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Hain‐Saunders N, Knight DR, Bruce M, Riley TV. Clostridioides difficile
infection and One Health: An Equine Perspective. Environ Microbiol 2022; 24:985-997. [PMID: 35001483 PMCID: PMC9304292 DOI: 10.1111/1462-2920.15898] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 01/04/2022] [Accepted: 01/05/2022] [Indexed: 11/29/2022]
Abstract
Clostridioides (Clostridium) difficile presents a significant health risk to humans and animals. The complexity of the bacterial–host interaction affecting pathogenesis and disease development creates an ongoing challenge for epidemiological studies, control strategies and prevention planning. The recent emergence of human disease caused by strains of C. difficile found in animals adds to mounting evidence that C. difficile infection (CDI) may be a zoonosis. In equine populations, C. difficile is a known cause of diarrhoea and gastrointestinal inflammation, with considerable mortality and morbidity. This has a significant impact on both the well‐being of the animal and, in the case of performance and production animals, it may have an adverse economic impact on relevant industries. While C. difficile is regularly isolated from horses, many questions remain regarding the impact of asymptomatic carriage as well as optimization of diagnosis, testing and treatment. This review provides an overview of our understanding of equine CDI while also identifying knowledge gaps and the need for a holistic One Health approach to a complicated issue.
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Affiliation(s)
- Natasza Hain‐Saunders
- Biosecurity and One Health Research Centre, Harry Butler Institute Murdoch University Murdoch Western Australia Australia
| | - Daniel R. Knight
- Biosecurity and One Health Research Centre, Harry Butler Institute Murdoch University Murdoch Western Australia Australia
- School of Biomedical Sciences, The University of Western Australia, Queen Elizabeth II Medical Centre Nedlands 6009 WA Australia
| | - Mieghan Bruce
- School of Veterinary Medicine, Centre for Biosecurity and One Health Murdoch University Murdoch Western Australia Australia
| | - Thomas V. Riley
- Biosecurity and One Health Research Centre, Harry Butler Institute Murdoch University Murdoch Western Australia Australia
- School of Biomedical Sciences, The University of Western Australia, Queen Elizabeth II Medical Centre Nedlands 6009 WA Australia
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia Australia
- Department of Microbiology, PathWest Laboratory Medicine, Queen Elizabeth II Medical Centre Nedlands Western Australia Australia
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Su T, Chen W, Wang D, Cui Y, Ni Q, Jiang C, Dong D, Peng Y. Complete Genome Sequencing and Comparative Phenotypic Analysis Reveal the Discrepancy Between Clostridioides difficile ST81 and ST37 Isolates. Front Microbiol 2021; 12:776892. [PMID: 34992586 PMCID: PMC8725731 DOI: 10.3389/fmicb.2021.776892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 11/22/2021] [Indexed: 11/26/2022] Open
Abstract
Toxin A-negative, toxin B-positive Clostridioides difficile strains, which primarily include the ST81 and ST37 genotypes, are predominant in C. difficile infections leading to antibiotic-associated diarrhea in China. Recently, ST81 has been reported as the most prevalent genotype rather than ST37, although the genetic and functional characteristics of the two genotypes remain ambiguous. In this study, we conducted comprehensive comparative analysis of these two genotypes through complete genome sequencing and phenotypic profiling. The whole genome sequencing revealed that the ST81 and ST37 isolates were closely related genetically with similar gene compositions, and high rate of the core genome shared. The integrative and conjugative elements identified in ST81 were similar to those in ST37, albeit with more diverse and insertion regions. By characterizing the phenotypes related to colonization or survival in the host, we found that the ST81 isolates exhibited robust colonization ability and survival both in vitro and in vivo, enhanced spore production, and slightly increased motility, which may be attributable to the discrepancy in non-synonymous single-nucleotide polymorphisms in the relevant functional genes. Furthermore, the ST81 isolates displayed a significantly higher rate of resistance to fluoroquinolones compared with the ST37 isolates (94.12% vs. 62.5%) and mostly carried the amino acid substitution Asp426Val in GyrB. In summary, the results of our study indicate that ST81 isolates exhibit enhanced ability to transmit between hosts and survive in harsh environments, providing key genetic insights for further epidemiological investigations and surveillance of C. difficile infection.
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Affiliation(s)
- Tongxuan Su
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wei Chen
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Daosheng Wang
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yingchao Cui
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qi Ni
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Cen Jiang
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Danfeng Dong
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- *Correspondence: Danfeng Dong,
| | - Yibing Peng
- Faculty of Medical Laboratory Science, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Yibing Peng,
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Genotyping and Antimicrobial Susceptibility of Clostridium perfringens and Clostridioides difficile in Camel Minced Meat. Pathogens 2021; 10:pathogens10121640. [PMID: 34959595 PMCID: PMC8708398 DOI: 10.3390/pathogens10121640] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 12/11/2021] [Accepted: 12/17/2021] [Indexed: 12/19/2022] Open
Abstract
The present study aimed to determine the occurrence, genotypes, and antimicrobial resistance of Clostridium perfringens (C. perfringens) and Clostridioides difficile (C. difficile) in camel minced meat samples collected from small butcher shops and supermarkets in Al-Ahsa Governorate, Saudi Arabia. A total of 100 camel minced meat samples were randomly collected from small butcher’s shops (n = 50) and supermarkets (n = 50) in Al-Ahsa Governorate, Saudi Arabia. C. perfringens and C. difficile were isolated and identified using the VITEK-2 compact system and 16S rRNA gene amplification. Genotypes, toxin genes, and antimicrobial susceptibility of the isolates were determined. Moreover, ELISA was used to detect C. perfringens and C. difficile toxins. C. perfringens and C. difficile were isolated from 14% and 4% of the tested minced meat samples, respectively. Out of the 14 C. perfringens isolates, type A (64.3%), type B (7.1%), type C (21.5%), and type D (7.1%) were detected. However, out of the four C. difficile isolates, three (75%) were type A+B+ and one (25%) was type A−B+. None of the C. perfringens or C. difficile toxins were identified using ELISA. C. perfringens and C. difficile isolates exhibited a high rate of resistance to tetracycline (56% and 75%, respectively). However, all isolates were susceptible to amoxicillin-clavulanate. Multidrug resistance was observed in three (21.4%) C. perfringens and one (25%) C. difficile isolates. In conclusion, camel minced meat was contaminated with C. perfringens and C. difficile, which present a potential risk of food poisoning. The majority of the isolates were resistant to at least one antimicrobial, and some isolates were multidrug-resistant. Therefore, food safety standards and frequent inspections of abattoirs, small butcher shops, and supermarkets should be enforced.
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Gu W, Wang W, Li W, Li N, Wang Y, Zhang W, Lu C, Tong P, Han Y, Sun X, Lu J, Wu Y, Dai J. New ribotype Clostridioides difficile from ST11 group revealed higher pathogenic ability than RT078. Emerg Microbes Infect 2021; 10:687-699. [PMID: 33682630 PMCID: PMC8023612 DOI: 10.1080/22221751.2021.1900748] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 02/07/2021] [Accepted: 03/04/2021] [Indexed: 11/14/2022]
Abstract
Clostridioides difficile is the predominant antibiotic-associated enteropathogen associated with diarrhoea or pseudomembranous colitis in patients worldwide. Previously, we identified C. difficile RT078 isolates (CD21062) from elderly patients in China, including two new ribotype strains (CD10010 and CD12038) belonging to the ST11 group, and their genomic features were also investigated. This study compared sporulation, spore germination, toxin expression, flagellar characteristics, and adhesion among these strains in vitro and analysed their pathogenic ability in vivo using animal models. The results showed sporulation and spore germination did not significantly differ among the three C. difficile strains. CD10010 and CD12038 showed higher transcriptional levels of toxins until 48 h; thereafter, the transcriptional levels of toxins remained constant among RT078, CD10010, and CD12038. RT078 showed a loss of flagellum and its related genes, whereas CD12038 showed the highest motility in vitro. Both CD10010 and CD12038 initially showed flg phase OFF, and the flagellar switch reversed to phase ON after 48 h in swim agar. Flagellar proteins and toxins were both upregulated when flg phase OFF changed to flg phase ON status, enhancing their pathogenic ability. CD12038 showed the highest adhesion to Hep-2 cells. Histopathology and inflammation scores demonstrated that CD12038 caused the most severe tissue damage and infection in vivo. The new ribotype strains, particularly CD12038, exhibit higher pathogenic ability than the typical RT078 strain, both in vitro and in vivo. Therefore, more attention should be paid to this new C. difficile strain in epidemiological research; further studies are warranted.
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Affiliation(s)
- Wenpeng Gu
- Center of Tree Shrew Germplasm Resources, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Yunnan Innovation Team of Standardization and Application Research in Tree Shrew, Kunming, China
- Department of Acute Infectious Diseases Control and Prevention, Yunnan Provincial Centre for Disease Control and Prevention, Kunming, China
| | - Wenguang Wang
- Center of Tree Shrew Germplasm Resources, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Yunnan Innovation Team of Standardization and Application Research in Tree Shrew, Kunming, China
| | - Wenge Li
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Na Li
- Center of Tree Shrew Germplasm Resources, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Yunnan Innovation Team of Standardization and Application Research in Tree Shrew, Kunming, China
| | - Yuanyuan Wang
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Wenzhu Zhang
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Caixia Lu
- Center of Tree Shrew Germplasm Resources, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Yunnan Innovation Team of Standardization and Application Research in Tree Shrew, Kunming, China
| | - Pinfen Tong
- Center of Tree Shrew Germplasm Resources, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Yunnan Innovation Team of Standardization and Application Research in Tree Shrew, Kunming, China
| | - Yuanyuan Han
- Center of Tree Shrew Germplasm Resources, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Yunnan Innovation Team of Standardization and Application Research in Tree Shrew, Kunming, China
| | - Xiaomei Sun
- Center of Tree Shrew Germplasm Resources, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Yunnan Innovation Team of Standardization and Application Research in Tree Shrew, Kunming, China
| | - Jinxing Lu
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yuan Wu
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jiejie Dai
- Center of Tree Shrew Germplasm Resources, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Yunnan Innovation Team of Standardization and Application Research in Tree Shrew, Kunming, China
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Weiss A, Lopez CA, Beavers WN, Rodriguez J, Skaar EP. Clostridioides difficile strain-dependent and strain-independent adaptations to a microaerobic environment. Microb Genom 2021; 7:000738. [PMID: 34908523 PMCID: PMC8767335 DOI: 10.1099/mgen.0.000738] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Clostridioides difficile (formerly Clostridium difficile) colonizes the gastrointestinal tract following disruption of the microbiota and can initiate a spectrum of clinical manifestations ranging from asymptomatic to life-threatening colitis. Following antibiotic treatment, luminal oxygen concentrations increase, exposing gut microbes to potentially toxic reactive oxygen species. Though typically regarded as a strict anaerobe, C. difficile can grow at low oxygen concentrations. How this bacterium adapts to a microaerobic environment and whether those responses to oxygen are conserved amongst strains is not entirely understood. Here, two C. difficile strains (630 and CD196) were cultured in 1.5% oxygen and the transcriptional response to long-term oxygen exposure was evaluated via RNA-sequencing. During growth in a microaerobic environment, several genes predicted to protect against oxidative stress were upregulated, including those for rubrerythrins and rubredoxins. Transcription of genes involved in metal homeostasis was also positively correlated with increased oxygen levels and these genes were amongst the most differentially transcribed. To directly compare the transcriptional landscape between C. difficile strains, a 'consensus-genome' was generated. On the basis of the identified conserved genes, basal transcriptional differences as well as variations in the response to oxygen were evaluated. While several responses were similar between the strains, there were significant differences in the abundance of transcripts involved in amino acid and carbohydrate metabolism. Furthermore, intracellular metal concentrations significantly varied both in an oxygen-dependent and oxygen-independent manner. Overall, these results indicate that C. difficile adapts to grow in a low oxygen environment through transcriptional changes, though the specific strategy employed varies between strains.
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Affiliation(s)
- Andy Weiss
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Christopher A. Lopez
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Biological Sciences, California State University Sacramento, Sacramento, CA, USA
| | - William N. Beavers
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jhoana Rodriguez
- Department of Biological Sciences, California State University Sacramento, Sacramento, CA, USA
| | - Eric P. Skaar
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN, USA
- *Correspondence: Eric P. Skaar,
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56
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Huang J, Zhao Z, Zhang Q, Zhang S, Zhang S, Chen M, Qiu H, Cao Y, Li B. Phylogenetic Analysis Reveals Distinct Evolutionary Trajectories of the Fluoroquinolones-Resistant Escherichia coli ST1193 From Fuzhou, China. Front Microbiol 2021; 12:746995. [PMID: 34803966 PMCID: PMC8602892 DOI: 10.3389/fmicb.2021.746995] [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] [Received: 07/25/2021] [Accepted: 10/13/2021] [Indexed: 01/27/2023] Open
Abstract
Escherichia coli (E. coli) ST1193 is an emerging fluoroquinolones-resistant and virulent lineage. Large gaps remain in our understanding of the evolutionary processes and differences of this lineage. Therefore, we used 76 E. coli ST1193 genomes to detect strain-level genetic diversity and phylogeny of this lineage globally. All E. coli ST1193 possessed fimH64, filCH5, and fumC14. There was 94.7% of isolates classified as O-type O75. There was 9.33% of E. coli ST1193 that possessed K5 capsular, while 90.67% of isolates possessed K1 capsular. The core genome analysis revealed that all isolates were divided into two phylogenetic clades (clade A and B). Clade A included 25 non-Chinese E. coli ST1193, and clade B contained all isolates collected from Fuzhou, China, respectively. The results of comparative genomics indicated Indels were identified in 150 clade-specific genes, which were enriched into the biological process and molecular function. Accessory genome phylogenetic tree showed a high degree of correlation between accessory genome clusters and core genome clades. There was significant difference in antibiotic resistance genes (ARGs) [bla CTX-M-55 , bla TEM-1 , sul2, tet(B), tet(R), APH(6)-Id, and AAC(3)-IId], virulence factors (cia, neuC, gad, and traT), and plasmid replicon types (IncQ1, Col156, and IncB/O/K/Z) between clade A (non-Chinese isolates) and clade B (Chinese isolates) (p < 0.05). Further analysis of the genetic environments of bla CTX-M-55 demonstrated that the flanking contexts of bla CTX-M-55 were diverse. In conclusion, our results reveal the distinct evolutionary trajectories of the spread of E. coli ST1193 in Fuzhou, China and non-China regions. This supports both global transmission and localized lineage expansion of this lineage following specific introductions into a geographic locality.
