New York, New York, USA
| | - Robert Gibson
- New Hampshire Veterinary Diagnostic Laboratory, Durham, NH, USA
| | - Isabella W. Martin
- Dartmouth-Hitchcock Medical Center and Dartmouth College Geisel School of Medicine, Lebanon, NH, USA
| | - Cheryl P. Andam
- Department of Biological Sciences, University at Albany, State University of New York, New York, USA,Corresponding author
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25
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Chong CE, Bengtsson RJ, Horsburgh MJ. Comparative genomics of Staphylococcus capitis reveals species determinants. Front Microbiol 2022; 13:1005949. [PMID: 36246238 PMCID: PMC9563023 DOI: 10.3389/fmicb.2022.1005949] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 09/05/2022] [Indexed: 11/27/2022] Open
Abstract
Staphylococcus capitis is primarily described as a human skin commensal but is now emergent as an opportunistic pathogen isolated from the bloodstream and prosthetic joint infections, and neonatal intensive care unit (NICU)-associated sepsis. We used comparative genomic analyses of S. capitis to provide new insights into commensal scalp isolates from varying skin states (healthy, dandruff lesional, and non-lesional), and to expand our current knowledge of the species populations (scalp isolates, n = 59; other skin isolates, n = 7; publicly available isolates, n = 120). A highly recombinogenic population structure was revealed, with genomes including the presence of a range of previously described staphylococcal virulence factors, cell wall-associated proteins, and two-component systems. Genomic differences between the two described S. capitis subspecies were explored, which revealed the determinants associated exclusively with each subspecies. The subspecies ureolyticus was distinguished from subspecies capitis based on the differences in antimicrobial resistance genes, β-lactam resistance genes, and β-class phenol soluble modulins and gene clusters linked to biofilm formation and survival on skin. This study will aid further research into the classification of S. capitis and virulence-linked phylogroups to monitor the spread and evolution of S. capitis.
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26
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Hibifolin, a Natural Sortase A Inhibitor, Attenuates the Pathogenicity of Staphylococcus aureus and Enhances the Antibacterial Activity of Cefotaxime. Microbiol Spectr 2022; 10:e0095022. [PMID: 35913166 PMCID: PMC9430695 DOI: 10.1128/spectrum.00950-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This study aimed to identify hibifolin as a sortase A (SrtA) inhibitor and to determine whether it could attenuate the virulence of methicillin-resistant Staphylococcus aureus (MRSA). We employed a fluorescence resonance energy transfer (FRET) assay to screen a library of natural molecules to identify compounds that inhibit SrtA activity. Fluorescence quenching assay and molecular docking were performed to verify the direct binding interaction between SrtA and hibifolin. The pneumonia model was established using C57BL/6J mice by MRAS nasal administration for evaluating the effect of hibifolin on the pathogenicity of MRSA. Herein, we found that hibifolin was able to inhibit SrtA activity with an IC50 of 31.20 μg/mL. Further assays showed that the capacity of adhesion of bacteria to the host cells and biofilm formation was decreased in hibifolin-treated USA300. Results obtained from fluorescence quenching assay and molecular docking indicated that hibifolin was capable of targeting SrtA protein directly. This interaction was further confirmed by the finding that the inhibition activities of hibifolin on mutant SrtA were substantially reduced after mutating the binding sites (TRP-194, ALA-104, THR-180, ARG-197, ASN-114). The in vivo study showed that hibifolin in combination with cefotaxime protected mice from USA300 infection-induced pneumonia, which was more potent than cefotaxime alone, and no significant cytotoxicity of hibifolin was observed. Taken together, we identified that hibifolin attenuated the pathogenicity of S. aureus by directly targeting SrtA, which may be utilized in the future as adjuvant therapy for S. aureus infections. IMPORTANCE We identified hibifolin as a sortase A (SrtA) inhibitor by screening the natural compounds library, which effectively inhibited the activity of SrtA with an IC50 value of 31.20 μg/mL. Hibifolin attenuated the pathogenic behavior of Staphylococcus aureus, including adhesion, invasion, and biofilm formation. Binding assays showed that hibifolin bound to SrtA protein directly. Hibifolin improved the survival of pneumonia induced by S. aureus USA300 in mice and alleviated the pathological damage. Moreover, hibifolin showed a synergistic antibacterial effect with cefotaxime in USA300-infected mice.
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27
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Jin Y, Wang Q, Zhang H, Zhao N, Yang Z, Wang H, Li M, Liu Q. Phenol-soluble modulin contributes to the dispersal of Staphylococcus epidermidis isolates from catheters. Front Microbiol 2022; 13:934358. [PMID: 35958143 PMCID: PMC9358717 DOI: 10.3389/fmicb.2022.934358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 07/04/2022] [Indexed: 11/13/2022] Open
Abstract
Staphylococcus epidermidis (S. epidermidis), a human commensal, has been implicated in invasive infection in humans due to their ability to form biofilm. It is assumed that when a biofilm is dispersed it will subsequently cause a more severe infection. The clinical significance of S. epidermidis isolated from sterile body fluid (BF) remains unclear, and might be related to dispersal from catheter-associated biofilm infection. To evaluate this relationship, we evaluated S. epidermidis isolates from catheters (CA) or BF in hospitalized patients. Sequence type 2 (ST2) is the most prevalent type isolated from infection sites. Although the specific STs were also observed in isolates from different sites, we observed that the main sequence type was ST2, followed by ST59, among all the 114 isolates from different infection sites. Interestingly, ST2 strains isolated from BF exhibited significantly thicker biofilm than those from CA. The thicker biofilm was due to the higher expression of accumulation-associated protein (aap) but not intercellular adhesion (ica) operon. Moreover, the transcription of PSMδ and PSMε were significantly increased in ST2 strains isolated from BF. Although the bacterial loads on catheters were similar infected by CA- or BF-originated strains in mouse biofilm-associated infection model, we observed a higher CFU in peri-catheter tissues infected by ST2 clones isolated from BF, suggesting that S. epidermidis with thicker biofilm formation might be able to disperse. Taken together, our data suggested that S. epidermidis originated from diverse infection sites exhibited different biofilm forming capacity. The major ST2 clone isolated from BF exhibited thicker biofilm by increasing the expression of Aap. The higher expression of PSM of these strains may contribute to bacteria dispersal from biofilm and the following bacterial spread.
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28
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Sands K, Carvalho MJ, Spiller OB, Portal EAR, Thomson K, Watkins WJ, Mathias J, Dyer C, Akpulu C, Andrews R, Ferreira A, Hender T, Milton R, Nieto M, Zahra R, Shirazi H, Muhammad A, Akif S, Jan MH, Iregbu K, Modibbo F, Uwaezuoke S, Chan GJ, Bekele D, Solomon S, Basu S, Nandy RK, Naha S, Mazarati JB, Rucogoza A, Gaju L, Mehtar S, Bulabula ANH, Whitelaw A, Walsh TR. Characterisation of Staphylococci species from neonatal blood cultures in low- and middle-income countries. BMC Infect Dis 2022; 22:593. [PMID: 35790903 PMCID: PMC9254428 DOI: 10.1186/s12879-022-07541-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 06/15/2022] [Indexed: 11/14/2022] Open
Abstract
Background In low- and middle-income countries (LMIC) Staphylococcus aureus is regarded as one of the leading bacterial causes of neonatal sepsis, however there is limited knowledge on the species diversity and antimicrobial resistance caused by Gram-positive bacteria (GPB). Methods We characterised GPB isolates from neonatal blood cultures from LMICs in Africa (Ethiopia, Nigeria, Rwanda, and South Africa) and South-Asia (Bangladesh and Pakistan) between 2015–2017. We determined minimum inhibitory concentrations and performed whole genome sequencing (WGS) on Staphylococci isolates recovered and clinical data collected related to the onset of sepsis and the outcome of the neonate up to 60 days of age. Results From the isolates recovered from blood cultures, Staphylococci species were most frequently identified. Out of 100 S. aureus isolates sequenced, 18 different sequence types (ST) were found which unveiled two small epidemiological clusters caused by methicillin resistant S. aureus (MRSA) in Pakistan (ST8) and South Africa (ST5), both with high mortality (n = 6/17). One-third of S. aureus was MRSA, with methicillin resistance also detected in Staphylococcus epidermidis, Staphylococcus haemolyticus and Mammaliicoccus sciuri. Through additional WGS analysis we report a cluster of M. sciuri in Pakistan identified between July-November 2017. Conclusions In total we identified 14 different GPB bacterial species, however Staphylococci was dominant. These findings highlight the need of a prospective genomic epidemiology study to comprehensively assess the true burden of GPB neonatal sepsis focusing specifically on mechanisms of resistance and virulence across species and in relation to neonatal outcome. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-022-07541-w.
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29
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Stogov MV, Emanov AA, Goodovykh NV, Ovchinnikov EN, Tushina NV, Kuznetsov VP. Microbiological Profile of the Implantation Zone under Different Mechanical Compression of Percutaneous Implants: Experimental Study. TRAUMATOLOGY AND ORTHOPEDICS OF RUSSIA 2022; 28:38-47. [DOI: 10.17816/2311-2905-1725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/03/2023]
Abstract
Background. Infection of percutaneous implants in patients with limb amputation is the most common complication.
Aim of the study evaluation of the microflora in the implantation zone depending on the mechanical compression of the implant in conditions of its additional external fixation.
Methods. The study was performed on 36 male rabbits. The tibia of all the rabbits was sawn at the border of the upper and middle parts. The medullary canal was reamed and a percutaneous implant was placed in the tibial stump. The segment and the implant were fixed with an Ilizarov apparatus. An additional compression device was installed in 30 animals. We used 5 compression modes, accordingly, 6 experimental groups were formed, 6 animals in each: group 1 without compression, group 2 compression on the implant with force of 0.053 N/mm2, group 3 compression on the implant with force of 0.105 N/mm2, group 4 compression on the implant with force of 0.158 N/mm2, group 5 compression on the implant with force of 0.211 N/mm2, group 6 compression on the implant with force of 0.263 N/mm2. The restraint was removed 6 weeks after implantation for a total follow-up of 26 weeks. The microflora of the place where the implant enters the skin (the implant / skin interface) was investigated, the level of blood leukocytes and the level of C-reactive protein in blood serum were determined.
Results. On days 9-10 after implantation, significant differences in the microbial landscape were found at the site of the exit of the metal implant in animals of different groups. The largest number of strains was found in animals of groups 1, 5 and 6, the smallest in groups 2 and 3. The most frequently detected strains: S. saprophyticus and Enterococcus spp. It was found that the greatest statistically significant increase in the level of CRP in the blood serum was observed in animals of group 6. The level of leukocytes in animals of all groups did not change statistically significantly relative to preoperative values. Animals with better osseointegration (groups 2 and 3 no cases of implant loss) showed a minimal number of growing strains.
Conclusions. The microbiological profile of the implantation zone of percutaneous implants changes depending on the amount of mechanical compression. The optimal mode is 0.053-0.105 N/mm2.
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30
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Sheppard SK. Strain wars and the evolution of opportunistic pathogens. Curr Opin Microbiol 2022; 67:102138. [DOI: 10.1016/j.mib.2022.01.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 01/13/2022] [Accepted: 01/20/2022] [Indexed: 01/28/2023]
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31
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Kong HH, Oh J. State of Residency: Microbial Strain Diversity in the Skin. J Invest Dermatol 2022; 142:1260-1264. [PMID: 34688614 PMCID: PMC9021319 DOI: 10.1016/j.jid.2021.10.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 10/04/2021] [Accepted: 10/09/2021] [Indexed: 12/31/2022]
Abstract
Human skin hosts a diversity of microbiota. Advances in sequencing and analytical methods have increasingly illuminated the importance of the finest resolution in understanding the genetic diversity of the skin microbiota, highlighting strain-level differences and their functional implications. Such genetic diversity, which exists within an individual and is strongly individual specific underscores the difficulty in elucidating functionality. Integrated investigations of the microbial strain diversity through sequencing and culture-based approaches with host immunology and physiology will be critical in expanding our understanding of the roles of the skin microbiome.
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Affiliation(s)
- Heidi H Kong
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Julia Oh
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA.
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32
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Chaguza C, Ebruke C, Senghore M, Lo SW, Tientcheu PE, Gladstone RA, Tonkin-Hill G, Cornick JE, Yang M, Worwui A, McGee L, Breiman RF, Klugman KP, Kadioglu A, Everett DB, Mackenzie G, Croucher NJ, Roca A, Kwambana-Adams BA, Antonio M, Bentley SD. Comparative Genomics of Disease and Carriage Serotype 1 Pneumococci. Genome Biol Evol 2022; 14:evac052. [PMID: 35439297 PMCID: PMC9048925 DOI: 10.1093/gbe/evac052] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/12/2022] [Indexed: 11/14/2022] Open
Abstract
The isolation of Streptococcus pneumoniae serotypes in systemic tissues of patients with invasive disease versus the nasopharynx of healthy individuals with asymptomatic carriage varies widely. Some serotypes are hyper-invasive, particularly serotype 1, but the underlying genetics remain poorly understood due to the rarity of carriage isolates, reducing the power of comparison with invasive isolates. Here, we use a well-controlled genome-wide association study to search for genetic variation associated with invasiveness of serotype 1 pneumococci from a serotype 1 endemic setting in Africa. We found no consensus evidence that certain genomic variation is overrepresented among isolates from patients with invasive disease than asymptomatic carriage. Overall, the genomic variation explained negligible phenotypic variability, suggesting a minimal effect on the disease status. Furthermore, changes in lineage distribution were seen with lineages replacing each other over time, highlighting the importance of continued pathogen surveillance. Our findings suggest that the hyper-invasiveness is an intrinsic property of the serotype 1 strains, not specific for a "disease-associated" subpopulation disproportionately harboring unique genomic variation.
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Affiliation(s)
- Chrispin Chaguza
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Darwin College, University of Cambridge, Silver Street, Cambridge, UK
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Chinelo Ebruke
- Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Madikay Senghore
- Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
- Department of Epidemiology, Center for Communicable Disease Dynamics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Stephanie W. Lo
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Peggy-Estelle Tientcheu
- Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Rebecca A. Gladstone
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Department of Biostatistics, University of Oslo, Oslo, Norway
| | - Gerry Tonkin-Hill
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Jennifer E. Cornick
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Marie Yang
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Archibald Worwui
- Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Lesley McGee
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Robert F. Breiman
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Keith P. Klugman
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Aras Kadioglu
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Dean B. Everett
- College of Medicine and Health Sciences, Khalifa University, Abu Dhabi, UAE
| | - Grant Mackenzie
- Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
- Murdoch Children’s Research Institute, Parkville, Melbourne, VIC, Australia
- London School of Hygiene & Tropical Medicine, London, UK
| | - Nicholas J. Croucher
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK
| | - Anna Roca
- Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
- London School of Hygiene & Tropical Medicine, London, UK
| | - Brenda A. Kwambana-Adams
- Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
- NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection and Immunity, University College London, London, UK
| | - Martin Antonio
- Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
- London School of Hygiene & Tropical Medicine, London, UK
- Warwick Medical School, University of Warwick, Coventry, UK
| | - Stephen D. Bentley
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
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Keller LJ, Lakemeyer M, Bogyo M. Integration of bioinformatic and chemoproteomic tools for the study of enzyme conservation in closely related bacterial species. Methods Enzymol 2022; 664:1-22. [PMID: 35331369 DOI: 10.1016/bs.mie.2021.11.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Activity-based protein profiling (ABPP) is a commonly utilized technique to globally characterize the endogenous activity of multiple enzymes within a related family. While it has been used extensively to identify enzymes that are differentially active across various mammalian tissues, recent efforts have expanded this technique to studying bacteria. As ABPP is applied to diverse sets of bacterial strains found in microbial communities, there is also an increasing need for robust tools for assessing the conservation of enzymes across closely related bacterial species and strains. In this chapter, we detail the integration of gel-based ABPP with basic bioinformatic tools to enable the analysis of enzyme activity, distribution, and homology. We use as an example the family of serine hydrolases identified in the skin commensal bacterium Staphylococcus epidermidis.
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Affiliation(s)
- Laura J Keller
- Department of Chemical & Systems Biology, Stanford University, Stanford, CA, United States
| | - Markus Lakemeyer
- Department of Pathology, Stanford University, Stanford, CA, United States
| | - Matthew Bogyo
- Department of Pathology, Stanford University, Stanford, CA, United States; Department of Microbiology and Immunology, Stanford University, Stanford, CA, United States.