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Affiliation(s)
- Jiangqing Huang
- Department of Clinical Laboratory, Fujian Medical University Union Hospital, Fuzhou, China
| | - Zhichang Zhao
- Department of Pharmacy, Fujian Medical University Union Hospital, Fuzhou, China
| | - Qianwen Zhang
- Department of Clinical Laboratory, Fujian Medical University Union Hospital, Fuzhou, China
| | - Shengcen Zhang
- Department of Clinical Laboratory, Fujian Medical University Union Hospital, Fuzhou, China
| | - Shuyu Zhang
- Department of Laboratory Medicine, Fujian Medical University, Fuzhou, China
| | - Min Chen
- Department of Laboratory Medicine, Fujian Medical University, Fuzhou, China
| | - Hongqiang Qiu
- Department of Pharmacy, Fujian Medical University Union Hospital, Fuzhou, China
| | - Yingping Cao
- Department of Clinical Laboratory, Fujian Medical University Union Hospital, Fuzhou, China
| | - Bin Li
- Department of Clinical Laboratory, Fujian Medical University Union Hospital, Fuzhou, China
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An aniline-substituted bile salt analog protects both mice and hamsters from multiple Clostridioides difficile strains. Antimicrob Agents Chemother 2021; 66:e0143521. [PMID: 34780262 DOI: 10.1128/aac.01435-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Clostridioides difficile infection (CDI) is the major identifiable cause of antibiotic-associated diarrhea. The emergence of hypervirulent C. difficile strains has led to increases in both hospital- and community-acquired CDI. Furthermore, CDI relapse from hypervirulent strains can reach up to 25%. Thus, standard treatments are rendered less effective, making new methods of prevention and treatment more critical. Previously, the bile salt analog CamSA was shown to inhibit spore germination in vitro and protect mice and hamsters from C. difficile strain 630. Here, we show that CamSA was less active at preventing spore germination of other C. difficile ribotypes, including the hypervirulent strain R20291. Strain-specific in vitro germination activity of CamSA correlated with its ability to prevent CDI in mice. Additional bile salt analogs were screened for in vitro germination inhibition activity against strain R20291, and the most active compounds were tested against other strains. An aniline-substituted bile salt analog, (CaPA), was found to be a better anti-germinant than CamSA against eight different C. difficile strains. In addition, CaPA was capable of reducing, delaying, or preventing murine CDI signs in all strains tested. CaPA-treated mice showed no obvious toxicity and showed minor effects on their gut microbiome. CaPA's efficacy was further confirmed by its ability to prevent CDI in hamsters infected with strain 630. These data suggest that C. difficile spores respond to germination inhibitors in a strain-dependent manner. However, careful screening can identify anti-germinants with broad CDI prophylaxis activity.
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Ebselen Not Only Inhibits Clostridioides difficile Toxins but Displays Redox-Associated Cellular Killing. Microbiol Spectr 2021; 9:e0044821. [PMID: 34468187 PMCID: PMC8557875 DOI: 10.1128/spectrum.00448-21] [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: 11/20/2022] Open
Abstract
Ebselen, a reactive organoselenium compound, was shown to inhibit toxins TcdA and TcdB by covalently binding to their cysteine protease domains. It was suggested that ebselen lacked antimicrobial activity against Clostridioides difficile. However, this perception conflicts with C. difficile having essential cysteine-containing enzymes that could be potential targets and the reported antimicrobial activity of ebselen against other species. Hence, we reevaluated the anti-C. difficile properties of ebselen. Susceptibility testing revealed that its activity was either slightly reduced by pyruvate found in Wilkins-Chalgren agar or obliterated by blood in brucella agar. In brain heart infusion (BHI) agar, ebselen inhibited most C. difficile strains (MICs of 2 to 8 μg/ml), except for ribotype 078 that was intrinsically resistant (MIC = 32 to 128 μg/ml). Against C. difficile R20291, at concentrations below its minimal bactericidal concentration (MBC), 16 μg/ml, ebselen inhibited production of toxins and spores. Transcriptome analysis revealed that ebselen altered redox-associated processes and cysteine metabolism and enhanced expression of Stickland proline metabolism, likely to regenerate NAD+ from NADH. In cellular assays, ebselen induced uptake of cysteine, depleted nonprotein thiols, and disrupted the NAD+/NADH ratio. Taken together, killing of C. difficile cells by ebselen occurs by a multitarget action that includes disrupting intracellular redox, which is consistent with ebselen being a reactive molecule. However, the physiological relevance of these antimicrobial actions in treating acute C. difficile infection (CDI) is likely to be undermined by host factors, such as blood, which protect C. difficile from killing by ebselen. IMPORTANCE We show that ebselen kills pathogenic C. difficile by disrupting its redox homeostasis, changing the normal concentrations of NAD+ and NADH, which are critical for various metabolic functions in cells. However, this antimicrobial action is hampered by host components, namely, blood. Future discovery of ebselen analogues, or mechanistically similar compounds, that remain active in blood could be drug leads for CDI or probes to study C. difficile redox biology in vivo.
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Harrison MA, Kaur H, Wren BW, Dawson LF. Production of p-cresol by Decarboxylation of p-HPA by All Five Lineages of Clostridioides difficile Provides a Growth Advantage. Front Cell Infect Microbiol 2021; 11:757599. [PMID: 34778108 PMCID: PMC8588808 DOI: 10.3389/fcimb.2021.757599] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 10/05/2021] [Indexed: 11/19/2022] Open
Abstract
Clostridioides difficile is the leading cause of antibiotic-associated diarrhea and is capable of causing severe symptoms, such as pseudomembranous colitis and toxic megacolon. An unusual feature of C. difficile is the distinctive production of high levels of the antimicrobial compound para-cresol. p-Cresol production provides C. difficile with a competitive colonization advantage over gut commensal species, in particular, Gram-negative species. p-Cresol is produced by the conversion of para-hydroxyphenylacetic acid (p-HPA) via the actions of HpdBCA decarboxylase coded by the hpdBCA operon. Host cells and certain bacterial species produce p-HPA; however, the effects of p-HPA on the viability of C. difficile and other gut microbiota are unknown. Here we show that representative strains from all five C. difficile clades are able to produce p-cresol by two distinct mechanisms: (i) via fermentation of p-tyrosine and (ii) via uptake and turnover of exogenous p-HPA. We observed strain-specific differences in p-cresol production, resulting from differential efficiency of p-tyrosine fermentation; representatives of clade 3 (CD305) and clade 5 (M120) produced the highest levels of p-cresol via tyrosine metabolism, whereas the toxin A-/B+ isolate from clade 4 (M68) produced the lowest level of p-cresol. All five lineages share at least 97.3% homology across the hpdBCA operon, responsible for decarboxylation of p-HPA to p-cresol, suggesting that the limiting step in p-cresol production may result from tyrosine to p-HPA conversion. We identified that elevated intracellular p-HPA, modulated indirectly via CodY, controls p-cresol production via inducing the expression of HpdBCA decarboxylase ubiquitously in C. difficile populations. Efficient turnover of p-HPA is advantageous to C. difficile as p-HPA has a deleterious effect on the growth of C. difficile and other representative Gram-negative gut bacteria, transduced potentially by the disruption of membrane permeability and release of intracellular phosphate. This study provides insights into the importance of HpdBCA decarboxylase in C. difficile pathogenesis, both in terms of p-cresol production and detoxification of p-HPA, highlighting its importance to cell survival and as a highly specific therapeutic target for the inhibition of p-cresol production across C. difficile species.
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Affiliation(s)
- Mark A. Harrison
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Harparkash Kaur
- Department of Clinical Research, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Brendan W. Wren
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Lisa F. Dawson
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
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Thomas P, Abdel-Glil MY, Eichhorn I, Semmler T, Werckenthin C, Baumbach C, Murmann W, Bodenthin-Drauschke A, Zimmermann P, Schotte U, Galante D, Slavic D, Wagner M, Wieler LH, Neubauer H, Seyboldt C. Genome Sequence Analysis of Clostridium chauvoei Strains of European Origin and Evaluation of Typing Options for Outbreak Investigations. Front Microbiol 2021; 12:732106. [PMID: 34659160 PMCID: PMC8513740 DOI: 10.3389/fmicb.2021.732106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 08/31/2021] [Indexed: 01/08/2023] Open
Abstract
Black quarter caused by Clostridium (C.) chauvoei is an important bacterial disease that affects cattle and sheep with high mortality. A comparative genomics analysis of 64 C. chauvoei strains, most of European origin and a few of non-European and unknown origin, was performed. The pangenome analysis showed limited new gene acquisition for the species. The accessory genome involved prophages and genomic islands, with variations in gene composition observed in a few strains. This limited accessory genome may indicate that the species replicates only in the host or that an active CRISPR/Cas system provides immunity to foreign genetic elements. All strains contained a CRISPR type I-B system and it was confirmed that the unique spacer sequences therein can be used to differentiate strains. Homologous recombination events, which may have contributed to the evolution of this pathogen, were less frequent compared to other related species from the genus. Pangenome single nucleotide polymorphism (SNP) based phylogeny and clustering indicate diverse clusters related to geographical origin. Interestingly the identified SNPs were mostly non-synonymous. The study demonstrates the possibility of the existence of polymorphic populations in one host, based on strain variability observed for strains from the same animal and strains from different animals of one outbreak. The study also demonstrates that new outbreak strains are mostly related to earlier outbreak strains from the same farm/region. This indicates the last common ancestor strain from one farm can be crucial to understand the genetic changes and epidemiology occurring at farm level. Known virulence factors for the species were highly conserved among the strains. Genetic elements involved in Nicotinamide adenine dinucleotide (NAD) precursor synthesis (via nadA, nadB, and nadC metabolic pathway) which are known as potential anti-virulence loci are completely absent in C. chauvoei compared to the partial inactivation in C. septicum. A novel core-genome MLST based typing method was compared to sequence typing based on CRISPR spacers to evaluate the usefulness of the methods for outbreak investigations.
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Affiliation(s)
- Prasad Thomas
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Jena, Germany
| | - Mostafa Y Abdel-Glil
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Jena, Germany
| | - Inga Eichhorn
- Department of Veterinary Medicine, Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
| | | | - Christiane Werckenthin
- Lower Saxony State Office for Consumer Protection and Food Safety (LAVES), Food and Veterinary Institute Oldenburg, Oldenburg, Germany
| | - Christina Baumbach
- State Office for Agriculture, Food Safety and Fisheries Mecklenburg-Western Pomerania, Rostock, Germany
| | - Wybke Murmann
- Chemical and Veterinary Investigations Office, Freiburg, Germany
| | | | - Pia Zimmermann
- Bavarian Health and Food Safety Authority (LGL), Laboratory of Food Microbiology, Oberschleißheim, Germany
| | - Ulrich Schotte
- Department A-Veterinary Medicine, Central Institute of the Bundeswehr Medical Service Kiel, Kronshagen, Germany
| | - Domenico Galante
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Foggia, Italy
| | - Durda Slavic
- Animal Health Laboratory, Laboratory Services Division, University of Guelph, Guelph, ON, Canada
| | - Martin Wagner
- Unit for Food Microbiology, Institute for Food Safety, Technology and Veterinary Public Health, University for Veterinary Medicine, Vienna, Austria
| | | | - Heinrich Neubauer
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Jena, Germany
| | - Christian Seyboldt
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Jena, Germany
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Genetic Relatedness of 5-Year Isolates of Clostridioides difficile Polymerase Chain Reaction Ribotype 017 Strains in a Hospital. Antibiotics (Basel) 2021; 10:antibiotics10101229. [PMID: 34680810 PMCID: PMC8532766 DOI: 10.3390/antibiotics10101229] [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: 09/03/2021] [Revised: 09/29/2021] [Accepted: 10/07/2021] [Indexed: 11/24/2022] Open
Abstract
The objective of this study was to analyse the genetic relatedness of Clostridioides difficile polymerase chain reaction ribotype 017 (RT017) strains from patients with hospital-acquired C. difficile infection (HA-CDI) in a hospital with a high RT017 prevalence. From 2009 to 2013, 200 RT017 strains (26.8%) were collected from 745 HA-CDI patient isolates. They comprised 64 MLVA types, and 197 (98.5%) strains were genetically related to 5 clonal complexes (CCs). The largest cluster, CC-A, included 163 isolates of 40 MLVA types. CC-A accounted for 20% of RT017 strains in 2009 and sharply increased to 94.9% in 2010, 94% in 2011, 86.2% in 2012, and 73.5% in 2013. The other 4 CCs included 20 isolates with 7 MLVA types. The resistance rates of antimicrobials were as follows: clindamycin 100%, moxifloxacin 99%, rifaximin 88.5%, and vancomycin 1%. All isolates were susceptible to metronidazole and piperacillin/tazobactam. Comparing antibiotic resistance among CCs, the geometric mean of the minimum inhibitory concentrations of moxifloxacin, vancomycin, and piperacillin/tazobactam were significantly higher for CC-A isolates than for the other CCs. RT017 clones constantly evolved over the 5 years studied with regard to genetic relatedness. The levels of antibiotic resistance may contribute to the persistence of organisms in the institution.
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Ressler A, Wang J, Rao K. Defining the black box: a narrative review of factors associated with adverse outcomes from severe Clostridioides difficile infection. Therap Adv Gastroenterol 2021; 14:17562848211048127. [PMID: 34646358 PMCID: PMC8504270 DOI: 10.1177/17562848211048127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 08/31/2021] [Indexed: 02/04/2023] Open
Abstract
In the United States, Clostridioides difficile infection (CDI) is the leading cause of healthcare-associated infection, affecting nearly half a million people and resulting in more than 20,000 in-hospital deaths every year. It is therefore imperative to better characterize the intricate interplay between C. difficile microbial factors, host immunologic signatures, and clinical features that are associated with adverse outcomes of severe CDI. In this narrative review, we discuss the implications of C. difficile genetics and virulence factors in the molecular epidemiology of CDI, and the utility of early biomarkers in predicting the clinical trajectory of patients at risk of developing severe CDI. Furthermore, we identify associations between host immune factors and CDI outcomes in both animal models and human studies. Next, we highlight clinical factors including renal dysfunction, aging, blood biomarkers, level of care, and chronic illnesses that can affect severe CDI diagnosis and outcome. Finally, we present our perspectives on two specific treatments pertinent to patient outcomes: metronidazole administration and surgery. Together, this review explores the various venues of CDI research and highlights the importance of integrating microbial, host, and clinical data to help clinicians make optimal treatment decisions based on accurate prediction of disease progression.
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Affiliation(s)
- Adam Ressler
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Joyce Wang
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
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63
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Ahn SW, Lee SH, Kim UJ, Jang HC, Choi HJ, Choy HE, Kang SJ, Roh SW. Genomic characterization of nine Clostridioides difficile strains isolated from Korean patients with Clostridioides difficile infection. Gut Pathog 2021; 13:55. [PMID: 34530913 PMCID: PMC8447795 DOI: 10.1186/s13099-021-00451-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 09/08/2021] [Indexed: 12/14/2022] Open
Abstract
Background Clostridioides difficile infection (CDI) is an infectious nosocomial disease caused by Clostridioides difficile, an opportunistic pathogen that occurs in the intestine after extensive antibiotic regimens. Results Nine C. difficile strains (CBA7201–CBA7209) were isolated from nine patients diagnosed with CDI at the national university hospital in Korea, and the whole genomes of these strains were sequenced to identify their genomic characteristics. Comparative genomic analysis was performed using 51 reference strains and the nine isolated herein. Phylogenetic analysis based on 16S rRNA gene sequences confirmed that all 60 C. difficile strains belong to the genus Clostridioides, while core-genome tree indicated that they were divided into five groups, which was consistent with the results of MLST clade analysis. All strains were confirmed to have a clindamycin antibiotic resistance gene, but the other antibiotic resistance genes differ depending on the MLST clade. Interestingly, the six strains belonging to the sequence type 17 among the nine C. difficile strains isolated here exhibited unique genomic characteristics for PaLoc and CdtLoc, the two toxin gene loci identified in this study, and harbored similar antibiotic resistance genes. Conclusion In this study, we identified the specific genomic characteristics of Korean C. difficile strains, which could serve as basic information for CDI prevention and treatment in Korea. Supplementary Information The online version contains supplementary material available at 10.1186/s13099-021-00451-3.
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Affiliation(s)
- Seung Woo Ahn
- Microbiology and Functionality Research Group, World Institute of Kimchi, 86, Kimchi-ro, Nam-gu, 61755, Gwangju, Republic of Korea
| | - Se Hee Lee
- Microbiology and Functionality Research Group, World Institute of Kimchi, 86, Kimchi-ro, Nam-gu, 61755, Gwangju, Republic of Korea
| | - Uh Jin Kim
- Department of Infectious Diseases, Chonnam National University Hospital, 61469, Gwangju, Republic of Korea
| | - Hee-Chang Jang
- Department of Infectious Diseases, Chonnam National University Hospital, 61469, Gwangju, Republic of Korea
| | - Hak-Jong Choi
- Microbiology and Functionality Research Group, World Institute of Kimchi, 86, Kimchi-ro, Nam-gu, 61755, Gwangju, Republic of Korea
| | - Hyon E Choy
- Department of Microbiology, Chonnam National University Medical School, 61469, Gwangju, Republic of Korea
| | - Seung Ji Kang
- Department of Infectious Diseases, Chonnam National University Hospital, 61469, Gwangju, Republic of Korea.
| | - Seong Woon Roh
- Microbiology and Functionality Research Group, World Institute of Kimchi, 86, Kimchi-ro, Nam-gu, 61755, Gwangju, Republic of Korea.
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64
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Midani FS, Collins J, Britton RA. AMiGA: Software for Automated Analysis of Microbial Growth Assays. mSystems 2021; 6:e0050821. [PMID: 34254821 PMCID: PMC8409736 DOI: 10.1128/msystems.00508-21] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 06/16/2021] [Indexed: 12/18/2022] Open
Abstract
The analysis of microbial growth is one of the central methods in the field of microbiology. Microbial growth dynamics can be characterized by meaningful parameters, including carrying capacity, exponential growth rate, and growth lag. However, microbial assays with clinical isolates, fastidious organisms, or microbes under stress often produce atypical growth shapes that do not follow the classical microbial growth pattern. Here, we introduce the analysis of microbial growth assays (AMiGA) software, which streamlines the analysis of growth curves without any assumptions about their shapes. AMiGA can pool replicates of growth curves and infer summary statistics for biologically meaningful growth parameters. In addition, AMiGA can quantify death phases and characterize diauxic shifts. It can also statistically test for differential growth under distinct experimental conditions. Altogether, AMiGA streamlines the organization, analysis, and visualization of microbial growth assays. IMPORTANCE Our current understanding of microbial physiology relies on the simple method of measuring microbial populations' sizes over time and under different conditions. Many advances have increased the throughput of those assays and enabled the study of nonlab-adapted microbes under diverse conditions that widely affect their growth dynamics. Our software provides an all-in-one tool for estimating the growth parameters of microbial cultures and testing for differential growth in a high-throughput and user-friendly fashion without any underlying assumptions about how microbes respond to their growth conditions.
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Affiliation(s)
- Firas S. Midani
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, Texas, USA
| | - James Collins
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, Texas, USA
| | - Robert A. Britton
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, Texas, USA
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65
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Complete Genome Assemblies of Three Highly Prevalent, Toxigenic Clostridioides difficile Strains Causing Health Care-Associated Infections in Australia. Microbiol Resour Announc 2021; 10:e0059921. [PMID: 34351229 PMCID: PMC8340868 DOI: 10.1128/mra.00599-21] [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] [Indexed: 11/20/2022] Open
Abstract
Clostridioides difficile infection (CDI) is the leading cause of life-threatening health care-related gastrointestinal illness worldwide. Phylogenetically appropriate closed reference genomes are essential for studies of C. difficile transmission and evolution. Here, we provide high-quality complete hybrid genome assemblies for the three most prevalent C. difficile strains causing CDI in Australia.
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66
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Noori M, Ghalavand Z, Azimirad M, Yadegar A, Eslami G, Krutova M, Brajerova M, Goudarzi M, Zali MR. Genetic diversity and phylogenetic analysis of the surface layer protein A gene (slpA) among Clostridioides difficile clinical isolates from Tehran, Iran. Anaerobe 2021; 70:102403. [PMID: 34111549 DOI: 10.1016/j.anaerobe.2021.102403] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 05/24/2021] [Accepted: 06/04/2021] [Indexed: 12/15/2022]
Abstract
Clostridioides difficile is the most common causative agent of healthcare-associated diarrhea. C. difficile strains produce a crystalline surface layer protein (SlpA), encoded by the slpA gene. Previous studies have shown that SlpA varies among C. difficile strains. In this study, we used the SlpA sequence-based typing system (SlpAST) for the molecular genotyping of C. difficile clinical isolates identified in Iran; the PCR ribotypes (RTs) and toxin profiles of the isolates were also characterized. Forty-eight C. difficile isolates were obtained from diarrheal patients, and characterized by capillary electrophoresis (CE) PCR ribotyping and the detection of toxin genes. In addition, the genetic diversity of the slpA gene was investigated by Sanger sequencing. The most common RTs were RT126 (20.8%), followed by RT001 (12.5%) and RT084 (10.4%). The intact PaLoc arrangement representing cdu2+/tcdR+/tcdB+/tcdE+/tcdA+/tcdC+/cdd3+ profile was the predominant pattern and cdtA and cdtB genes were found in one-third of the isolates. Using the SlpA genotyping, 12 main genotypes and 16 subtypes were identified. The SlpA type 078-1 was the most prevalent genotype (20.8%), and identified within the isolates of RT126. The yok-1, gr-1, cr-1 and kr-3 genotypes were detected in 14.5%, 12.5%, 12.5% and 8.3% of isolates, respectively. Almost all the isolates with the same RT were clustered in similar SlpA sequence types. In comparison to PCR ribotyping, SlpAST, as a simple and highly reproducible sequenced-based technique, can discriminate well between C. difficile isolates. This typing method appears to be a valuable tool for the epidemiological study of C. difficile isolates worldwide.
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Affiliation(s)
- Maryam Noori
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Zohreh Ghalavand
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Masoumeh Azimirad
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Abbas Yadegar
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Gita Eslami
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Marcela Krutova
- Department of Medical Microbiology, Charles University, 2nd Faculty of Medicine and Motol University Hospital, Prague, Czech Republic
| | - Marie Brajerova
- Department of Medical Microbiology, Charles University, 2nd Faculty of Medicine and Motol University Hospital, Prague, Czech Republic
| | - Mehdi Goudarzi
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Zali
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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67
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Cationic Peptidomimetic Amphiphiles Having a N-Aryl- or N-Naphthyl-1,2,3-Triazole Core Structure Targeting Clostridioides ( Clostridium) difficile: Synthesis, Antibacterial Evaluation, and an In Vivo C. difficile Infection Model. Antibiotics (Basel) 2021; 10:antibiotics10080913. [PMID: 34438963 PMCID: PMC8388771 DOI: 10.3390/antibiotics10080913] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 07/15/2021] [Accepted: 07/21/2021] [Indexed: 12/17/2022] Open
Abstract
Clostridioides (also known as Clostridium) difficile is a Gram-positive anaerobic, spore producing bacterial pathogen that causes severe gastrointestinal infection in humans. The current chemotherapeutic options are inadequate, expensive, and limited, and thus inexpensive drug treatments for C. difficile infection (CDI) with improved efficacy and specificity are urgently needed. To improve the solubility of our cationic amphiphilic 1,1′-binaphthylpeptidomimetics developed earlier that showed promise in an in vivo murine CDI model we have synthesized related compounds with an N-arytriazole or N-naphthyltriazole moiety instead of the 1,1′-biphenyl or 1,1′-binaphthyl moiety. This modification was made to increase the polarity and thus water solubility of the overall peptidomimetics, while maintaining the aromatic character. The dicationic N-naphthyltriazole derivative 40 was identified as a C. difficile-selective antibacterial with MIC values of 8 µg/mL against C. difficile strains ATCC 700057 and 132 (both ribotype 027). This compound displayed increased water solubility and reduced hemolytic activity (32 µg/mL) in an in vitro hemolysis assay and reduced cytotoxicity (CC50 32 µg/mL against HEK293 cells) relative to lead compound 2. Compound 40 exhibited mild efficacy (with 80% survival observed after 24 h compared to the DMSO control of 40%) in an in vivo murine model of C. difficile infection by reducing the severity and slowing the onset of disease.
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68
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Discovery and mining of enzymes from the human gut microbiome. Trends Biotechnol 2021; 40:240-254. [PMID: 34304905 DOI: 10.1016/j.tibtech.2021.06.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 06/24/2021] [Accepted: 06/25/2021] [Indexed: 12/19/2022]
Abstract
Advances in technological and bioinformatics approaches have led to the generation of a plethora of human gut metagenomic datasets. Metabolomics has also provided substantial data regarding the small metabolites produced and modified by the microbiota. Comparatively, the microbial enzymes mediating the transformation of metabolites have not been intensively investigated. Here, we discuss the recent efforts and technologies used for discovering and mining enzymes from the human gut microbiota. The wealth of knowledge on metabolites, reactions, genome sequences, and structures of proteins, may drive the development of strategies for enzyme mining. Ongoing efforts to annotate gut microbiota enzymes will explain catalytic mechanisms that may guide the clinical applications of the gut microbiome for diagnostic and therapeutic purposes.
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69
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Riedel T, Neumann-Schaal M, Wittmann J, Schober I, Hofmann JD, Lu CW, Dannheim A, Zimmermann O, Lochner M, Groß U, Overmann J. Characterization of Clostridioides difficile DSM 101085 with A-B-CDT+ Phenotype from a Late Recurrent Colonization. Genome Biol Evol 2021; 12:566-577. [PMID: 32302381 PMCID: PMC7250501 DOI: 10.1093/gbe/evaa072] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/10/2020] [Indexed: 12/29/2022] Open
Abstract
During the last decades, hypervirulent strains of Clostridioides difficile with frequent disease recurrence and increased mortality appeared. Clostridioides difficile DSM 101085 was isolated from a patient who suffered from several recurrent infections and colonizations, likely contributing to a fatal outcome. Analysis of the toxin repertoire revealed the presence of a complete binary toxin locus and an atypical pathogenicity locus consisting of only a tcdA pseudogene and a disrupted tcdC gene sequence. The pathogenicity locus shows upstream a transposon and has been subject to homologous recombination or lateral gene transfer events. Matching the results of the genome analysis, neither TcdA nor TcdB production but the expression of cdtA and cdtB was detected. This highlights a potential role of the binary toxin C. difficile toxin in this recurrent colonization and possibly further in a host-dependent virulence. Compared with the C. difficile metabolic model strains DSM 28645 (630Δerm) and DSM 27147 (R20291), strain DSM 101085 showed a specific metabolic profile, featuring changes in the threonine degradation pathways and alterations in the central carbon metabolism. Moreover, products originating from Stickland pathways processing leucine, aromatic amino acids, and methionine were more abundant in strain DSM 101085, indicating a more efficient use of these substrates. The particular characteristics of strain C. difficile DSM 101085 may represent an adaptation to a low-protein diet in a patient with recurrent infections.
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Affiliation(s)
- Thomas Riedel
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.,German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Braunschweig, Germany
| | - Meina Neumann-Schaal
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.,Department of Bioinformatics and Biochemistry and Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Germany
| | - Johannes Wittmann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Isabel Schober
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Julia Danielle Hofmann
- Department of Bioinformatics and Biochemistry and Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Germany
| | - Chia-Wen Lu
- Institute of Infection Immunology, TWINCORE, Centre for Experimental and Clinical Infection Research, a Joint Venture between the Medical School Hannover (MHH) and the Helmholtz Centre for Infection Research (HZI), Hannover, Germany
| | - Antonia Dannheim
- Department of Bioinformatics and Biochemistry and Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Germany
| | - Ortrud Zimmermann
- Institute of Medical Microbiology, University Medical Center Göttingen, Germany
| | - Matthias Lochner
- Institute of Infection Immunology, TWINCORE, Centre for Experimental and Clinical Infection Research, a Joint Venture between the Medical School Hannover (MHH) and the Helmholtz Centre for Infection Research (HZI), Hannover, Germany
| | - Uwe Groß
- Institute of Medical Microbiology, University Medical Center Göttingen, Germany.,Göttingen International Health Network, Göttingen, Germany
| | - Jörg Overmann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.,German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Braunschweig, Germany.,Institute of Microbiology, Technical University of Braunschweig, Germany
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70
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Xu X, Bian Q, Luo Y, Song X, Lin S, Chen H, Liang Q, Wang M, Ye G, Zhu B, Chen L, Tang YW, Wang X, Jin D. Comparative Whole Genome Sequence Analysis and Biological Features of Clostridioides difficile Sequence Type 2 ‡. Front Microbiol 2021; 12:651520. [PMID: 34290677 PMCID: PMC8287029 DOI: 10.3389/fmicb.2021.651520] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 05/31/2021] [Indexed: 01/05/2023] Open
Abstract
Clostridioides difficile sequence type 2 (ST2) has been increasingly recognized as one of the major genotypes in China, while the genomic characteristics and biological phenotypes of Chinese ST2 strains remain to be determined. We used whole-genome sequencing and phylogenetic analysis to investigate the genomic features of 182 ST2 strains, isolated between 2011 and 2017. PCR ribotyping (RT) was performed, and antibiotic resistance, toxin concentration, and sporulation capacity were measured. The core genome Maximum-likelihood phylogenetic analysis showed that ST2 strains were distinctly segregated into two genetically diverse lineages [L1 (67.0% from Northern America) and L2], while L2 further divided into two sub-lineages, SL2a and SL2b (73.5% from China). The 36 virulence-related genes were widely distributed in ST2 genomes, but in which only 11 antibiotic resistance-associated genes were dispersedly found. Among the 25 SL2b sequenced isolates, RT014 (40.0%, n = 10) and RT020 (28.0%, n = 7) were two main genotypes with no significant difference on antibiotic resistance (χ2 = 0.024-2.667, P > 0.05). A non-synonymous amino acid substitution was found in tcdB (Y1975D) which was specific to SL2b. Although there was no significant difference in sporulation capacity between the two lineages, the average toxin B concentration (5.11 ± 3.20 ng/μL) in SL2b was significantly lower in comparison to those in L1 (10.49 ± 15.82 ng/μL) and SL2a (13.92 ± 2.39 ng/μL) (χ2 = 12.30, P < 0.05). This study described the genomic characteristics of C. difficile ST2, with many virulence loci and few antibiotic resistance elements. The Chinese ST2 strains with the mutation in codon 1975 of the tcdB gene clustering in SL2b circulating in China express low toxin B, which may be associated with mild or moderate C. difficile infection.