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A One Health Approach Molecular Analysis of Staphylococcus aureus Reveals Distinct Lineages in Isolates from Miranda Donkeys (Equus asinus) and Their Handlers. Antibiotics (Basel) 2022; 11:antibiotics11030374. [PMID: 35326837 PMCID: PMC8944429 DOI: 10.3390/antibiotics11030374] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 02/24/2022] [Accepted: 03/04/2022] [Indexed: 12/11/2022] Open
Abstract
Donkeys (Equus asinus) are in decline in Europe. Occupational exposure to farm animals has been associated with increased staphylococci carriage. We aimed to isolate S. aureus and coagulase-negative staphylococci (CoNS) from donkeys and handlers and characterize the antimicrobial resistance profiles and genetic lineages of S. aureus strains. Oral and nasal swab samples were collected from 49 Miranda donkeys and 23 handlers from 15 different farms. Staphylococci species were identified by MALDI-TOF MS. The presence of antimicrobial resistance genes and virulence factors was investigated by PCR. Molecular typing was performed in S. aureus isolates. From the 49 donkey samples, 4 S. aureus (8.2%) and 21 CoNS (42.9%) were isolated. Ten handlers (43.5%) were carriers of S. aureus and 4 (17.4%) carried CoNS. The CoNS isolates showed resistance to several classes of antimicrobials encoded by the mecA, aph (3′)-IIIa, ant (4′)-Ia, tetM, tetK, lnuA, ermB, ermC, dfrA and dfrG genes. S. aureus isolates were resistant to penicillin, aminoglicosides and tetracycline harboring the blaZ, aph (3′)-IIIa, tetL, tetM and tetK genes. All S. aureus isolates from donkeys belonged to ST49 and spa-type t208 while the strains isolated from the handlers were ascribed to 3 STs and 7 spa-types. However, human isolates were from different STs than the donkey isolates. Donkeys are mainly colonized by methicillin-resistant S. sciuri. S. aureus transmission between donkeys and their handlers appears not to have occurred since the isolates belonged to different genetic lineages.
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Zheng Y, Hunt RL, Villaruz AE, Fisher EL, Liu R, Liu Q, Cheung GYC, Li M, Otto M. Commensal Staphylococcus epidermidis contributes to skin barrier homeostasis by generating protective ceramides. Cell Host Microbe 2022; 30:301-313.e9. [PMID: 35123653 PMCID: PMC8917079 DOI: 10.1016/j.chom.2022.01.004] [Citation(s) in RCA: 79] [Impact Index Per Article: 39.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 12/07/2021] [Accepted: 01/11/2022] [Indexed: 12/19/2022]
Abstract
Previously either regarded as insignificant or feared as potential sources of infection, the bacteria living on our skin are increasingly recognized for their role in benefitting human health. Skin commensals modulate mucosal immune defenses and directly interfere with pathogens; however, their contribution to the skin's physical integrity is less understood. Here, we show that the abundant skin commensal Staphylococcus epidermidis contributes to skin barrier integrity. S. epidermidis secretes a sphingomyelinase that acquires essential nutrients for the bacteria and assists the host in producing ceramides, the main constituent of the epithelial barrier that averts skin dehydration and aging. In mouse models, S. epidermidis significantly increases skin ceramide levels and prevents water loss of damaged skin in a fashion entirely dependent on its sphingomyelinase. Our findings reveal a symbiotic mechanism that demonstrates an important role of the skin microbiota in the maintenance of the skin's protective barrier.
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Affiliation(s)
- Yue Zheng
- Pathogen Molecular Genetics Section, Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases, US National Institutes of Health, Bethesda, MD 20814, USA
| | - Rachelle L Hunt
- Pathogen Molecular Genetics Section, Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases, US National Institutes of Health, Bethesda, MD 20814, USA
| | - Amer E Villaruz
- Pathogen Molecular Genetics Section, Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases, US National Institutes of Health, Bethesda, MD 20814, USA
| | - Emilie L Fisher
- Pathogen Molecular Genetics Section, Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases, US National Institutes of Health, Bethesda, MD 20814, USA
| | - Ryan Liu
- Pathogen Molecular Genetics Section, Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases, US National Institutes of Health, Bethesda, MD 20814, USA
| | - Qian Liu
- Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Gordon Y C Cheung
- Pathogen Molecular Genetics Section, Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases, US National Institutes of Health, Bethesda, MD 20814, USA
| | - Min Li
- Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Michael Otto
- Pathogen Molecular Genetics Section, Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases, US National Institutes of Health, Bethesda, MD 20814, USA.
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Diversity of transcription activator-like effectors and pathogenicity in strains of Xanthomonas oryzae pv. oryzicola from Yunnan. World J Microbiol Biotechnol 2022; 38:71. [PMID: 35258706 DOI: 10.1007/s11274-022-03230-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 01/07/2022] [Indexed: 10/18/2022]
Abstract
The present study aimed to evaluate transcriptional activator-like effector (TALE) genes in 86 Xanthomonas oryzae pv. oryzicola strains collected from 8 rice-growing regions in Yunnan, and to examine the relationship between TALE genotypes and virulence in 6 differential rice lines. Besides, the geographical areas, distribution of these genotypes were studied in detail. Genetic diversity was analyzed through the number and size of putative TALE genes based on TALE gene avrXa3 as a probe. We found that X. oryzae pv. oryzicola strains consist of variable number (13-27) of avrXa3-hybridizing fragments (putative TALE genes). Test strains were classified into 8 genotypes (G1-G8) with major genotypes G3 and G7 widely distributed in Yunnan. Pathogenicity of X. oryzae pv. oryzicola was evaluated by inoculating 6 differential rice lines with a single resistance gene into 9 pathotypes clusters (I-IX), the dominant Genotypes G3 and G7 consist of pathotypes I, II, and IV. Furthermore, we also detected the known TALE target genes expression in susceptible rice cultivar (cv. nipponbare) after inoculating 8 genotypes-representative X. oryzae pv. oryzicola strain. Correlation between the numbers of putative TALE genes of X. oryzae pv. oryzicola and relevant target genes in nipponbare confirmed up-regulation. Altogether, this study has given insights into the population structure of X. oryzae pv. oryzicola that may inform strategies to control BLS in rice.
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Peng Z, Maciel-Guerra A, Baker M, Zhang X, Hu Y, Wang W, Rong J, Zhang J, Xue N, Barrow P, Renney D, Stekel D, Williams P, Liu L, Chen J, Li F, Dottorini T. Whole-genome sequencing and gene sharing network analysis powered by machine learning identifies antibiotic resistance sharing between animals, humans and environment in livestock farming. PLoS Comput Biol 2022; 18:e1010018. [PMID: 35333870 PMCID: PMC8986120 DOI: 10.1371/journal.pcbi.1010018] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 04/06/2022] [Accepted: 03/14/2022] [Indexed: 01/26/2023] Open
Abstract
Anthropogenic environments such as those created by intensive farming of livestock, have been proposed to provide ideal selection pressure for the emergence of antimicrobial-resistant Escherichia coli bacteria and antimicrobial resistance genes (ARGs) and spread to humans. Here, we performed a longitudinal study in a large-scale commercial poultry farm in China, collecting E. coli isolates from both farm and slaughterhouse; targeting animals, carcasses, workers and their households and environment. By using whole-genome phylogenetic analysis and network analysis based on single nucleotide polymorphisms (SNPs), we found highly interrelated non-pathogenic and pathogenic E. coli strains with phylogenetic intermixing, and a high prevalence of shared multidrug resistance profiles amongst livestock, human and environment. Through an original data processing pipeline which combines omics, machine learning, gene sharing network and mobile genetic elements analysis, we investigated the resistance to 26 different antimicrobials and identified 361 genes associated to antimicrobial resistance (AMR) phenotypes; 58 of these were known AMR-associated genes and 35 were associated to multidrug resistance. We uncovered an extensive network of genes, correlated to AMR phenotypes, shared among livestock, humans, farm and slaughterhouse environments. We also found several human, livestock and environmental isolates sharing closely related mobile genetic elements carrying ARGs across host species and environments. In a scenario where no consensus exists on how antibiotic use in the livestock may affect antibiotic resistance in the human population, our findings provide novel insights into the broader epidemiology of antimicrobial resistance in livestock farming. Moreover, our original data analysis method has the potential to uncover AMR transmission pathways when applied to the study of other pathogens active in other anthropogenic environments characterised by complex interconnections between host species. Livestock have been suggested as an important source of antimicrobial-resistant (AMR) Escherichia coli, capable of infecting humans and carrying resistance to drugs used in human medicine. China has a large intensive livestock farming industry, poultry being the second most important source of meat in the country, and is the largest user of antibiotics for food production in the world. Here we studied antimicrobial resistance gene overlap between E. coli isolates collected from humans, livestock and their shared environments in a large-scale Chinese poultry farm and associated slaughterhouse. By using a computational approach that integrates machine learning, whole-genome sequencing, gene sharing network and mobile genetic elements analysis we characterized the E. coli community structure, antimicrobial resistance phenotypes and the genetic relatedness of non-pathogenic and pathogenic E. coli strains. We uncovered the network of genes, associated with AMR, shared across host species (animals and workers) and environments (farm and slaughterhouse). Our approach opens up new avenues for the development of a fast, affordable and effective computational solutions that provide novel insights into the broader epidemiology of antimicrobial resistance in livestock farming.