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Affiliation(s)
- Xingxing Xu
- Department of Clinical Laboratory, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China.,School of Laboratory Medicine, Hangzhou Medical College, Hangzhou, China
| | - Qiao Bian
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Yun Luo
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Xiaojun Song
- Centre of Laboratory Medicine, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, China
| | - Shan Lin
- School of Laboratory Medicine, Hangzhou Medical College, Hangzhou, China
| | - Huan Chen
- Key Laboratory of Microorganism Technology and Bioinformatics Research of Zhejiang Province, Hangzhou, China.,NMPA Key Laboratory for Testing and Risk Warning of Pharmaceutical Microbiology, Hangzhou, China
| | - Qian Liang
- Key Laboratory of Microorganism Technology and Bioinformatics Research of Zhejiang Province, Hangzhou, China.,NMPA Key Laboratory for Testing and Risk Warning of Pharmaceutical Microbiology, Hangzhou, China
| | - Meixia Wang
- Key Laboratory of Microorganism Technology and Bioinformatics Research of Zhejiang Province, Hangzhou, China.,NMPA Key Laboratory for Testing and Risk Warning of Pharmaceutical Microbiology, Hangzhou, China
| | - Guangyong Ye
- Department of Clinical Laboratory, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Bo Zhu
- Department of Clinical Laboratory, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Liang Chen
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, Untied States.,Department of Medical Sciences, Hackensack Meridian School of Medicine, Nutley, NJ, Untied States
| | - Yi-Wei Tang
- Cepheid, Danaher Diagnostic Platform, Shanghai, China
| | - Xianjun Wang
- Department of Clinical Laboratory, Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Dazhi Jin
- School of Laboratory Medicine, Hangzhou Medical College, Hangzhou, China.,Centre of Laboratory Medicine, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, China
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71
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Kartalidis P, Skoulakis A, Tsilipounidaki K, Florou Z, Petinaki E, Fthenakis GC. Clostridioides difficile as a Dynamic Vehicle for the Dissemination of Antimicrobial-Resistance Determinants: Review and In Silico Analysis. Microorganisms 2021; 9:microorganisms9071383. [PMID: 34202117 PMCID: PMC8307371 DOI: 10.3390/microorganisms9071383] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/21/2021] [Accepted: 06/22/2021] [Indexed: 01/11/2023] Open
Abstract
The present paper is divided into two parts. The first part focuses on the role of Clostridioides difficile in the accumulation of genes associated with antimicrobial resistance and then the transmission of them to other pathogenic bacteria occupying the same human intestinal niche. The second part describes an in silico analysis of the genomes of C. difficile available in GenBank, with regard to the presence of mobile genetic elements and antimicrobial resistance genes. The diversity of the C. difficile genome is discussed, and the current status of resistance of the organisms to various antimicrobial agents is reviewed. The role of transposons associated with antimicrobial resistance is appraised; the importance of plasmids associated with antimicrobial resistance is discussed, and the significance of bacteriophages as a potential shuttle for antimicrobial resistance genes is presented. In the in silico study, 1101 C. difficile genomes were found to harbor mobile genetic elements; Tn6009, Tn6105, CTn7 and Tn6192, Tn6194 and IS256 were the ones more frequently identified. The genes most commonly harbored therein were: ermB, blaCDD, vanT, vanR, vanG and vanS. Tn6194 was likely associated with resistance to erythromycin, Tn6192 and CTn7 with resistance to the β-lactams and vancomycin, IS256 with resistance to aminoglycoside and Tn6105 to vancomycin.
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Affiliation(s)
- Philip Kartalidis
- Department of Clinical and Laboratory Research, Faculty of Medicine, School of Health Sciences, University of Thessaly, 41110 Larissa, Greece; (P.K.); (A.S.); (K.T.); (Z.F.); (E.P.)
| | - Anargyros Skoulakis
- Department of Clinical and Laboratory Research, Faculty of Medicine, School of Health Sciences, University of Thessaly, 41110 Larissa, Greece; (P.K.); (A.S.); (K.T.); (Z.F.); (E.P.)
| | - Katerina Tsilipounidaki
- Department of Clinical and Laboratory Research, Faculty of Medicine, School of Health Sciences, University of Thessaly, 41110 Larissa, Greece; (P.K.); (A.S.); (K.T.); (Z.F.); (E.P.)
| | - Zoi Florou
- Department of Clinical and Laboratory Research, Faculty of Medicine, School of Health Sciences, University of Thessaly, 41110 Larissa, Greece; (P.K.); (A.S.); (K.T.); (Z.F.); (E.P.)
| | - Efthymia Petinaki
- Department of Clinical and Laboratory Research, Faculty of Medicine, School of Health Sciences, University of Thessaly, 41110 Larissa, Greece; (P.K.); (A.S.); (K.T.); (Z.F.); (E.P.)
| | - George C. Fthenakis
- Veterinary Faculty, University of Thessaly, 43100 Karditsa, Greece
- Correspondence:
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72
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Ramírez-Vargas G, Rodríguez C. Putative Conjugative Plasmids with tcdB and cdtAB Genes in Clostridioides difficile. Emerg Infect Dis 2021; 26:2287-2290. [PMID: 32818425 PMCID: PMC7454092 DOI: 10.3201/eid2609.191447] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The major toxins of Clostridioides difficile (TcdA, TcdB, CDT) are chromosomally encoded in nearly all known strains. Following up on previous findings, we identified 5 examples of a family of putative conjugative plasmids with tcdB and cdtAB in clinical C. difficile isolates from multilocus sequence typing clades C-I, 2, and 4.
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73
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Xu X, Luo Y, Chen H, Song X, Bian Q, Wang X, Liang Q, Zhao J, Li C, Song G, Yang J, Sun L, Jiang J, Wang H, Zhu B, Ye G, Chen L, Tang YW, Jin D. Genomic evolution and virulence association of Clostridioides difficile sequence type 37 (ribotype 017) in China. Emerg Microbes Infect 2021; 10:1331-1345. [PMID: 34125660 PMCID: PMC8253194 DOI: 10.1080/22221751.2021.1943538] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Clostridioides difficile sequence type (ST) 37 (ribotype 017) is one of the most prevalent genotypes circulating in China. However, its genomic evolution and virulence determinants were rarely explored. Whole-genome sequencing, phylogeographic and phylogenetic analyses were conducted for C. difficile ST37 isolates. The 325 ST37 genomes from six continents, including North America (n = 66), South America (n = 4), Oceania (n = 7), Africa (n = 9), Europe (n = 138) and Asia (n = 101), were clustered into six major lineages, with region-dependent distributions, harbouring an array of antibiotic-resistance genes. The ST37 strains from China were divided into four distinct sublineages, showing five importation times and international sources. Isolates associated with severe infections exhibited significantly higher toxin productions, tcdB mRNA levels, and sporulation capacities (P < 0.001). Kyoto Encyclopedia of Genes and Genomes analysis showed 10 metabolic pathways were significantly enriched in the mutations among isolates associated with severe CDI (P < 0.05). Gene mutations in glycometabolism, amino acid metabolism and biosynthesis virtually causing instability in protein activity were correlated positively to the transcription of tcdR and negatively to the expression of toxin repressor genes, ccpA and codY. In summary, our study firstly presented genomic insights into genetic characteristics and virulence association of C. difficile ST37 in China. Gene mutations in certain important metabolic pathways are associated with severe symptoms and correlated with higher virulence in C. difficile ST37 isolates.
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Affiliation(s)
- Xingxing Xu
- Department of Clinical Laboratory, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, People's Republic of China.,School of Laboratory Medicine, Hangzhou Medical College, Hangzhou, People's Republic of China
| | - Yuo Luo
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Huan Chen
- Key Laboratory of Microorganism technology and bioinformatics research of Zhejiang Province, Hangzhou, People's Republic of China.,NMPA Key Laboratory For Testing and Risk Warning of Pharmaceutical Microbiology, Hangzhou, People's Republic of China
| | - Xiaojun Song
- Centre of Laboratory Medicine, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, People's Republic of China
| | - Qiao Bian
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, People's Republic of China
| | - Xianjun Wang
- Department of Laboratory Medicine, Hangzhou First People's Hospital, Hangzhou, People's Republic of China
| | - Qian Liang
- Key Laboratory of Microorganism technology and bioinformatics research of Zhejiang Province, Hangzhou, People's Republic of China.,NMPA Key Laboratory For Testing and Risk Warning of Pharmaceutical Microbiology, Hangzhou, People's Republic of China
| | - Jianhong Zhao
- Department of Clinical Microbiology, Second Hospital of Hebei Medical University, Hebei Provincial Center for Clinical Laboratories, Shijiazhuang, People's Republic of China
| | - Chunhui Li
- Infection Control Center, Xiangya Hospital of Central South University, Changsha, People's Republic of China
| | - Guangzhong Song
- School of Laboratory Medicine, Hangzhou Medical College, Hangzhou, People's Republic of China
| | - Jun Yang
- School of Laboratory Medicine, Hangzhou Medical College, Hangzhou, People's Republic of China
| | - Lingli Sun
- Key Laboratory of Microorganism technology and bioinformatics research of Zhejiang Province, Hangzhou, People's Republic of China.,NMPA Key Laboratory For Testing and Risk Warning of Pharmaceutical Microbiology, Hangzhou, People's Republic of China
| | - Jianmin Jiang
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, People's Republic of China
| | - Huanying Wang
- Key Laboratory of Microorganism technology and bioinformatics research of Zhejiang Province, Hangzhou, People's Republic of China.,NMPA Key Laboratory For Testing and Risk Warning of Pharmaceutical Microbiology, Hangzhou, People's Republic of China
| | - Bo Zhu
- Department of Clinical Laboratory, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, People's Republic of China
| | - Guangyong Ye
- Department of Clinical Laboratory, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, People's Republic of China
| | - Liang Chen
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA.,Department of Medical Sciences, Hackensack Meridian School of Medicine, Nutley, NJ, USA
| | - Yi-Wei Tang
- Cepheid, Danaher Diagnostic Platform, Shanghai, People's Republic of China
| | - Dazhi Jin
- School of Laboratory Medicine, Hangzhou Medical College, Hangzhou, People's Republic of China.,Centre of Laboratory Medicine, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, People's Republic of China
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74
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Knight DR, Imwattana K, Kullin B, Guerrero-Araya E, Paredes-Sabja D, Didelot X, Dingle KE, Eyre DW, Rodríguez C, Riley TV. Major genetic discontinuity and novel toxigenic species in Clostridioides difficile taxonomy. eLife 2021; 10:64325. [PMID: 34114561 PMCID: PMC8241443 DOI: 10.7554/elife.64325] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 06/08/2021] [Indexed: 12/17/2022] Open
Abstract
Clostridioides difficile infection (CDI) remains an urgent global One Health threat. The genetic heterogeneity seen across C. difficile underscores its wide ecological versatility and has driven the significant changes in CDI epidemiology seen in the last 20 years. We analysed an international collection of over 12,000 C. difficile genomes spanning the eight currently defined phylogenetic clades. Through whole-genome average nucleotide identity, and pangenomic and Bayesian analyses, we identified major taxonomic incoherence with clear species boundaries for each of the recently described cryptic clades CI–III. The emergence of these three novel genomospecies predates clades C1–5 by millions of years, rewriting the global population structure of C. difficile specifically and taxonomy of the Peptostreptococcaceae in general. These genomospecies all show unique and highly divergent toxin gene architecture, advancing our understanding of the evolution of C. difficile and close relatives. Beyond the taxonomic ramifications, this work may impact the diagnosis of CDI.
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Affiliation(s)
- Daniel R Knight
- Medical, Molecular and Forensic Sciences, Murdoch University, Murdoch, Australia.,School of Biomedical Sciences, the University of Western Australia, Nedlands, Australia
| | - Korakrit Imwattana
- School of Biomedical Sciences, the University of Western Australia, Nedlands, Australia.,Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Brian Kullin
- Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Enzo Guerrero-Araya
- Microbiota-Host Interactions and Clostridia Research Group, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile.,Millenium Nucleus in the Biology of Intestinal Microbiota, Santiago, Chile
| | - Daniel Paredes-Sabja
- Microbiota-Host Interactions and Clostridia Research Group, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile.,Millenium Nucleus in the Biology of Intestinal Microbiota, Santiago, Chile.,Department of Biology, Texas A&M University, College Station, United States
| | - Xavier Didelot
- School of Life Sciences and Department of Statistics, University of Warwick, Coventry, United Kingdom
| | - Kate E Dingle
- Nuffield Department of Clinical Medicine, University of Oxford, National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom
| | - David W Eyre
- Big Data Institute, Nuffield Department of Population Health, University of Oxford, National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom
| | - César Rodríguez
- Facultad de Microbiología & Centro de Investigación en Enfermedades Tropicales (CIET), Universidad de Costa Rica, San José, Costa Rica
| | - Thomas V Riley
- Medical, Molecular and Forensic Sciences, Murdoch University, Murdoch, Australia.,School of Biomedical Sciences, the University of Western Australia, Nedlands, Australia.,Department of Microbiology, PathWest Laboratory Medicine, Queen Elizabeth II Medical Centre, Nedlands, Australia.,School of Medical and Health Sciences, Edith Cowan University, Joondalup, Australia
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75
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Seth-Smith HMB, Biggel M, Roloff T, Hinic V, Bodmer T, Risch M, Casanova C, Widmer A, Sommerstein R, Marschall J, Tschudin-Sutter S, Egli A. Transition From PCR-Ribotyping to Whole Genome Sequencing Based Typing of Clostridioides difficile. Front Cell Infect Microbiol 2021; 11:681518. [PMID: 34141631 PMCID: PMC8204696 DOI: 10.3389/fcimb.2021.681518] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 05/04/2021] [Indexed: 11/13/2022] Open
Abstract
Clostridioides difficile causes nosocomial outbreaks which can lead to severe and even life-threatening colitis. Rapid molecular diagnostic tests allow the identification of toxin-producing, potentially hypervirulent strains, which is critical for patient management and infection control. PCR-ribotyping has been used for decades as the reference standard to investigate transmission in suspected outbreaks. However, the introduction of whole genome sequencing (WGS) for molecular epidemiology provides a realistic alternative to PCR-ribotyping. In this transition phase it is crucial to understand the strengths and weaknesses of the two technologies, and to assess their correlation. We aimed to investigate ribotype prediction from WGS data, and options for analysis at different levels of analytical granularity. Ribotypes cannot be directly determined from short read Illumina sequence data as the rRNA operons including the ribotype-defining ISR fragments collapse in genome assemblies, and comparison with traditional PCR-ribotyping results becomes impossible. Ribotype extraction from long read Oxford nanopore data also requires optimization. We have compared WGS-based typing with PCR-ribotyping in nearly 300 clinical and environmental isolates from Switzerland, and in addition from the Enterobase database (n=1778). Our results show that while multi-locus sequence type (MLST) often correlates with a specific ribotype, the agreement is not complete, and for some ribotypes the resolution is insufficient. Using core genome MLST (cgMLST) analysis, there is an improved resolution and ribotypes can often be predicted within clusters, using cutoffs of 30-50 allele differences. The exceptions are ribotypes within known ribotype complexes such as RT078/RT106, where the genome differences in cgMLST do not reflect the ribotype segregation. We show that different ribotype clusters display different degrees of diversity, which could be important for the definition of ribotype cluster specific cutoffs. WGS-based analysis offers the ultimate resolution to the SNP level, enabling exploration of patient-to-patient transmission. PCR-ribotyping does not sufficiently discriminate to prove nosocomial transmission with certainty. We discuss the associated challenges and opportunities in a switch to WGS from conventional ribotyping for C. difficile.