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Affiliation(s)
- Zixin Peng
- NHC Key Laboratory of Food Safety Risk Assessment, Chinese Academy of Medical Science Research Unit (2019RU014), China National Center for Food Safety Risk Assessment, Beijing, People’s Republic of China
| | - Alexandre Maciel-Guerra
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, United Kingdom
| | - Michelle Baker
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, United Kingdom
| | - Xibin Zhang
- Qingdao Tian run Food Co., Ltd, New Hope, Beijing, People’s Republic of China
| | - Yue Hu
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, United Kingdom
| | - Wei Wang
- NHC Key Laboratory of Food Safety Risk Assessment, Chinese Academy of Medical Science Research Unit (2019RU014), China National Center for Food Safety Risk Assessment, Beijing, People’s Republic of China
| | - Jia Rong
- Qingdao Tian run Food Co., Ltd, New Hope, Beijing, People’s Republic of China
| | - Jing Zhang
- NHC Key Laboratory of Food Safety Risk Assessment, Chinese Academy of Medical Science Research Unit (2019RU014), China National Center for Food Safety Risk Assessment, Beijing, People’s Republic of China
| | - Ning Xue
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, United Kingdom
| | - Paul Barrow
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, United Kingdom
- School of Veterinary Medicine, University of Surrey, Guildford, Surrey, United Kingdom
| | - David Renney
- Nimrod Veterinary Products Limited, Moreton-in-Marsh, United Kingdom
| | - Dov Stekel
- School of Biosciences, University of Nottingham, Sutton Bonington, United Kingdom
| | - Paul Williams
- Biodiscovery Institute and School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Longhai Liu
- Qingdao Tian run Food Co., Ltd, New Hope, Beijing, People’s Republic of China
| | - Junshi Chen
- NHC Key Laboratory of Food Safety Risk Assessment, Chinese Academy of Medical Science Research Unit (2019RU014), China National Center for Food Safety Risk Assessment, Beijing, People’s Republic of China
| | - Fengqin Li
- NHC Key Laboratory of Food Safety Risk Assessment, Chinese Academy of Medical Science Research Unit (2019RU014), China National Center for Food Safety Risk Assessment, Beijing, People’s Republic of China
- * E-mail: (FL); (TD)
| | - Tania Dottorini
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, United Kingdom
- * E-mail: (FL); (TD)
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Ruan SF, Hu Y, Wu WF, Du QQ, Wang ZX, Chen TT, Shen Q, Liu L, Jiang CP, Li H, Yi Y, Shen CY, Zhu HX, Liu Q. Explore the Anti-Acne Mechanism of Licorice Flavonoids Based on Metabonomics and Microbiome. Front Pharmacol 2022; 13:832088. [PMID: 35211023 PMCID: PMC8861462 DOI: 10.3389/fphar.2022.832088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 01/17/2022] [Indexed: 11/13/2022] Open
Abstract
Acne vulgaris is one of the most common inflammatory dermatoses in dermatological practice and can affect any gender or ethnic group. Although in previous studies, we had found that licorice flavonoids (LCF) play an anti-acne role by inhibiting PI3K-Akt signaling pathways and mitochondrial activity, the mechanism of LCF regulating skin metabolism, serum metabolism and skin microbes is still unclear. Here, we performed a full spectrum analysis of metabolites in the skin and serum using UHPLC-Triple TOF-MS. The results showed that LCF could treat acne by regulating the metabolic balance of amino acids, lipids and fatty acids in serum and skin. Similarly, we performed Illumina Hiseq sequencing of DNA from the skin microbes using 16S ribosomal DNA identification techniques. The results showed that LCF could treat acne by regulating the skin microbes to interfere with acne and make the microecology close to the normal skin state of rats. In summary, this study confirmed the anti-acne mechanism of LCF, namely by regulating metabolic balance and microbial balance. Therefore, this discovery will provide theoretical guidance for the preparation development and clinical application of the drug.
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Affiliation(s)
- Shi-Fa Ruan
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
| | - Yi Hu
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
| | - Wen-Feng Wu
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
| | - Qun-Qun Du
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
| | - Zhu-Xian Wang
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
| | - Ting-Ting Chen
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
| | - Qun Shen
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
| | - Li Liu
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
| | - Cui-Ping Jiang
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
| | - Hui Li
- Department of Traditional Chinese Medicine, Guangzhou Red Cross Hospital, Guangzhou, China
| | - Yankui Yi
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
| | - Chun-Yan Shen
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
| | - Hong-Xia Zhu
- Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
| | - Qiang Liu
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
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Pochtovyi AA, Vasina DV, Verdiev BI, Shchetinin AM, Yuzhakov AG, Ovchinnikov RS, Tkachuk AP, Gushchin VA, Gintsburg AL. Microbiological Characteristics of Some Stations of Moscow Subway. BIOLOGY 2022; 11:biology11020170. [PMID: 35205037 PMCID: PMC8869165 DOI: 10.3390/biology11020170] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/17/2022] [Accepted: 01/20/2022] [Indexed: 01/08/2023]
Abstract
Simple Summary Public transport facilities, including subway systems, provide the most suitable conditions for the transfer of microorganisms between people and the environment, contributing to the pathogenic potential of the urban habitat. Investigation of microbiome diversity and description of its characteristic properties, e.g., antibiotic-resistance profiles, leads to understanding of these interactions. In this study, we aimed to conduct an extended analysis of the bioaerosol and surface microbiome of the Moscow subway, using 16S rRNA gene sample sequencing and classical microbiology methods. The microbiomes of two subway stations (Novokosino and Cherkizovskaya) were reconstructed which differ in terms of passenger traffic and duration of exploitation. It was shown that most bacterial genera were ubiquitous; however, the unique genera were presented in aerosol samples. The relatively older Cherkizovskaya station possessed greater diversity in antibiotic resistance among the identified microorganisms compared to Novokosino station. We also provided a comparative analysis of these results with the previously published data, which allowed us to identify the distribution of microorganisms associated with the human microbiome and the environment regardless of the seasonal fluctuations. The obtained results provide valuable information on the diversity of bacterial communities in the Moscow subway, one of the most socially important facilities in metropolitan areas. Abstract The subway is one of the most actively used means of transport in the traffic infrastructure of large metropolitan areas. More than seven million passengers use the Moscow subway every day, which promotes the exchange of microorganisms between people and the surrounding subway environment. In this research, a study of the bacterial communities of two Moscow subway stations was conducted and the common subway microbiome was determined. However, there were differences in microbiological and antibiotic-resistance profiles, depending on the station. The station’s operational period since opening correlated with the taxonomic diversity and resistance of the identified bacteria. Moreover, differences between aerosol and surface bacterial communities were found at the two subway stations, indicating the importance of diversified sampling during the microbiome profiling of public areas. In this study, we also compared our data with previously published results obtained for the Moscow subway. Despite sample collection at different stations and seasons, we showed the presence of 15 common genera forming the core microbiome of the Moscow subway, which represents human commensal species, as well as widespread microorganisms from the surrounding environment.