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Affiliation(s)
- Helena M B Seth-Smith
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland.,Applied Microbiology Research, Department Biomedicine, University of Basel, Basel, Switzerland.,Swiss Institute for Bioinformatics, Basel, Switzerland
| | - Michael Biggel
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Tim Roloff
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland.,Applied Microbiology Research, Department Biomedicine, University of Basel, Basel, Switzerland.,Swiss Institute for Bioinformatics, Basel, Switzerland
| | - Vladimira Hinic
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland
| | - Thomas Bodmer
- Clinical Microbiology, Labormedizinisches Zentrum Dr Risch, Liebefeld, Switzerland
| | - Martin Risch
- Clinical Microbiology, Labormedizinisches Zentrum Dr Risch, Liebefeld, Switzerland
| | - Carlo Casanova
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Andreas Widmer
- Division of Infectious Diseases & Hospital Epidemiology, University Hospital Basel, University Basel, Basel, Switzerland
| | - Rami Sommerstein
- Department of Infectious Diseases, Bern University Hospital and University of Bern, Bern, Switzerland.,Infectious Diseases, Hirslanden Central Switzerland, Lucerne, Switzerland
| | - Jonas Marschall
- Department of Infectious Diseases, Bern University Hospital and University of Bern, Bern, Switzerland
| | - Sarah Tschudin-Sutter
- Division of Infectious Diseases & Hospital Epidemiology, University Hospital Basel, University Basel, Basel, Switzerland
| | - Adrian Egli
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland.,Applied Microbiology Research, Department Biomedicine, University of Basel, Basel, Switzerland
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Abstract
Clostridium difficile (C. difficile) is a kind of obligate anaerobic gram-positive Bacillus related with intestinal diseases and antibiotic treatment. In present study, the C. difficile genome was studied employing met genomic technology. Genome sequencing identified C. difficile LCL126 has total size of 4,301,949 bp with a 27.97% of GC content. Specifically, 4119 predicted coding genes, 188 repeat sequences, 13 prophages and 8 gene islands were detected. Additionally, gene function analysis aspect of the function annotation, effector, and virulence were concluded that total of 3367 cluster of orthologous groups of proteins genes and classified into 24 categories, while the most outstanding class was metabolic process (1533) and catalytic activity (1498). The carbohydrate-active enzymes have been detected 127 genes, pathogenicity analysis revealed that 133 reduced and 22 increased virulence (hypervirulence) genes, while 54 unaffected and 10 loss of pathogenicity genes were found. Furthermore, perform the visualization and methylation expression were revealed that the dominant types comprised m4C, m5C, and m6C with the number of 6989, 36,666, and 3534, respectively. Overall, whole genome sequence information of C. difficile LCL126 was obtained and functional prediction was revealed its possible toxicological potential genes existence.
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Affiliation(s)
- Jianfeng Wang
- School of Life Sciences, Lanzhou University, Lanzhou, Gansu Province, China.,Laboratory of Clostridium, Lanzhou Institute of Biological Products, Lanzhou, Gansu Province, China
| | - Chu Yang
- Laboratory of Clostridium, Lanzhou Institute of Biological Products, Lanzhou, Gansu Province, China
| | - Chao Zhang
- Laboratory of Clostridium, Lanzhou Institute of Biological Products, Lanzhou, Gansu Province, China
| | - Xiaoyan Mao
- Laboratory of Clostridium, Lanzhou Institute of Biological Products, Lanzhou, Gansu Province, China
| | - An Lizhe
- School of Life Sciences, Lanzhou University, Lanzhou, Gansu Province, China
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77
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Imwattana K, Knight DR, Riley TV. Can sequencing improve the diagnosis and management of Clostridioides difficile infection? Expert Rev Mol Diagn 2021; 21:429-431. [PMID: 33843381 DOI: 10.1080/14737159.2021.1915774] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Korakrit Imwattana
- School of Biomedical Sciences, The University of Western Australia, Crawley, Australia.,Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Daniel R Knight
- School of Biomedical Sciences, The University of Western Australia, Crawley, Australia.,Medical, Molecular and Forensic Sciences, Murdoch University, Murdoch, Australia
| | - Thomas V Riley
- School of Biomedical Sciences, The University of Western Australia, Crawley, Australia.,Medical, Molecular and Forensic Sciences, Murdoch University, Murdoch, Australia.,School of Medical and Health Sciences, Edith Cowan University, Joondalup, Australia.,PathWest Laboratory Medicine, Queen Elizabeth II Medical Centre, Nedlands, Australia
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78
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Global Landscape of Clostridioides Difficile Phylogeography, Antibiotic Susceptibility, and Toxin Polymorphisms by Post-Hoc Whole-Genome Sequencing from the MODIFY I/II Studies. Infect Dis Ther 2021; 10:853-870. [PMID: 33751421 PMCID: PMC8116447 DOI: 10.1007/s40121-021-00426-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 02/26/2021] [Indexed: 12/31/2022] Open
Abstract
INTRODUCTION Clostridioides (Clostridium) difficile infection, the leading cause of healthcare-associated diarrhea, represents a significant burden on global healthcare systems. Despite being a global issue, information on C. difficile from a global perspective is lacking. The aim of this study is to model the global phylogeography of clinical C. difficile. METHODS Using samples collected from the MODIFY I and II studies (NCT01241552, NCT01513239), we performed whole-genome sequencing of 1501 clinical isolates including 37 novel sequence types (STs), representing the largest worldwide collection to date. RESULTS Our data showed ribotypes, multi-locus sequence typing clades, and whole-genome phylogeny were in good accordance. The clinical C. difficile genome was found to be more conserved than previously reported (61% core genes), and modest recombination rates of 1.4-5.0 were observed across clades. We observed a significant continent distribution preference among five C. difficile clades (Benjamini-Hochberg corrected Fisher's exact test P < 0.01); moreover, weak association between geographic and genetic distance among ribotypes suggested sources beyond healthcare-related transmission. Markedly different trends of antibiotic susceptibility among lineages and regions were identified, and three novel mutations (in pyridoxamine 5'-phosphate oxidase family protein: Tyr130Ser, Tyr130Cys, and a promoter SNP) associated with metronidazole-reduced susceptibility were discovered on a nim-related gene and its promotor by genome-wide association study. Toxin gene polymorphisms were shown to vary within and between prevalent ribotypes, and novel severe mutations were found on the tcdC toxin regulator protein. CONCLUSION Our systematic characterization of a global set of clinical trial C. difficile isolates from infected individuals demonstrated the complexity of the genetic makeup of this pathogenic organism. The geographic variability of clades, variability in toxin genes, and mutations associated with antibiotic susceptibility indicate a highly complex interaction of C. difficile between host and environment. This dataset will provide a useful resource for validation of findings and future research of C. difficile.
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79
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Clostridioides difficile in Calves in Central Italy: Prevalence, Molecular Typing, Antimicrobial Susceptibility and Association with Antibiotic Administration. Animals (Basel) 2021; 11:ani11020515. [PMID: 33669325 PMCID: PMC7920295 DOI: 10.3390/ani11020515] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/09/2021] [Accepted: 02/12/2021] [Indexed: 12/28/2022] Open
Abstract
Simple Summary Clostridioides difficile is a leading cause of nosocomial and community-acquired diarrhoea in men. The infection most commonly occurs in people who have recently been treated with antibiotics. Indistinguishable C. difficile strains have been isolated from livestock and humans, which has shed light on a possible zoonotic origin of this infection. This study aimed to assess the prevalence and risk factors of C. difficile in calves bred in dairy and beef cattle farms of the Umbria, central Italy. We estimated a 19.8% prevalence of farms positive for C. difficile. The C. difficile isolates from calves were potentially toxigenic and resistant to antibiotics, including lincosamides, quinolones, vancomycin and linezolid. Isolates belonging to ribotype RT-126, which is also commonly reported in humans, showed the highest number of resistance to the antimicrobials tested. Furthermore, we observed an almost sixfold increased risk for C. difficile on farms where penicillins had been prescribed. This, together with the detection of toxigenic and antibiotic-resistant isolates, strongly suggests the need for a reduction of antibiotic use in cattle. Abstract The emergence of Clostridioides difficile as the main agent of antibiotic-associated diarrhoea has raised concerns about its potential zoonotic role in different animal species. The use of antimicrobials is a major risk factor for C. difficile infection. Here, we provide data on C. difficile infection in dairy and beef calves in Umbria, a region in central Italy. This cross-sectional study focuses on prevalence, risk factors, ribotypes, toxinotypes and antimicrobial resistance profiles of circulating ribotypes. A prevalence of 19.8% (CI95%, 12–27.6%) positive farms was estimated, and the prescription of penicillins on the farms was associated with C. difficile detection (OR = 5.58). Eleven different ribotypes were found, including the ST11 sublineages RT-126 and -078, which are also commonly reported in humans. Thirteen isolates out of 17 showed resistance to at least one of clindamycin, moxifloxacin, linezolid and vancomycin. Among them, multiple-drug resistance was observed in two isolates, belonging to RT-126. Furthermore, RT-126 isolates were positive for tetracycline resistance determinants, confirming that tetracycline resistance is widespread among ST11 isolates from cattle. The administration of penicillins increased the risk of C. difficile in calves: this, together with the recovery of multi-resistant strains, strongly suggests the need for minimising antibiotic misuse on cattle farms.
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80
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Kulecka M, Waker E, Ambrozkiewicz F, Paziewska A, Skubisz K, Cybula P, Targoński Ł, Mikula M, Walewski J, Ostrowski J. Higher genome variability within metabolism genes associates with recurrent Clostridium difficile infection. BMC Microbiol 2021; 21:36. [PMID: 33509087 PMCID: PMC7842062 DOI: 10.1186/s12866-021-02090-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 01/08/2021] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Clostridium difficile (C. difficile) is a major source of healthcare-associated infection with a high risk of recurrence, attributable to many factors such as usage of antibiotics, older age and immunocompromised status of the patients. C. difficile has also a highly diverse genome, which may contribute to its high virulence. Herein we examined whether the genome conservation, measured as non-synonymous to synonymous mutations ratio (dN/dS) in core genes, presence of single genes, plasmids and prophages increased the risk of reinfection in a subset of 134 C. difficile isolates from our previous study in a singly hemato-oncology ward. METHODS C. difficile isolates were subjected to whole-genome sequencing (WGS) on Ion Torrent PGM sequencer. Genomes were assembled with MIRA5 and annotated with prokka and VRprofile. Logistic regression was used to asses the relationship between single gene presence and the odds of infection recurrence. DN/dS ratios were computed with codeml. Functional annotation was conducted with eggNOG-Mapper. RESULTS We have found that the presence of certain genes, associated with carbon metabolism and oxidative phosphorylation, increased the odds of infection recurrence. More core genes were under positive selective pressure in recurrent disease isolates - they were mostly associated with the metabolism of aminoacids. Finally, prophage elements were more prevalent in single infection isolates and plasmids did not influence the odds of recurrence. CONCLUSIONS Our findings suggest higher genetic plasticity in isolates causing recurrent infection, associated mainly with metabolism. On the other hand, the presence of prophages seems to reduce the isolates' virulence.
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Affiliation(s)
- Maria Kulecka
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, Roentgena 5, 02-781, Warsaw, Poland
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, 02-781, Warsaw, Poland
| | - Edyta Waker
- Department of Clinical Microbiology, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781, Warsaw, Poland
| | - Filip Ambrozkiewicz
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, Roentgena 5, 02-781, Warsaw, Poland
| | - Agnieszka Paziewska
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, Roentgena 5, 02-781, Warsaw, Poland
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, 02-781, Warsaw, Poland
| | - Karolina Skubisz
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, 02-781, Warsaw, Poland
| | - Patrycja Cybula
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, 02-781, Warsaw, Poland
| | - Łukasz Targoński
- Department of Lymphoproliferative Diseases, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781, Warsaw, Poland
| | - Michał Mikula
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, Roentgena 5, 02-781, Warsaw, Poland
| | - Jan Walewski
- Department of Lymphoproliferative Diseases, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781, Warsaw, Poland
| | - Jerzy Ostrowski
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, Roentgena 5, 02-781, Warsaw, Poland.
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, 02-781, Warsaw, Poland.
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81
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Azimirad M, Krutova M, Yadegar A, Shahrokh S, Olfatifar M, Aghdaei HA, Fawley WN, Wilcox MH, Zali MR. Clostridioides difficile ribotypes 001 and 126 were predominant in Tehran healthcare settings from 2004 to 2018: a 14-year-long cross-sectional study. Emerg Microbes Infect 2021; 9:1432-1443. [PMID: 32520657 PMCID: PMC7473134 DOI: 10.1080/22221751.2020.1780949] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Clostridioides difficile infection (CDI) remains a major healthcare problem worldwide, however, little is known about CDI epidemiology in Iran. Between December 2004 and November 2018, 3649 stool samples were collected from patients in 69 hospitals and medical centres in Tehran and were cultured for the presence of C. difficile; isolates were characterized by PCR ribotyping and toxin genes detection. A total of 582 C. difficile isolates were obtained and the overall CDI prevalence was 15.9%; 290 (49.8%) cases were healthcare-associated (HA) and 292 (50.2%) cases were community-associated (CA). Of these, DNA of 513 isolates submitted for ribotyping. The ribotype and/or WEBRIBO type could be assessed in 366 (62.9%) isolates. The most frequent RTs were 001 (n = 75, 12.9%), 126 (n = 65, 11.2%) and 084 (n = 19, 3.3%); the toxin gene profile tcdA + B + /cdtA + B + (n = 112, 19.2%) was the most common. Fifteen C. difficile isolates (2.6%) did not carry any toxin genes. There was no difference between frequently found RTs in HA-CDI and CA-CDI, except for RT 029 which was more likely to be associated with healthcare origin (12/15, p-value = 0.02). No isolate of RTs 027 or 078 was identified. Importantly, RTs 031, 038, 039, 084, 085 reported previously as RTs with an absence of toxin genes, revealed the presence of toxin genes in our study. Using Simpson's reciprocal index of diversity, we found that RT diversity decreased as the prevalence of the RT 084 increased (R = -0.78, p-value = 0.041). Different patterns in CDI epidemiology underscore the importance of local surveillance and infection control measures in Tehran healthcare settings.