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Affiliation(s)
- Andrei A. Pochtovyi
- Federal State Budget Institution “National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N F Gamaleya” of the Ministry of Health of the Russian Federation, 123098 Moscow, Russia; (D.V.V.); (B.I.V.); (A.M.S.); (A.G.Y.); (R.S.O.); (A.P.T.); (A.L.G.)
- Department of Virology, Biological Faculty, Lomonosov Moscow State University, 119991 Moscow, Russia
- Correspondence: (A.A.P.); (V.A.G.); Tel.: +7-499-193-30-01 (A.A.P.)
| | - Daria V. Vasina
- Federal State Budget Institution “National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N F Gamaleya” of the Ministry of Health of the Russian Federation, 123098 Moscow, Russia; (D.V.V.); (B.I.V.); (A.M.S.); (A.G.Y.); (R.S.O.); (A.P.T.); (A.L.G.)
| | - Bakhtiyar I. Verdiev
- Federal State Budget Institution “National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N F Gamaleya” of the Ministry of Health of the Russian Federation, 123098 Moscow, Russia; (D.V.V.); (B.I.V.); (A.M.S.); (A.G.Y.); (R.S.O.); (A.P.T.); (A.L.G.)
| | - Alexey M. Shchetinin
- Federal State Budget Institution “National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N F Gamaleya” of the Ministry of Health of the Russian Federation, 123098 Moscow, Russia; (D.V.V.); (B.I.V.); (A.M.S.); (A.G.Y.); (R.S.O.); (A.P.T.); (A.L.G.)
| | - Anton G. Yuzhakov
- Federal State Budget Institution “National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N F Gamaleya” of the Ministry of Health of the Russian Federation, 123098 Moscow, Russia; (D.V.V.); (B.I.V.); (A.M.S.); (A.G.Y.); (R.S.O.); (A.P.T.); (A.L.G.)
- Laboratory of Biochemistry and Molecular Biology, Federal State Budget Scientific Institution “Federal Scientific Center VIEV”, 109428 Moscow, Russia
| | - Roman S. Ovchinnikov
- Federal State Budget Institution “National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N F Gamaleya” of the Ministry of Health of the Russian Federation, 123098 Moscow, Russia; (D.V.V.); (B.I.V.); (A.M.S.); (A.G.Y.); (R.S.O.); (A.P.T.); (A.L.G.)
- Laboratory of Mycology and Antibiotics, Federal Research Center “All-Russian Research Institute of Experimental Veterinary Medicine (VIEV) Named after K.I. Skryabin and Y.R. Kovalenko“ of Russian Academy of Science, 109428 Moscow, Russia
| | - Artem P. Tkachuk
- Federal State Budget Institution “National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N F Gamaleya” of the Ministry of Health of the Russian Federation, 123098 Moscow, Russia; (D.V.V.); (B.I.V.); (A.M.S.); (A.G.Y.); (R.S.O.); (A.P.T.); (A.L.G.)
| | - Vladimir A. Gushchin
- Federal State Budget Institution “National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N F Gamaleya” of the Ministry of Health of the Russian Federation, 123098 Moscow, Russia; (D.V.V.); (B.I.V.); (A.M.S.); (A.G.Y.); (R.S.O.); (A.P.T.); (A.L.G.)
- Department of Virology, Biological Faculty, Lomonosov Moscow State University, 119991 Moscow, Russia
- Correspondence: (A.A.P.); (V.A.G.); Tel.: +7-499-193-30-01 (A.A.P.)
| | - Alexander L. Gintsburg
- Federal State Budget Institution “National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N F Gamaleya” of the Ministry of Health of the Russian Federation, 123098 Moscow, Russia; (D.V.V.); (B.I.V.); (A.M.S.); (A.G.Y.); (R.S.O.); (A.P.T.); (A.L.G.)
- Department of Infectiology and Virology, Federal State Autonomous Educational Institution of Higher Education I M Sechenov, First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 119435 Moscow, Russia
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Look Who's Talking: Host and Pathogen Drivers of Staphylococcus epidermidis Virulence in Neonatal Sepsis. Int J Mol Sci 2022; 23:ijms23020860. [PMID: 35055041 PMCID: PMC8775791 DOI: 10.3390/ijms23020860] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 01/10/2022] [Accepted: 01/10/2022] [Indexed: 02/04/2023] Open
Abstract
Preterm infants are at increased risk for invasive neonatal bacterial infections. S. epidermidis, a ubiquitous skin commensal, is a major cause of late-onset neonatal sepsis, particularly in high-resource settings. The vulnerability of preterm infants to serious bacterial infections is commonly attributed to their distinct and developing immune system. While developmentally immature immune defences play a large role in facilitating bacterial invasion, this fails to explain why only a subset of infants develop infections with low-virulence organisms when exposed to similar risk factors in the neonatal ICU. Experimental research has explored potential virulence mechanisms contributing to the pathogenic shift of commensal S. epidermidis strains. Furthermore, comparative genomics studies have yielded insights into the emergence and spread of nosocomial S. epidermidis strains, and their genetic and functional characteristics implicated in invasive disease in neonates. These studies have highlighted the multifactorial nature of S. epidermidis traits relating to pathogenicity and commensalism. In this review, we discuss the known host and pathogen drivers of S. epidermidis virulence in neonatal sepsis and provide future perspectives to close the gap in our understanding of S. epidermidis as a cause of neonatal morbidity and mortality.
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Tuft S, Somerville TF, Li JPO, Neal T, De S, Horsburgh MJ, Fothergill JL, Foulkes D, Kaye S. Bacterial keratitis: identifying the areas of clinical uncertainty. Prog Retin Eye Res 2021; 89:101031. [PMID: 34915112 DOI: 10.1016/j.preteyeres.2021.101031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 11/24/2021] [Accepted: 11/29/2021] [Indexed: 12/12/2022]
Abstract
Bacterial keratitis is a common corneal infection that is treated with topical antimicrobials. By the time of presentation there may already be severe visual loss from corneal ulceration and opacity, which may persist despite treatment. There are significant differences in the associated risk factors and the bacterial isolates between high income and low- or middle-income countries, so that general management guidelines may not be appropriate. Although the diagnosis of bacterial keratitis may seem intuitive there are multiple uncertainties about the criteria that are used, which impacts the interpretation of investigations and recruitment to clinical studies. Importantly, the concept that bacterial keratitis can only be confirmed by culture ignores the approximately 50% of cases clinically consistent with bacterial keratitis in which investigations are negative. The aetiology of these culture-negative cases is unknown. Currently, the estimation of bacterial susceptibility to antimicrobials is based on data from systemic administration and achievable serum or tissue concentrations, rather than relevant corneal concentrations and biological activity in the cornea. The provision to the clinician of minimum inhibitory concentrations of the antimicrobials for the isolated bacteria would be an important step forward. An increase in the prevalence of antimicrobial resistance is a concern, but the effect this has on disease outcomes is yet unclear. Virulence factors are not routinely assessed although they may affect the pathogenicity of bacteria within species and affect outcomes. New technologies have been developed to detect and kill bacteria, and their application to bacterial keratitis is discussed. In this review we present the multiple areas of clinical uncertainty that hamper research and the clinical management of bacterial keratitis, and we address some of the assumptions and dogma that have become established in the literature.
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Affiliation(s)
- Stephen Tuft
- Moorfields Eye Hospital NHS Foundation Trust, 162 City Road, London, EC1V 2PD, UK.
| | - Tobi F Somerville
- Department of Eye and Vision Sciences, University of Liverpool, 6 West Derby Street, Liverpool, L7 8TX, UK.
| | - Ji-Peng Olivia Li
- Moorfields Eye Hospital NHS Foundation Trust, 162 City Road, London, EC1V 2PD, UK.
| | - Timothy Neal
- Department of Clinical Microbiology, Liverpool Clinical Laboratories, Liverpool University Hospital NHS Foundation Trust, Prescot Street, Liverpool, L7 8XP, UK.
| | - Surjo De
- Department of Clinical Microbiology, University College London Hospitals NHS Foundation Trust, 250 Euston Road, London, NW1 2PG, UK.
| | - Malcolm J Horsburgh
- Department of Infection and Microbiomes, University of Liverpool, Crown Street, Liverpool, L69 7BX, UK.
| | - Joanne L Fothergill
- Department of Eye and Vision Sciences, University of Liverpool, 6 West Derby Street, Liverpool, L7 8TX, UK.
| | - Daniel Foulkes
- Department of Eye and Vision Sciences, University of Liverpool, 6 West Derby Street, Liverpool, L7 8TX, UK.
| | - Stephen Kaye
- Department of Eye and Vision Sciences, University of Liverpool, 6 West Derby Street, Liverpool, L7 8TX, UK.
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Altwiley D, Brignoli T, Edwards A, Recker M, Lee JC, Massey RC. A functional menadione biosynthesis pathway is required for capsule production by Staphylococcus aureus. MICROBIOLOGY (READING, ENGLAND) 2021; 167. [PMID: 34825882 PMCID: PMC8743628 DOI: 10.1099/mic.0.001108] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Staphylococcus aureus is a major human pathogen that utilises a wide array of pathogenic and immune evasion strategies to cause disease. One immune evasion strategy, common to many bacterial pathogens, is the ability of S. aureus to produce a capsule that protects the bacteria from several aspects of the human immune system. To identify novel regulators of capsule production by S. aureus, we applied a genome wide association study (GWAS) to a collection of 300 bacteraemia isolates that represent the two major MRSA clones in UK and Irish hospitals: CC22 and CC30. One of the loci associated with capsule production, the menD gene, encodes an enzyme critical to the biosynthesis of menadione. Mutations in this gene that result in menadione auxotrophy induce the slow growing small-colony variant (SCV) form of S. aureus often associated with chronic infections due to their increased resistance to antibiotics and ability to survive inside phagocytes. Utilising such an SCV, we functionally verified this association between menD and capsule production. Although the clinical isolates with polymorphisms in the menD gene in our collections had no apparent growth defects, they were more resistant to gentamicin when compared to those with the wild-type menD gene. Our work suggests that menadione is involved in the production of the S. aureus capsule, and that amongst clinical isolates polymorphisms exist in the menD gene that confer the characteristic increased gentamicin resistance, but not the major growth defect associated with SCV phenotype.
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Affiliation(s)
- Dina Altwiley
- School of Cellular and Molecular Medicine, University of Bristol, BS8 1TD, UK.,University of Jeddah, Saudi Arabia
| | - Tarcisio Brignoli
- School of Cellular and Molecular Medicine, University of Bristol, BS8 1TD, UK
| | - Andrew Edwards
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, SW7 2AZ, UK
| | - Mario Recker
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, TR10 9FE, UK
| | - Jean C Lee
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Ruth C Massey
- School of Cellular and Molecular Medicine, University of Bristol, BS8 1TD, UK.,Schools of Microbiology and Medicine, and APC Microbiome Ireland, University College Cork, Ireland
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Viability-Resolved Metagenomics Reveals Antagonistic Colonization Dynamics of Staphylococcus epidermidis Strains on Preterm Infant Skin. mSphere 2021; 6:e0053821. [PMID: 34523979 PMCID: PMC8550141 DOI: 10.1128/msphere.00538-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Preterm infants are at increased risk of infections caused by coagulase-negative staphylococci (CoNS) that colonize skin. Technical barriers in sequencing low-microbial-biomass skin swabs from preterm infants hinder attempts to gain a strain-level understanding of CoNS colonization dynamics within their developing skin microbiome. Here, the microbiome of five skin sites and available stool was studied from four preterm infants hospitalized over their first 2 months of life. We used propidium monoazide treatment of samples to enrich for the viable microbiome and metagenomic shotgun sequencing to resolve species and strains. The microbiome of different skin sites overlapped with each other, was dominated by the CoNS species Staphylococcus epidermidis and Staphylococcus capitis, and was distinct from stool. Species diversity on skin increased over time despite antibiotic exposure. Evidence of antagonism between the most common S. epidermidis strains, ST2 and ST59, included negative relationships for species correlation networks and in situ replication rates and that ST2 colonized skin earlier but was often replaced by ST59 over time. Experiments done with reference isolates showed that ST2 produced more biofilm than ST59 on plastic surfaces, which was reduced in mixed culture. We also discovered that a rare S. epidermidis strain, ST5, grew rapidly in stool in association with Stenotrophomonas maltophilia from a suspected episode of infection. Viability treatment of samples and moderate throughput shotgun sequencing provides strain-level information about CoNS colonization dynamics of preterm infant skin that ultimately might be exploited to prevent infections. IMPORTANCE The skin is a habitat for microbes that commonly infect preterm infants, but the use of sequencing for fine-scale study of the microbial communities of skin that develop in these infants has been limited by technical barriers. We treated skin swabs of preterm infants with a photoreactive dye that eliminates DNA from nonviable microbes and then sequenced the remaining DNA. We found that two strains of the most common species, Staphylococcus epidermidis, showed an antagonistic relationship on skin by cooccurring with different species, replicating fastest in different samples, and dominating skin sites at different times. Representatives of these strains also differed in their ability to stick to plastic surfaces—an important pathogenicity trait of this species. Our study shows the feasibility of gaining detailed information about strain colonization dynamics from this difficult-to-sequence body site of preterm infants, which might be used to guide novel approaches to prevent infections.
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Widerström M, Stegger M, Johansson A, Gurram BK, Larsen AR, Wallinder L, Edebro H, Monsen T. Heterogeneity of Staphylococcus epidermidis in prosthetic joint infections: time to reevaluate microbiological criteria? Eur J Clin Microbiol Infect Dis 2021; 41:87-97. [PMID: 34599708 PMCID: PMC8732909 DOI: 10.1007/s10096-021-04352-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 09/17/2021] [Indexed: 11/24/2022]
Abstract
Prosthetic joint infection (PJI) is a feared and challenging to diagnose complication after arthroplasty, with Staphylococcus epidermidis as the major pathogen. One important criteria to define PJI is the detection of phenotypically indistinguishable microorganisms with identical antibiotic susceptibility pattern in at least two different samples. However, owing to phenotypical variation within genetic clones and clonal variation within a phenotype, the criteria may be ambiguous. We investigated the extent of diversity among coagulase-negative staphylococci (CoNS) in PJI and characterised S. epidermidis isolates from PJI samples, specifically multiple S. epidermidis isolates identified in individual PJI patients. We performed a retrospective cohort study on 62 consecutive patients with PJI caused by CoNS from two hospitals in Northern Sweden. In 16/62 (26%) PJIs, multiple S. epidermidis isolates were available for whole-genome analyses. Hospital-adapted multidrug-resistant genetic clones of S. epidermidis were identified in samples from 40/62 (65%) of the patients using a combination of pulsed-field gel electrophoresis and multilocus sequence typing. Whole-genome sequencing showed the presence of multiple sequence types (STs) in 7/16 (44%) PJIs where multiple S. epidermidis isolates were available. Within-patient phenotypical variation in the antibiotic susceptibility and/or whole-genome antibiotic resistance gene content was frequent (11/16, 69%) among isolates with the same ST. The results highlight the ambiguity of S. epidermidis phenotypic characterisation as a diagnostic method in PJI and call for larger systematic studies for determining the frequency of CoNS diversity in PJIs, the implications of such diversity for microbiological diagnostics, and the therapeutic outcomes in patients.