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Affiliation(s)
- Masoumeh Azimirad
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Marcela Krutova
- Department of Medical Microbiology, Charles University, 2nd Faculty of Medicine and Motol University Hospital, Prague, Czech Republic.,European Society of Clinical Microbiology and Infectious Diseases (ESCMID) Study Group for Clostridioides Difficile (ESGCD)
| | - Abbas Yadegar
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Shabnam Shahrokh
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Meysam Olfatifar
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hamid Asadzadeh Aghdaei
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Warren N Fawley
- European Society of Clinical Microbiology and Infectious Diseases (ESCMID) Study Group for Clostridioides Difficile (ESGCD).,Healthcare Associated Infections Research Group, Leeds Teaching Hospitals NHS Trust & University of Leeds, Leeds, UK
| | - Mark H Wilcox
- European Society of Clinical Microbiology and Infectious Diseases (ESCMID) Study Group for Clostridioides Difficile (ESGCD).,Healthcare Associated Infections Research Group, Leeds Teaching Hospitals NHS Trust & University of Leeds, Leeds, UK
| | - Mohammad Reza Zali
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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82
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Successful Experience of Fecal Transplantation in a Patient with Severe Pseudomembranous Colitis. ACTA BIOMEDICA SCIENTIFICA 2021. [DOI: 10.29413/abs.2020-5.6.32] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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83
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Aguilar-Zamora E, Weimer BC, Torres RC, Gómez-Delgado A, Ortiz-Olvera N, Aparicio-Ozores G, Barbero-Becerra VJ, Torres J, Camorlinga-Ponce M. Molecular Epidemiology and Antimicrobial Resistance of Clostridioides difficile in Hospitalized Patients From Mexico. Front Microbiol 2021; 12:787451. [PMID: 35360652 PMCID: PMC8960119 DOI: 10.3389/fmicb.2021.787451] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 12/29/2021] [Indexed: 01/05/2023] Open
Abstract
Clostridioides difficile is a global public health problem, which is a primary cause of antibiotic-associated diarrhea in humans. The emergence of hypervirulent and antibiotic-resistant strains is associated with the increased incidence and severity of the disease. There are limited studies on genomic characterization of C. difficile in Latin America. We aimed to learn about the molecular epidemiology and antimicrobial resistance in C. difficile strains from adults and children in hospitals of México. We studied 94 C. difficile isolates from seven hospitals in Mexico City from 2014 to 2018. Whole-genome sequencing (WGS) was used to determine the genotype and examine the toxigenic profiles. Susceptibility to antibiotics was determined by E-test. Multilocus sequence typing (MLST) was used to determine allelic profiles. Results identified 20 different sequence types (ST) in the 94 isolates, mostly clade 2 and clade 1. ST1 was predominant in isolates from adult and children. Toxigenic strains comprised 87.2% of the isolates that were combinations of tcdAB and cdtAB (tcdA+/tcdB+/cdtA+/cdtB+, followed by tcdA+/tcdB+/cdtA-/cdtB-, tcdA-/tcdB+/cdtA-/ cdtB-, and tcdA-/tcdB-/cdtA+/cdtB+). Toxin profiles were more diverse in isolates from children. All 94 isolates were susceptible to metronidazole and vancomycin, whereas a considerable number of isolates were resistant to clindamycin, fluroquinolones, rifampicin, meropenem, and linezolid. Multidrug-resistant isolates (≥3 antibiotics) comprised 65% of the isolates. The correlation between resistant genotypes and phenotypes was evaluated by the kappa test. Mutations in rpoB and rpoC showed moderate concordance with resistance to rifampicin and mutations in fusA substantial concordance with fusidic acid resistance. cfrE, a gene recently described in one Mexican isolate, was present in 65% of strains linezolid resistant, all ST1 organisms. WGS is a powerful tool to genotype and characterize virulence and antibiotic susceptibility patterns.
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Affiliation(s)
- Emmanuel Aguilar-Zamora
- Unidad de Investigación Medica en Enfermedades Infecciosas y Parasitarias, UMAE Pediatría, CMN Siglo XXI, IMSS, México City, Mexico
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, México City, Mexico
| | - Bart C. Weimer
- Department of Population Health and Reproduction, School of Veterinary Medicine, 100K Pathogen Genome Project, University of California, Davis, Davis, CA, United States
| | - Roberto C. Torres
- Unidad de Investigación Medica en Enfermedades Infecciosas y Parasitarias, UMAE Pediatría, CMN Siglo XXI, IMSS, México City, Mexico
| | - Alejandro Gómez-Delgado
- Unidad de Investigación Medica en Enfermedades Infecciosas y Parasitarias, UMAE Pediatría, CMN Siglo XXI, IMSS, México City, Mexico
| | - Nayeli Ortiz-Olvera
- Departamento de Gastroenterología, UMAE Hospital de Especialidades, Instituto Mexicano del Seguro Social, México City, Mexico
| | - Gerardo Aparicio-Ozores
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, México City, Mexico
| | | | - Javier Torres
- Unidad de Investigación Medica en Enfermedades Infecciosas y Parasitarias, UMAE Pediatría, CMN Siglo XXI, IMSS, México City, Mexico
- *Correspondence: Javier Torres,
| | - Margarita Camorlinga-Ponce
- Unidad de Investigación Medica en Enfermedades Infecciosas y Parasitarias, UMAE Pediatría, CMN Siglo XXI, IMSS, México City, Mexico
- Margarita Camorlinga-Ponce,
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84
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Phylogenomics of 8,839 Clostridioides difficile genomes reveals recombination-driven evolution and diversification of toxin A and B. PLoS Pathog 2020; 16:e1009181. [PMID: 33370413 PMCID: PMC7853461 DOI: 10.1371/journal.ppat.1009181] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 02/02/2021] [Accepted: 11/23/2020] [Indexed: 12/15/2022] Open
Abstract
Clostridioides difficile is the major worldwide cause of antibiotic-associated gastrointestinal infection. A pathogenicity locus (PaLoc) encoding one or two homologous toxins, toxin A (TcdA) and toxin B (TcdB), is essential for C. difficile pathogenicity. However, toxin sequence variation poses major challenges for the development of diagnostic assays, therapeutics, and vaccines. Here, we present a comprehensive phylogenomic analysis of 8,839 C. difficile strains and their toxins including 6,492 genomes that we assembled from the NCBI short read archive. A total of 5,175 tcdA and 8,022 tcdB genes clustered into 7 (A1-A7) and 12 (B1-B12) distinct subtypes, which form the basis of a new method for toxin-based subtyping of C. difficile. We developed a haplotype coloring algorithm to visualize amino acid variation across all toxin sequences, which revealed that TcdB has diversified through extensive homologous recombination throughout its entire sequence, and formed new subtypes through distinct recombination events. In contrast, TcdA varies mainly in the number of repeats in its C-terminal repetitive region, suggesting that recombination-mediated diversification of TcdB provides a selective advantage in C. difficile evolution. The application of toxin subtyping is then validated by classifying 351 C. difficile clinical isolates from Brigham and Women's Hospital in Boston, demonstrating its clinical utility. Subtyping partitions TcdB into binary functional and antigenic groups generated by intragenic recombinations, including two distinct cell-rounding phenotypes, whether recognizing frizzled proteins as receptors, and whether it can be efficiently neutralized by monoclonal antibody bezlotoxumab, the only FDA-approved therapeutic antibody. Our analysis also identifies eight universally conserved surface patches across the TcdB structure, representing ideal targets for developing broad-spectrum therapeutics. Finally, we established an open online database (DiffBase) as a central hub for collection and classification of C. difficile toxins, which will help clinicians decide on therapeutic strategies targeting specific toxin variants, and allow researchers to monitor the ongoing evolution and diversification of C. difficile.
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85
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Werner A, Mölling P, Fagerström A, Dyrkell F, Arnellos D, Johansson K, Sundqvist M, Norén T. Whole genome sequencing of Clostridioides difficile PCR ribotype 046 suggests transmission between pigs and humans. PLoS One 2020; 15:e0244227. [PMID: 33347506 PMCID: PMC7751860 DOI: 10.1371/journal.pone.0244227] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 12/04/2020] [Indexed: 01/16/2023] Open
Abstract
Background A zoonotic association has been suggested for several PCR ribotypes (RTs) of Clostridioides difficile. In central parts of Sweden, RT046 was found dominant in neonatal pigs at the same time as a RT046 hospital C. difficile infection (CDI) outbreak occurred in the southern parts of the country. Objective To detect possible transmission of RT046 between pig farms and human CDI cases in Sweden and investigate the diversity of RT046 in the pig population using whole genome sequencing (WGS). Methods WGS was performed on 47 C. difficile isolates from pigs (n = 22), the farm environment (n = 7) and human cases of CDI (n = 18). Two different core genome multilocus sequencing typing (cgMLST) schemes were used together with a single nucleotide polymorphisms (SNP) analysis and the results were related to time and location of isolation of the isolates. Results The pig isolates were closely related (≤6 cgMLST alleles differing in both cgMLST schemes) and conserved over time and were clearly separated from isolates from the human hospital outbreak (≥76 and ≥90 cgMLST alleles differing in the two cgMLST schemes). However, two human isolates were closely related to the pig isolates, suggesting possible transmission. The SNP analysis was not more discriminate than cgMLST. Conclusion No general pattern suggesting zoonotic transmission was apparent between pigs and humans, although contrasting results from two isolates still make transmission possible. Our results support the need for high resolution WGS typing when investigating hospital and environmental transmission of C. difficile.
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Affiliation(s)
- Anders Werner
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Göteborg, Region Västra Götaland, Sweden
- * E-mail:
| | - Paula Mölling
- Faculty of Medicine and Health, Department of Laboratory Medicine, National Reference Laboratory for Clostridioides difficile, Clinical Microbiology, Örebro University, Örebro, Sweden
| | - Anna Fagerström
- Faculty of Medicine and Health, Department of Laboratory Medicine, National Reference Laboratory for Clostridioides difficile, Clinical Microbiology, Örebro University, Örebro, Sweden
| | | | | | - Karin Johansson
- Faculty of Medicine and Health, Department of Laboratory Medicine, National Reference Laboratory for Clostridioides difficile, Clinical Microbiology, Örebro University, Örebro, Sweden
| | - Martin Sundqvist
- Faculty of Medicine and Health, Department of Laboratory Medicine, National Reference Laboratory for Clostridioides difficile, Clinical Microbiology, Örebro University, Örebro, Sweden
| | - Torbjörn Norén
- Faculty of Medicine and Health, Department of Laboratory Medicine, National Reference Laboratory for Clostridioides difficile, Clinical Microbiology, Örebro University, Örebro, Sweden
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86
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Sekiya H, Tamai E, Kawasaki J, Murakami K, Kamitori S. Structural and biochemical characterizations of the novel autolysin Acd24020 from Clostridioides difficile and its full-function catalytic domain as a lytic enzyme. Mol Microbiol 2020; 115:684-698. [PMID: 33140473 DOI: 10.1111/mmi.14636] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 10/13/2020] [Accepted: 10/28/2020] [Indexed: 12/17/2022]
Abstract
Autolysin is a lytic enzyme that hydrolyzes peptidoglycans of the bacterial cell wall, with a catalytic domain and cell wall-binding (CWB) domains, to be involved in different physiological functions that require bacterial cell wall remodeling. We identified a novel autolysin, Acd24020, from Clostridioides (Clostridium) difficile (C. difficile), with an endopeptidase catalytic domain belonging to the NlpC/P60 family and three bacterial Src-homology 3 domains as CWB domains. The catalytic domain of Acd24020 (Acd24020-CD) exhibited C. difficile-specific lytic activity equivalent to Acd24020, indicating that Acd24020-CD has full-function as a lytic enzyme by itself. To elucidate the specific peptidoglycan-recognition and catalytic reaction mechanisms of Acd24020-CD, biochemical characterization, X-ray structure determination, a modeling study of the enzyme/substrate complex, and mutagenesis analysis were performed. Acd24020-CD has an hourglass-shaped substrate-binding groove across the molecule, which is responsible for recognizing the direct 3-4 cross-linking structure unique to C. difficile peptidoglycan. Based on the X-ray structure and modeling study, we propose a dynamic Cys/His catalyzing mechanism, in which the catalytic Cys299 and His354 residues dynamically change their conformations to complement each step of the enzyme catalytic reaction.
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Affiliation(s)
- Hiroshi Sekiya
- Department of Infectious Disease, College of Pharmaceutical Science, Matsuyama University, Matsuyama, Japan
| | - Eiji Tamai
- Department of Infectious Disease, College of Pharmaceutical Science, Matsuyama University, Matsuyama, Japan.,Life Science Research Center and Faculty of Medicine, Kagawa University, Miki-cho, Kita-gun, Japan
| | - Jurina Kawasaki
- Department of Infectious Disease, College of Pharmaceutical Science, Matsuyama University, Matsuyama, Japan
| | - Kaho Murakami
- Department of Infectious Disease, College of Pharmaceutical Science, Matsuyama University, Matsuyama, Japan
| | - Shigehiro Kamitori
- Life Science Research Center and Faculty of Medicine, Kagawa University, Miki-cho, Kita-gun, Japan
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87
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McLean K, Balada-Llasat JM, Waalkes A, Pancholi P, Salipante SJ. Whole-genome sequencing of clinical Clostridioides difficile isolates reveals molecular epidemiology and discrepancies with conventional laboratory diagnostic testing. J Hosp Infect 2020; 108:64-71. [PMID: 33227298 DOI: 10.1016/j.jhin.2020.11.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 10/06/2020] [Accepted: 11/16/2020] [Indexed: 12/29/2022]
Abstract
BACKGROUND The high clinical burden of Clostridioides difficile infections merits rapid and sensitive identification of affected individuals. However, effective diagnosis remains challenging. Current best practice guidelines recommend molecular and/or direct toxin detection-based screening for symptomatic individuals, but previous work has called into question the concordance and performance of extant clinical assays. AIM To better correlate the genomic and phenotypic properties of clinical C. difficile isolates with laboratory testing outcomes in both C. difficile-infected patients and asymptomatic carriers. METHODS Whole-genome sequencing of clinical C. difficile isolates collected from an inpatient population at a single healthcare institution was performed, enabling examination of their molecular epidemiology and toxigenic gene content. Genomic findings were compared with clinical testing outcomes, identifying multiple diagnostic discrepancies. FINDINGS Toxigenic culture, considered a 'reference standard', provided perfect sensitivity and specificity in predicting toxigenic gene content, whereas reduced performance was observed for Simplexa C. difficile Direct Assay (100% specificity, 88% sensitivity), Gene Xpert CD/Epi Assay (86% specificity, 83% sensitivity), and Quick Check Complete Tox A/B (100% specificity, 30% sensitivity). Genomic analysis additionally revealed variability in toxin gene sequences among C. difficile strains, phylogenomic equivalency between isolates from affected patients and carriers, and patient carriage with uncommon environmentally derived C. difficile lineages, as well as presenting opportunities for tracing pathogen transmission events. CONCLUSION These results highlight the variable performance of clinical stool-based testing approaches as well as the potential diagnostic utility of whole-genome sequencing as an alternative to conventional testing algorithms.
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Affiliation(s)
- K McLean
- University of Washington Department of Laboratory Medicine, Seattle, WA, USA
| | - J-M Balada-Llasat
- Ohio State University Wexner Medical Center, Department of Pathology, Columbus, OH, USA
| | - A Waalkes
- University of Washington Department of Laboratory Medicine, Seattle, WA, USA
| | - P Pancholi
- Ohio State University Wexner Medical Center, Department of Pathology, Columbus, OH, USA.
| | - S J Salipante
- University of Washington Department of Laboratory Medicine, Seattle, WA, USA.