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Affiliation(s)
- Micael Widerström
- Department of Clinical Microbiology, Umeå University, SE-901 85, Umeå, Sweden.
| | - Marc Stegger
- Department of Bacteria, Parasites, and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Anders Johansson
- Department of Clinical Microbiology, Umeå University, SE-901 85, Umeå, Sweden
| | - Bharat Kumar Gurram
- Department of Clinical Microbiology, Umeå University, SE-901 85, Umeå, Sweden
| | - Anders Rhod Larsen
- Department of Bacteria, Parasites, and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Lars Wallinder
- Department of Orthopaedics, University Hospital of Umeå, Umeå, Sweden
| | - Helen Edebro
- Department of Clinical Microbiology, Umeå University, SE-901 85, Umeå, Sweden
| | - Tor Monsen
- Department of Clinical Microbiology, Umeå University, SE-901 85, Umeå, Sweden
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45
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Gallegos-Alcalá P, Jiménez M, Cervantes-García D, Salinas E. The Keratinocyte as a Crucial Cell in the Predisposition, Onset, Progression, Therapy and Study of the Atopic Dermatitis. Int J Mol Sci 2021; 22:ijms221910661. [PMID: 34639001 PMCID: PMC8509070 DOI: 10.3390/ijms221910661] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 09/27/2021] [Accepted: 09/27/2021] [Indexed: 12/24/2022] Open
Abstract
The keratinocyte (KC) is the main functional and structural component of the epidermis, the most external layer of the skin that is highly specialized in defense against external agents, prevention of leakage of body fluids and retention of internal water within the cells. Altered epidermal barrier and aberrant KC differentiation are involved in the pathophysiology of several skin diseases, such as atopic dermatitis (AD). AD is a chronic inflammatory disease characterized by cutaneous and systemic immune dysregulation and skin microbiota dysbiosis. Nevertheless, the pathological mechanisms of this complex disease remain largely unknown. In this review, we summarize current knowledge about the participation of the KC in different aspects of the AD. We provide an overview of the genetic predisposing and environmental factors, inflammatory molecules and signaling pathways of the KC that participate in the physiopathology of the AD. We also analyze the link among the KC, the microbiota and the inflammatory response underlying acute and chronic skin AD lesions.
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Affiliation(s)
- Pamela Gallegos-Alcalá
- Department of Microbiology, Center of Basic Science, Autonomous University of Aguascalientes, Aguascalientes 20100, Mexico; (P.G.-A.); (M.J.); (D.C.-G.)
| | - Mariela Jiménez
- Department of Microbiology, Center of Basic Science, Autonomous University of Aguascalientes, Aguascalientes 20100, Mexico; (P.G.-A.); (M.J.); (D.C.-G.)
| | - Daniel Cervantes-García
- Department of Microbiology, Center of Basic Science, Autonomous University of Aguascalientes, Aguascalientes 20100, Mexico; (P.G.-A.); (M.J.); (D.C.-G.)
- National Council of Science and Technology, Ciudad de México 03940, Mexico
| | - Eva Salinas
- Department of Microbiology, Center of Basic Science, Autonomous University of Aguascalientes, Aguascalientes 20100, Mexico; (P.G.-A.); (M.J.); (D.C.-G.)
- Correspondence: ; Tel.: +52-449-9108424
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Pistone D, Meroni G, Panelli S, D’Auria E, Acunzo M, Pasala AR, Zuccotti GV, Bandi C, Drago L. A Journey on the Skin Microbiome: Pitfalls and Opportunities. Int J Mol Sci 2021; 22:9846. [PMID: 34576010 PMCID: PMC8469928 DOI: 10.3390/ijms22189846] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/07/2021] [Accepted: 09/08/2021] [Indexed: 12/22/2022] Open
Abstract
The human skin microbiota is essential for maintaining homeostasis and ensuring barrier functions. Over the years, the characterization of its composition and taxonomic diversity has reached outstanding goals, with more than 10 million bacterial genes collected and cataloged. Nevertheless, the study of the skin microbiota presents specific challenges that need to be addressed in study design. Benchmarking procedures and reproducible and robust analysis workflows for increasing comparability among studies are required. For various reasons and because of specific technical problems, these issues have been investigated in gut microbiota studies, but they have been largely overlooked for skin microbiota. After a short description of the skin microbiota, the review tackles methodological aspects and their pitfalls, covering NGS approaches and high throughput culture-based techniques. Recent insights into the "core" and "transient" types of skin microbiota and how the manipulation of these communities can prevent or combat skin diseases are also covered. Finally, this review includes an overview of the main dermatological diseases, the changes in the microbiota composition associated with them, and the recommended skin sampling procedures. The last section focuses on topical and oral probiotics to improve and maintain skin health, considering their possible applications for skin diseases.
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Affiliation(s)
- Dario Pistone
- Pediatric Clinical Research Center “Invernizzi”, Department of Biomedical and Clinical Sciences “L. Sacco”, University of Milan, 20157 Milan, Italy; (S.P.); (A.R.P.); (G.V.Z.)
- Department of Biomedical Sciences for Health, University of Milan, 20133 Milan, Italy;
| | - Gabriele Meroni
- Department of Biomedical Surgical and Dental Sciences-One Health Unit, University of Milan, 20133 Milan, Italy;
| | - Simona Panelli
- Pediatric Clinical Research Center “Invernizzi”, Department of Biomedical and Clinical Sciences “L. Sacco”, University of Milan, 20157 Milan, Italy; (S.P.); (A.R.P.); (G.V.Z.)
| | - Enza D’Auria
- Department of Pediatrics, Children’s Hospital Vittore Buzzi, University of Milan, 20154 Milan, Italy; (E.D.); (M.A.)
| | - Miriam Acunzo
- Department of Pediatrics, Children’s Hospital Vittore Buzzi, University of Milan, 20154 Milan, Italy; (E.D.); (M.A.)
| | - Ajay Ratan Pasala
- Pediatric Clinical Research Center “Invernizzi”, Department of Biomedical and Clinical Sciences “L. Sacco”, University of Milan, 20157 Milan, Italy; (S.P.); (A.R.P.); (G.V.Z.)
| | - Gian Vincenzo Zuccotti
- Pediatric Clinical Research Center “Invernizzi”, Department of Biomedical and Clinical Sciences “L. Sacco”, University of Milan, 20157 Milan, Italy; (S.P.); (A.R.P.); (G.V.Z.)
- Department of Pediatrics, Children’s Hospital Vittore Buzzi, University of Milan, 20154 Milan, Italy; (E.D.); (M.A.)
| | - Claudio Bandi
- Pediatric Clinical Research Center “Invernizzi”, Department of Biosciences, University of Milan, 20133 Milan, Italy;
| | - Lorenzo Drago
- Department of Biomedical Sciences for Health, University of Milan, 20133 Milan, Italy;
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47
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Smith JT, Andam CP. Extensive Horizontal Gene Transfer within and between Species of Coagulase-Negative Staphylococcus. Genome Biol Evol 2021; 13:evab206. [PMID: 34498042 PMCID: PMC8462280 DOI: 10.1093/gbe/evab206] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/01/2021] [Indexed: 01/10/2023] Open
Abstract
Members of the gram-positive bacterial genus Staphylococcus have historically been classified into coagulase-positive Staphylococcus (CoPS) and coagulase-negative Staphylococcus (CoNS) based on the diagnostic presentation of the coagulase protein. Previous studies have noted the importance of horizontal gene transfer (HGT) and recombination in the more well-known CoPS species Staphylococcus aureus, yet little is known of the contributions of these processes in CoNS evolution. In this study, we aimed to elucidate the phylogenetic relationships, genomic characteristics, and frequencies of HGT in CoNS, which are now being recognized as major opportunistic pathogens of humans. We compiled a data set of 1,876 publicly available named CoNS genomes. These can be delineated into 55 species based on allele differences in 462 core genes and variation in accessory gene content. CoNS species are a reservoir of transferrable genes associated with resistance to diverse classes of antimicrobials. We also identified nine types of the mobile genetic element SCCmec, which carries the methicillin resistance determinant mecA. Other frequently transferred genes included those associated with resistance to heavy metals, surface-associated proteins related to virulence and biofilm formation, type VII secretion system, iron capture, recombination, and metabolic enzymes. The highest frequencies of receipt and donation of recombined DNA fragments were observed in Staphylococcus capitis, Staphylococcus caprae, Staphylococcus hominis, Staphylococcus haemolyticus, and members of the Saprophyticus species group. The variable rates of recombination and biases in transfer partners imply that certain CoNS species function as hubs of gene flow and major reservoir of genetic diversity for the entire genus.
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Affiliation(s)
- Joshua T Smith
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, USA
| | - Cheryl P Andam
- Department of Biological Sciences, University at Albany, State University of New York, New York, USA
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48
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Peters S, Pascoe B, Wu Z, Bayliss SC, Zeng X, Edwinson A, Veerabadhran-Gurunathan S, Jawahir S, Calland JK, Mourkas E, Patel R, Wiens T, Decuir M, Boxrud D, Smith K, Parker CT, Farrugia G, Zhang Q, Sheppard SK, Grover M. Campylobacter jejuni genotypes are associated with post-infection irritable bowel syndrome in humans. Commun Biol 2021; 4:1015. [PMID: 34462533 PMCID: PMC8405632 DOI: 10.1038/s42003-021-02554-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 08/13/2021] [Indexed: 02/08/2023] Open
Abstract
Campylobacter enterocolitis may lead to post-infection irritable bowel syndrome (PI-IBS) and while some C. jejuni strains are more likely than others to cause human disease, genomic and virulence characteristics promoting PI-IBS development remain uncharacterized. We combined pangenome-wide association studies and phenotypic assays to compare C. jejuni isolates from patients who developed PI-IBS with those who did not. We show that variation in bacterial stress response (Cj0145_phoX), adhesion protein (Cj0628_CapA), and core biosynthetic pathway genes (biotin: Cj0308_bioD; purine: Cj0514_purQ; isoprenoid: Cj0894c_ispH) were associated with PI-IBS development. In vitro assays demonstrated greater adhesion, invasion, IL-8 and TNFα secretion on colonocytes with PI-IBS compared to PI-no-IBS strains. A risk-score for PI-IBS development was generated using 22 genomic markers, four of which were from Cj1631c, a putative heme oxidase gene linked to virulence. Our finding that specific Campylobacter genotypes confer greater in vitro virulence and increased risk of PI-IBS has potential to improve understanding of the complex host-pathogen interactions underlying this condition. Stephanie Peters, Ben Pascoe, et al. use whole-genome sequencing and phenotypic analysis of clinical strains from patients to identify potential genetic factors involved in irritable bowel syndrome resulting from Campylobacter jejuni infection. Their data suggest that genes involved in the bacterial stress response and biosynthetic pathways may contribute toward irritable bowel syndrome, providing further insight into links between Campylobacter genotypes and risk of disease.
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Affiliation(s)
- Stephanie Peters
- Department of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Ben Pascoe
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, UK
| | - Zuowei Wu
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA, USA
| | - Sion C Bayliss
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, UK
| | - Ximin Zeng
- Department of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Adam Edwinson
- Department of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | | | | | - Jessica K Calland
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, UK
| | - Evangelos Mourkas
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, UK
| | - Robin Patel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Terra Wiens
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Marijke Decuir
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - David Boxrud
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Kirk Smith
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Craig T Parker
- United States Department of Agriculture, Albany, CA, USA
| | - Gianrico Farrugia
- Department of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Qijing Zhang
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA, USA
| | - Samuel K Sheppard
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, UK.
| | - Madhusudan Grover
- Department of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA.
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49
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Abdullahi IN, Lozano C, Ruiz-Ripa L, Fernández-Fernández R, Zarazaga M, Torres C. Ecology and Genetic Lineages of Nasal Staphylococcus aureus and MRSA Carriage in Healthy Persons with or without Animal-Related Occupational Risks of Colonization: A Review of Global Reports. Pathogens 2021; 10:1000. [PMID: 34451464 PMCID: PMC8400700 DOI: 10.3390/pathogens10081000] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 07/30/2021] [Accepted: 08/02/2021] [Indexed: 01/16/2023] Open
Abstract
In this conceptual review, we thoroughly searched for appropriate English articles on nasal staphylococci carriage among healthy people with no reported risk of colonization (Group A), food handlers (Group B), veterinarians (Group C), and livestock farmers (Group D) published between 2000 and 2021. Random-effects analyses of proportions were performed to determine the pooled prevalence of S. aureus, MRSA, MRSA-CC398, and MSSA-CC398, as well as the prevalence of PVL-positive S. aureus from all eligible studies. A total of 166 eligible papers were evaluated for Groups A/B/C/D (n = 58/31/26/51). The pooled prevalence of S. aureus and MRSA in healthy humans of Groups A to D were 15.9, 7.8, 34.9, and 27.1%, and 0.8, 0.9, 8.6, and 13.5%, respectively. The pooled prevalence of MRSA-CC398 nasal carriage among healthy humans was as follows: Group A/B (<0.05%), Group C (1.4%), Group D (5.4%); and the following among Group D: pig farmers (8.4%) and dairy farmers (4.7%). The pooled prevalence of CC398 lineage among the MSSA and MRSA isolates from studies of the four groups were Group A (2.9 and 6.9%), B (1.5 and 0.0%), C (47.6% in MRSA), and D (11.5 and 58.8%). Moreover, MSSA-CC398 isolates of Groups A and B were mostly of spa-t571 (animal-independent clade), while those of Groups C and D were spa-t011 and t034. The MRSA-CC398 was predominately of t011 and t034 in all the groups (with few other spa-types, livestock-associated clades). The pooled prevalence of MSSA and MRSA isolates carrying the PVL encoding genes were 11.5 and 9.6% (ranges: 0.0-76.9 and 0.0-28.6%), respectively. Moreover, one PVL-positive MSSA-t011-CC398 isolate was detected in Group A. Contact with livestock and veterinary practice seems to increase the risk of carrying MRSA-CC398, but not in food handlers. Thus, this emphasizes the need for integrated molecular epidemiology of zoonotic staphylococci.
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Affiliation(s)
| | | | | | | | | | - Carmen Torres
- Area of Biochemistry and Molecular Biology, University of La Rioja, Madre de Dios 53, 26006 Logroño, Spain; (I.N.A.); (C.L.); (L.R.-R.); (R.F.-F.); (M.Z.)
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50
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Ahle CM, Stødkilde-Jørgensen K, Poehlein A, Streit WR, Hüpeden J, Brüggemann H. Comparison of three amplicon sequencing approaches to determine staphylococcal populations on human skin. BMC Microbiol 2021; 21:221. [PMID: 34320945 PMCID: PMC8320028 DOI: 10.1186/s12866-021-02284-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 07/21/2021] [Indexed: 02/08/2023] Open
Abstract
Background Staphylococci are important members of the human skin microbiome. Many staphylococcal species and strains are commensals of the healthy skin microbiota, while few play essential roles in skin diseases such as atopic dermatitis. To study the involvement of staphylococci in health and disease, it is essential to determine staphylococcal populations in skin samples beyond the genus and species level. Culture-independent approaches such as amplicon next-generation sequencing (NGS) are time- and cost-effective options. However, their suitability depends on the power of resolution. Results Here we compare three amplicon NGS schemes that rely on different targets within the genes tuf and rpsK, designated tuf1, tuf2 and rpsK schemes. The schemes were tested on mock communities and on human skin samples. To obtain skin samples and build mock communities, skin swab samples of healthy volunteers were taken. In total, 254 staphylococcal strains were isolated and identified to the species level by MALDI-TOF mass spectrometry. A subset of ten strains belonging to different staphylococcal species were genome-sequenced. Two mock communities with nine and eighteen strains, respectively, as well as eight randomly selected skin samples were analysed with the three amplicon NGS methods. Our results imply that all three methods are suitable for species-level determination of staphylococcal populations. However, the novel tuf2-NGS scheme was superior in resolution power. It unambiguously allowed identification of Staphylococcus saccharolyticus and distinguish phylogenetically distinct clusters of Staphylococcus epidermidis. Conclusions Powerful amplicon NGS approaches for the detection and relative quantification of staphylococci in human samples exist that can resolve populations to the species and, to some extent, to the subspecies level. Our study highlights strengths, weaknesses and pitfalls of three currently available amplicon NGS approaches to determine staphylococcal populations. Applied to the analysis of healthy and diseased skin, these approaches can be useful to attribute host-beneficial and -detrimental roles to skin-resident staphylococcal species and subspecies. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02284-1.
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Affiliation(s)
- Charlotte Marie Ahle
- Beiersdorf AG, Research & Development, Front End Innovation, 20245, Hamburg, Germany.,Department of Microbiology and Biotechnology, University of Hamburg, 22609, Hamburg, Germany
| | | | - Anja Poehlein
- Department of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, University of Göttingen, 37073, Göttingen, Germany
| | - Wolfgang R Streit
- Department of Microbiology and Biotechnology, University of Hamburg, 22609, Hamburg, Germany
| | - Jennifer Hüpeden
- Beiersdorf AG, Research & Development, Front End Innovation, 20245, Hamburg, Germany
| | - Holger Brüggemann
- Department of Biomedicine, Aarhus University, 8000, Aarhus, Denmark.
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