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88
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Lu J, Salzberg SL. Ultrafast and accurate 16S rRNA microbial community analysis using Kraken 2. MICROBIOME 2020; 8:124. [PMID: 32859275 PMCID: PMC7455996 DOI: 10.1186/s40168-020-00900-2] [Citation(s) in RCA: 113] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 07/24/2020] [Indexed: 05/23/2023]
Abstract
BACKGROUND For decades, 16S ribosomal RNA sequencing has been the primary means for identifying the bacterial species present in a sample with unknown composition. One of the most widely used tools for this purpose today is the QIIME (Quantitative Insights Into Microbial Ecology) package. Recent results have shown that the newest release, QIIME 2, has higher accuracy than QIIME, MAPseq, and mothur when classifying bacterial genera from simulated human gut, ocean, and soil metagenomes, although QIIME 2 also proved to be the most computationally expensive. Kraken, first released in 2014, has been shown to provide exceptionally fast and accurate classification for shotgun metagenomics sequencing projects. Bracken, released in 2016, then provided users with the ability to accurately estimate species or genus relative abundances using Kraken classification results. Kraken 2, which matches the accuracy and speed of Kraken 1, now supports 16S rRNA databases, allowing for direct comparisons to QIIME and similar systems. METHODS For a comprehensive assessment of each tool, we compare the computational resources and speed of QIIME 2's q2-feature-classifier, Kraken 2, and Bracken in generating the three main 16S rRNA databases: Greengenes, SILVA, and RDP. For an evaluation of accuracy, we evaluated each tool using the same simulated 16S rRNA reads from human gut, ocean, and soil metagenomes that were previously used to compare QIIME, MAPseq, mothur, and QIIME 2. We evaluated accuracy based on the accuracy of the final genera read counts assigned by each tool. Finally, as Kraken 2 is the only tool providing per-read taxonomic assignments, we evaluate the sensitivity and precision of Kraken 2's per-read classifications. RESULTS For both the Greengenes and SILVA database, Kraken 2 and Bracken are up to 100 times faster at database generation. For classification, using the same data as previous studies, Kraken 2 and Bracken are up to 300 times faster, use 100x less RAM, and generate results that more accurate at 16S rRNA profiling than QIIME 2's q2-feature-classifier. CONCLUSION Kraken 2 and Bracken provide a very fast, efficient, and accurate solution for 16S rRNA metataxonomic data analysis. Video Abstract.
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Affiliation(s)
- Jennifer Lu
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA.
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA.
| | - Steven L Salzberg
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA
- Departments of Computer Science and Biostatistics, Johns Hopkins University, Baltimore, MD, USA
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89
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Gu W, Li W, Wang W, Kuang D, Zhang W, Lu C, Li N, Tong P, Han Y, Sun X, Lu J, Wu Y, Dai J. Response of the gut microbiota during the Clostridioides difficile infection in tree shrews mimics those in humans. BMC Microbiol 2020; 20:260. [PMID: 32819295 PMCID: PMC7441558 DOI: 10.1186/s12866-020-01943-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 08/11/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Clostridioides difficile is a major cause of antibiotic associated diarrhea. Several animal models are used to study C. difficile infection (CDI). The tree shrew has recently been developed as a model of primate processes. C. difficile infection has not been examined in tree shrews. We infected tree shrews with hyper-virulent C. difficile strains and examined the alterations in gut microbiota using 16S rRNA gene sequencing. RESULTS C. difficile colonized the gastrointestinal tract of tree shrew and caused diarrhea and weight loss. Histopathologic examination indicated structures and mucosal cell destruction in ileal and colonic tissues. The gut microbial community was highly diversity before infection and was dominated by Firmicutes, Fusobacteria, Bacteroidetes, and Proteobacteria. Antibiotic administration decreased the diversity of the gut microbiota and led to an outgrowth of Lactobacillus. The relative abundance of Proteobacteria, Gammaproteobacteria, Enterobacteriales, Lachnospiraceae, Enterobacteriaceae, Escherichia, Blautia, and Tyzzerella increased following C. difficile infection. These taxa could be biomarkers for C. difficile colonization. CONCLUSIONS In general, the disease symptoms, histopathology, and gut microbiota changes following C. difficile infection in tree shrews were similar to those observed in humans.
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Affiliation(s)
- Wenpeng Gu
- Center of Tree Shrew Germplasm Resources, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Yunnan Innovation Team of Standardization and Application Research in Tree Shrew, Zhao zong Road 66, Kunming, 650118, China.,Department of Acute Infectious Diseases Control and Prevention, Yunnan Provincial Centre for Disease Control and Prevention, Kunming, 650022, China
| | - Wenge Li
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Chang bai Road 155, Chang ping District, Beijing, 102206, China
| | - Wenguang Wang
- Center of Tree Shrew Germplasm Resources, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Yunnan Innovation Team of Standardization and Application Research in Tree Shrew, Zhao zong Road 66, Kunming, 650118, China
| | - Dexuan Kuang
- Center of Tree Shrew Germplasm Resources, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Yunnan Innovation Team of Standardization and Application Research in Tree Shrew, Zhao zong Road 66, Kunming, 650118, China
| | - Wenzhu Zhang
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Chang bai Road 155, Chang ping District, Beijing, 102206, China
| | - Caixia Lu
- Center of Tree Shrew Germplasm Resources, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Yunnan Innovation Team of Standardization and Application Research in Tree Shrew, Zhao zong Road 66, Kunming, 650118, China
| | - Na Li
- Center of Tree Shrew Germplasm Resources, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Yunnan Innovation Team of Standardization and Application Research in Tree Shrew, Zhao zong Road 66, Kunming, 650118, China
| | - Pinfen Tong
- Center of Tree Shrew Germplasm Resources, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Yunnan Innovation Team of Standardization and Application Research in Tree Shrew, Zhao zong Road 66, Kunming, 650118, China
| | - Yuanyuan Han
- Center of Tree Shrew Germplasm Resources, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Yunnan Innovation Team of Standardization and Application Research in Tree Shrew, Zhao zong Road 66, Kunming, 650118, China
| | - Xiaomei Sun
- Center of Tree Shrew Germplasm Resources, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Yunnan Innovation Team of Standardization and Application Research in Tree Shrew, Zhao zong Road 66, Kunming, 650118, China
| | - Jinxing Lu
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Chang bai Road 155, Chang ping District, Beijing, 102206, China
| | - Yuan Wu
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Chang bai Road 155, Chang ping District, Beijing, 102206, China.
| | - Jiejie Dai
- Center of Tree Shrew Germplasm Resources, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Yunnan Innovation Team of Standardization and Application Research in Tree Shrew, Zhao zong Road 66, Kunming, 650118, China.
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90
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Shen E, Zhu K, Li D, Pan Z, Luo Y, Bian Q, He L, Song X, Zhen Y, Jin D, Tao L. Subtyping analysis reveals new variants and accelerated evolution of Clostridioides difficile toxin B. Commun Biol 2020; 3:347. [PMID: 32620855 PMCID: PMC7335066 DOI: 10.1038/s42003-020-1078-y] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 06/16/2020] [Indexed: 02/06/2023] Open
Abstract
Clostridioides difficile toxins (TcdA and TcdB) are major exotoxins responsible for C. difficile infection (CDI) associated diseases. The previously reported TcdB variants showed distinct biological features, immunoactivities, and potential pathogenicity in disease progression. Here, we performed global comparisons of amino acid sequences of both TcdA and TcdB from 3,269 C. difficile genomes and clustered them according to the evolutionary relatedness. We found that TcdB was much diverse and could be divided into eight subtypes, of which four were first described. Further analysis indicates that the tcdB gene undergoes accelerated evolution to maximize diversity. By tracing TcdB subtypes back to their original isolates, we found that the distribution of TcdB subtypes was not completely aligned with the phylogeny of C. difficile. These findings suggest that the tcdB genes not only frequently mutate, but also continuously transfer and exchange among C. difficile strains. Shen et al. compare the amino acid sequences of bacterial toxins TcdA and TcdB from 3,269 Clostridioides difficile genomes to identify four new TcdB subtypes. They find that TcdB was more diverse in amino acid sequence than TcdA. This study suggests that the tcdB genes not only frequently mutate, but they also continuously transfer and exchange among C. difficile strains.
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Affiliation(s)
- Enhui Shen
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, 310024, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, 310024, China
| | - Kangli Zhu
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, 310024, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, 310024, China
| | - Danyang Li
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, 310024, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, 310024, China
| | - Zhenrui Pan
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, 310024, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, 310024, China
| | - Yun Luo
- Department of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, Zhejiang, 310051, China.,School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Qiao Bian
- School of Medicine, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Liuqing He
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, 310024, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, 310024, China
| | - Xiaojun Song
- Centre of Laboratory Medicine, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, Zhejiang, 310014, China
| | - Ying Zhen
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, 310024, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, 310024, China
| | - Dazhi Jin
- Centre of Laboratory Medicine, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, Zhejiang, 310014, China.,School of Laboratory Medicine, Hangzhou Medical College, Hangzhou, Zhejiang, 310053, China
| | - Liang Tao
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, 310024, China. .,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, 310024, China.
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91
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Smith AB, Soto Ocana J, Zackular JP. From Nursery to Nursing Home: Emerging Concepts in Clostridioides difficile Pathogenesis. Infect Immun 2020; 88:IAI.00934-19. [PMID: 32122939 PMCID: PMC7309631 DOI: 10.1128/iai.00934-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Clostridioides difficile is a Gram-positive, spore-forming, anaerobic bacterium that infects the human gastrointestinal tract, causing a wide range of disorders that vary in severity from mild diarrhea to toxic megacolon and/or death. Over the past decade, incidence, severity, and costs associated with C. difficile infection (CDI) have increased dramatically in both the pediatric and adult populations. The factors driving this rapidly evolving epidemiology remain largely unknown but are likely due in part to previously unappreciated host, microbiota, and environmental factors. In this review, we will cover the risks and challenges of CDI in adult and pediatric populations and examine asymptomatic colonization in infants. We will also discuss the emerging role of diet, pharmaceutical drugs, and pathogen-microbiota interactions in C. difficile pathogenesis, as well as the impact of host-microbiota interactions in the manifestation of C. difficile-associated disease. Finally, we highlight new areas of research and novel strategies that may shed light on this complex infection and provide insights into the future of microbiota-based therapeutics for CDI.
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Affiliation(s)
- Alexander B Smith
- Division of Protective Immunity, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Joshua Soto Ocana
- Division of Protective Immunity, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Joseph P Zackular
- Division of Protective Immunity, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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92
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Martínez-Meléndez A, Morfin-Otero R, Villarreal-Treviño L, Baines SD, Camacho-Ortíz A, Garza-González E. Molecular epidemiology of predominant and emerging Clostridioides difficile ribotypes. J Microbiol Methods 2020; 175:105974. [PMID: 32531232 DOI: 10.1016/j.mimet.2020.105974] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 06/05/2020] [Accepted: 06/05/2020] [Indexed: 12/18/2022]
Abstract
There has been an increase in the incidence and severity of Clostridioides difficile infection (CDI) worldwide, and strategies to control, monitor, and diminish the associated morbidity and mortality have been developed. Several typing methods have been used for typing of isolates and studying the epidemiology of CDI; serotyping was the first typing method, but then was replaced by pulsed-field gel electrophoresis (PFGE). PCR ribotyping is now the gold standard method; however, multi locus sequence typing (MLST) schemes have been developed. New sequencing technologies have allowed comparing whole bacterial genomes to address genetic relatedness with a high level of resolution and discriminatory power to distinguish between closely related strains. Here, we review the most frequent C. difficile ribotypes reported worldwide, with a focus on their epidemiology and genetic characteristics.
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Affiliation(s)
- Adrián Martínez-Meléndez
- Universidad Autónoma de Nuevo León, Facultad de Ciencias Químicas, Pedro de Alba S/N, Ciudad Universitaria, CP 66450 San Nicolás de los Garza, Nuevo Leon, Mexico
| | - Rayo Morfin-Otero
- Hospital Civil de Guadalajara "Fray Antonio Alcalde" e Instituto de Patología Infecciosa y Experimental, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara. Sierra Mojada 950, Col. Independencia, CP 44350 Guadalajara, Jalisco, Mexico
| | - Licet Villarreal-Treviño
- Universidad Autónoma de Nuevo León, Facultad de Ciencias Biológicas, Departamento de Microbiología e Inmunología, Pedro de Alba S/N, Ciudad Universitaria, CP 66450 San Nicolás de los Garza, Nuevo Leon, Mexico
| | - Simon D Baines
- University of Hertfordshire, School of Life and Medical Sciences, Department of Biological and Environmental Sciences, Hatfield AL10 9AB, UK
| | - Adrián Camacho-Ortíz
- Universidad Autónoma de Nuevo León, Hospital Universitario "Dr. José Eleuterio González", Servicio de Infectología. Av. Francisco I. Madero Pte. S/N y Av. José E. González. Col. Mitras Centro, CP 64460 Monterrey, Nuevo Leon, Mexico
| | - Elvira Garza-González
- Universidad Autónoma de Nuevo León, Hospital Universitario "Dr. José Eleuterio González", Servicio de Infectología. Av. Francisco I. Madero Pte. S/N y Av. José E. González. Col. Mitras Centro, CP 64460 Monterrey, Nuevo Leon, Mexico.
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93
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Ma KGL, Lertpiriyapong K, Piersigilli A, Dobtsis I, Wipf JRK, Littmann ER, Leiner I, Pamer EG, Ricart Arbona RJ, Lipman NS. Outbreaks of Typhlocolitis Caused by Hypervirulent Group ST1 Clostridioides difficile in Highly Immunocompromised Strains of Mice. Comp Med 2020; 70:277-290. [PMID: 32404234 PMCID: PMC7287380 DOI: 10.30802/aalas-cm-19-000109] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 12/15/2019] [Accepted: 01/13/2020] [Indexed: 12/17/2022]
Abstract
Clostridioides difficile is an enteric pathogen that can cause significant clinical disease in both humans and animals. However, clinical disease arises most commonly after treatment with broad-spectrum antibiotics. The organism's ability to cause naturally occurring disease in mice is rare, and little is known about its clinical significance in highly immunocompromised mice. We report on 2 outbreaks of diarrhea associated with C. difficile in mice. In outbreak 1, 182 of approximately 2, 400 NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ (NSG) and related strains of mice became clinically ill after cessation of a 14-d course of 0.12% amoxicillin feed to control an increase in clinical signs associated with Corynebacterium bovis infection. Most mice had been engrafted with human tumors; the remainder were experimentally naïve. Affected animals exhibited 1 of 3 clinical syndromes: 1) peracute death; 2) severe diarrhea leading to euthanasia or death; or 3) mild to moderate diarrhea followed by recovery. A given cage could contain both affected and unaffected mice. Outbreak 2 involved a small breeding colony (approximately 50 mice) of NOD. CB17-Prkdcscid/NCrCrl (NOD-scid) mice that had not received antibiotics or experimental manipulations. In both outbreaks, C. difficile was isolated, and toxins A and B were detected in intestinal content or feces. Histopathologic lesions highly suggestive of C. difficile enterotoxemia included fibrinonecrotizing and neutrophilic typhlocolitis with characteristic 'volcano' erosions or pseudomembrane formation. Genomic analysis of 4 isolates (3 from outbreak 1 and 1 from outbreak 2) revealed that these isolates were closely related to a pathogenic human isolate, CD 196. To our knowledge, this report is the first to describe naturally occurring outbreaks of C. difficile-associated typhlocolitis with significant morbidity and mortality in highly immunocompromised strains of mice.
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Affiliation(s)
- Kathleen G L Ma
- Tri-Institutional Training Program in Laboratory Animal Medicine and Science, Memorial Sloan-Kettering Cancer Center, Weill Cornell Medicine, and The Rockefeller University, New York, New York
| | - Kvin Lertpiriyapong
- Tri-Institutional Training Program in Laboratory Animal Medicine and Science, Memorial Sloan-Kettering Cancer Center, Weill Cornell Medicine, and The Rockefeller University, New York, New York; Center for Comparative Medicine and Pathology, Memorial Sloan-Kettering Cancer Center and Weill Cornell Medicine, New York, New York
| | - Alessandra Piersigilli
- Tri-Institutional Training Program in Laboratory Animal Medicine and Science, Memorial Sloan-Kettering Cancer Center, Weill Cornell Medicine, and The Rockefeller University, New York, New York; Center for Comparative Medicine and Pathology, Memorial Sloan-Kettering Cancer Center and Weill Cornell Medicine, New York, New York; Laboratory for Comparative Pathology, Memorial Sloan-Kettering Cancer Center, Weill Cornell Medical College, and The Rockefeller University, New York, New York
| | - Irina Dobtsis
- Laboratory for Comparative Pathology, Memorial Sloan-Kettering Cancer Center, Weill Cornell Medical College, and The Rockefeller University, New York, New York
| | - Juliette R K Wipf
- Tri-Institutional Training Program in Laboratory Animal Medicine and Science, Memorial Sloan-Kettering Cancer Center, Weill Cornell Medicine, and The Rockefeller University, New York, New York; Center for Comparative Medicine and Pathology, Memorial Sloan-Kettering Cancer Center and Weill Cornell Medicine, New York, New York; Laboratory for Comparative Pathology, Memorial Sloan-Kettering Cancer Center, Weill Cornell Medical College, and The Rockefeller University, New York, New York
| | - Eric R Littmann
- Infectious Diseases Service, Department of Medicine, Immunology Program, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Ingrid Leiner
- Infectious Diseases Service, Department of Medicine, Immunology Program, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Eric G Pamer
- Infectious Diseases Service, Department of Medicine, Immunology Program, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Rodolfo J Ricart Arbona
- Tri-Institutional Training Program in Laboratory Animal Medicine and Science, Memorial Sloan-Kettering Cancer Center, Weill Cornell Medicine, and The Rockefeller University, New York, New York; Center for Comparative Medicine and Pathology, Memorial Sloan-Kettering Cancer Center and Weill Cornell Medicine, New York, New York
| | - Neil S Lipman
- Tri-Institutional Training Program in Laboratory Animal Medicine and Science, Memorial Sloan-Kettering Cancer Center, Weill Cornell Medicine, and The Rockefeller University, New York, New York; Center for Comparative Medicine and Pathology, Memorial Sloan-Kettering Cancer Center and Weill Cornell Medicine, New York, New York;,
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94
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Okada Y, Okugawa S, Ikeda M, Kobayashi T, Saito R, Higurashi Y, Moriya K. Genetic diversity and epidemiology of accessory gene regulator loci in Clostridioides difficile. Access Microbiol 2020; 2:acmi000134. [PMID: 32974597 PMCID: PMC7497831 DOI: 10.1099/acmi.0.000134] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 04/25/2020] [Indexed: 02/04/2023] Open
Abstract
Quorum sensing is known to regulate bacterial virulence, and the accessory gene regulator (agr) loci is one of the genetic loci responsible for its regulation. Recent reports examining Clostridioides difficile show that two agr loci, agr1 and agr2, regulate toxin production, but the diversity of agr loci and their epidemiology is unknown. In our study, in silico analysis was performed to research genetic diversity of agr, and C. difficile isolates from clinical samples underwent multilocus sequence typing (MLST) and PCR analysis of agr loci. To reveal the distribution of agr among different strains, phylogenetic analysis was also performed. In our in silico analysis, two different subtypes, named agr2R and agr2M, were found in agr2, which were previously reported. PCR analysis of 133 C . difficile isolates showed that 131 strains had agr1, 61 strains had agr2R, and 26 strains had agr2M; agr2R was mainly found in clade 1 or clade 2 organisms, whereas agr2M was only found in clade 4. With rare exception, agr1-negative sequence types (STs) belonged to clade C-Ⅰ and C-Ⅲ, and one clade 4 strain had agr2R. Our study revealed subtypes of agr2 not previously recognized, and the distribution of several agr loci in C. difficile . These findings provide a foundation for further functional and clinical research of the agr loci.
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Affiliation(s)
- Yuta Okada
- Department of Infectious Diseases, The University of Tokyo Hospital, Bunkyo-ku, Tokyo, Japan
| | - Shu Okugawa
- Department of Infectious Diseases, The University of Tokyo Hospital, Bunkyo-ku, Tokyo, Japan
| | - Mahoko Ikeda
- Department of Infectious Diseases, The University of Tokyo Hospital, Bunkyo-ku, Tokyo, Japan
- Department of Infection Control and Prevention, The University of Tokyo Hospital, Bunkyo-ku, Tokyo, Japan
| | - Tatsuya Kobayashi
- Department of Infectious Diseases, The University of Tokyo Hospital, Bunkyo-ku, Tokyo, Japan
| | - Ryoichi Saito
- Department of Molecular Microbiology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo, Japan
| | - Yoshimi Higurashi
- Department of Infection Control and Prevention, The University of Tokyo Hospital, Bunkyo-ku, Tokyo, Japan
| | - Kyoji Moriya
- Department of Infectious Diseases, The University of Tokyo Hospital, Bunkyo-ku, Tokyo, Japan
- Department of Infection Control and Prevention, The University of Tokyo Hospital, Bunkyo-ku, Tokyo, Japan
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95
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McLure A, Glass K. Some simple rules for estimating reproduction numbers in the presence of reservoir exposure or imported cases. Theor Popul Biol 2020; 134:182-194. [PMID: 32304644 PMCID: PMC7159883 DOI: 10.1016/j.tpb.2020.04.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 03/29/2020] [Accepted: 04/10/2020] [Indexed: 02/04/2023]
Abstract
For many diseases, the basic reproduction number (R0) is a threshold parameter for disease extinction or survival in isolated populations. However no human population is fully isolated from other human or animal populations. We use compartmental models to derive simple rules for the basic reproduction number in populations where an endemic disease is sustained by a combination of local transmission within the population and exposure from some other source: either a reservoir exposure or imported cases. We introduce the idea of a reservoir-driven or importation-driven disease: diseases that would become extinct in the population of interest without reservoir exposure or imported cases (since R0<1), but nevertheless may be sufficiently transmissible that many or most infections are acquired from humans in that population. We show that in the simplest case, R0<1 if and only if the proportion of infections acquired from the external source exceeds the disease prevalence and explore how population heterogeneity and the interactions of multiple strains affect this rule. We apply these rules in two case studies of Clostridium difficile infection and colonisation: C. difficile in the hospital setting accounting for imported cases, and C. difficile in the general human population accounting for exposure to animal reservoirs. We demonstrate that even the hospital-adapted, highly-transmissible NAP1/RT027 strain of C. difficile had a reproduction number <1 in a landmark study of hospitalised patients and therefore was sustained by colonised and infected admissions to the study hospital. We argue that C. difficile should be considered reservoir-driven if as little as 13.0% of transmission can be attributed to animal reservoirs.
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Affiliation(s)
- Angus McLure
- Research School of Population Health, Australian National University, 62 Mills Rd, Acton, 0200, ACT, Australia.
| | - Kathryn Glass
- Research School of Population Health, Australian National University, 62 Mills Rd, Acton, 0200, ACT, Australia
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96
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Saber T, Hawash YA, Ismail KA, Khalifa AS, Alsharif KF, Alghamdi SA, Saber T, Eed EM. Prevalence, toxin gene profile, genotypes and antibiotic susceptibility of Clostridium difficile in a tertiary care hospital in Taif, Saudi Arabia. Indian J Med Microbiol 2020; 38:176-182. [PMID: 32883931 DOI: 10.4103/ijmm.ijmm_20_300] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Purpose Clostridium difficile (C. difficile) is an important causative agent of nosocomial diarrhoea and has become a major worldwide public health concern. The current study was conducted to determine the prevalence of C. difficile infection (CDI) amongst patients with nosocomial diarrhoea in a large tertiary care hospital in Taif, Saudi Arabia, and to define molecular characteristics and antimicrobial sensitivity profiles of C. difficile strains isolated from those patients. Materials and Methods Stool specimens were collected from 456 patients and were cultured for C. difficile isolation. The isolates were subjected to multiplex polymerase chain reaction (PCR) for detecting genes encoding the toxins (toxin A, toxin B and binary toxin [CDT]), genotyping by PCR ribotyping method and antimicrobial sensitivity testing using E test strips. Results Seventy-four C. difficile strains were recovered, of which 44 (59.5%) were A+B+CDT-, 14 (18.9%) were A-B+CDT-, 4 (5.4%) were A+B+CDT+ and 12 (16.2%) were A-B-CDT-. Toxigenic strains, and hence CDI, were detected in 13.6% of the patients (62/456). Fourteen different ribotypes were distinguished amongst bacterial isolates, of which ribotypes 002, 001, 017, 014 and 020 were the most prevalent (20.3%, 18.9%, 18.9%, 9.5% and 8.1%, respectively). Four isolates (5.4%) belonged to ribotype 027. All bacterial isolates showed sensitivity to metronidazole, vancomycin and piperacillin-tazobactam. The isolates exhibited resistance to linezolid (2.7%), chloramphenicol (5.4%), rifampicin (13.5%), tetracycline (21.6%), moxifloxacin (48.6%), clindamycin (54%) and imipenem (83.8%). Multiple drug resistance was observed in 56.8% of the isolates. Conclusion Further larger studies are required for an accurate understanding of CDI epidemiology in Saudi Arabia.
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Affiliation(s)
- Taisir Saber
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia; Department of Medical Microbiology and Immunology, Faculty of Medicine, Zagazig University, Zagazig, Egypt
| | - Yousry A Hawash
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia; Department of Molecular and Clinical Parasitology, National Liver Institute, Menoufia University, Menoufia, Egypt
| | - Khadiga A Ismail
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia; Department of Parasitology, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Amany S Khalifa
- Department of Medical Microbiology and Immunology, Faculty of Pharmacy, Taif University, Taif, Saudi Arabia; Department of Clinical Pathology, Faculty of Medicine, Menoufia University, Menoufia, Egypt
| | - Khalaf F Alsharif
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
| | - Saleh A Alghamdi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
| | - Tamer Saber
- Department of Internal Medicine, Faculty of Medicine, Zagazig University, Zagazig, Egypt
| | - Emad M Eed
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia; Department of Medical Microbiology and Immunology, Faculty of Medicine, Menoufia University, Menoufia, Egypt
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97
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Quesada-Gómez C, Murillo T, Arce G, Badilla-Lobo A, Castro-Peña C, Molina J, López-Ureña D, González-Camacho S, Lomonte B, Chacón-Díaz C, Rodríguez C, Chaves-Olarte E. Proteogenomic analysis of the Clostridium difficile exoproteome reveals a correlation between phylogenetic distribution and virulence potential. Anaerobe 2020; 62:102151. [DOI: 10.1016/j.anaerobe.2020.102151] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 12/28/2019] [Accepted: 01/10/2020] [Indexed: 12/16/2022]
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98
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Le Maréchal C, Gateau C, Poezevara T, Couturier J, Rouxel S, Syed Zaidi R, Houard E, Pourcher AM, Denis M, Barbut F. Characterization of Clostridioides difficile strains isolated from manure and digestate in five agricultural biogas plants. Anaerobe 2020; 62:102180. [DOI: 10.1016/j.anaerobe.2020.102180] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 02/20/2020] [Indexed: 02/08/2023]
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99
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Zhang WZ, Li WG, Liu YQ, Gu WP, Zhang Q, Li H, Liu ZJ, Zhang X, Wu Y, Lu JX. The molecular characters and antibiotic resistance of Clostridioides difficile from economic animals in China. BMC Microbiol 2020; 20:70. [PMID: 32228454 PMCID: PMC7106571 DOI: 10.1186/s12866-020-01757-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 03/20/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND It has been performed worldwidely to explore the potential of animals that might be a reservoir for community associated human infections of Clostridioides difficile. Several genetically undistinguished PCR ribotypes of C. difficile from animals and human have been reported, illustrating potential transmission of C. difficile between them. Pig and calf were considered as the main origins of C. difficile with predominant RT078 and RT033, respectively. As more investigations involved, great diversity of molecular types from pig and calf were reported in Europe, North American and Australia. However, there were quite limited research on C. difficile isolates from meat animals in China, leading to non-comprehensive understanding of molecular epidemiology of C. difficile in China. RESULTS A total of 55 C. difficile were isolated from 953 animal stool samples, within which 51 strains were from newborn dairy calf less than 7 days in Shandong Province. These isolates were divided into 3 STs and 6 RTs, of which ST11/RT126 was predominant type, and responsible for majority antibiotic resistance isolates. All the isolates were resistant to at least one tested antibiotics, however, only two multidrug resistant (MDR) isolates were identified. Furthermore, erythromycin (ERY) and clindamycin (CLI) were the two main resistant antibiotics. None of the isolates were resistant to vancomycin (VAN), metronidazole (MTZ), tetracycline (TET), and rifampin (RIF). CONCLUSIONS In this study, we analyzed the prevalence, molecular characters and antibiotic resistance of C. difficile from calf, sheep, chicken, and pig in China. Some unique features were found here: first, RT126 not RT078 were the dominant type from baby calf, and none isolates were got from pig; second, on the whole, isolates from animals display relative lower resistant rate to these 11 tested antibiotics, compared with isolates from human in China in our previous report. Our study helps to deep understanding the situation of C. difficile from economic animals in China, and to further study the potential transmission of C. difficile between meat animals and human.
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Affiliation(s)
- Wen-Zhu Zhang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Prevention and Control, Beijing, China
| | - Wen-Ge Li
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Prevention and Control, Beijing, China
| | - Yu-Qing Liu
- Institute of Animal Science and Veterinary Medicine, Shandong academy of agricultural Sciences, Jinan, China
| | - Wen-Peng Gu
- Department of Acute Infectious Diseases Control and Prevention, Yunnan Provincial Centre for Disease Control and Prevention, Kunming, China
| | - Qing Zhang
- Institute of Animal Science and Veterinary Medicine, Shandong academy of agricultural Sciences, Jinan, China
| | - Hu Li
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Prevention and Control, Beijing, China.,Regional Center for Disease Prevention and Control, Aksu, Xinjiang, China
| | - Zheng-Jie Liu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Prevention and Control, Beijing, China
| | - Xin Zhang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Prevention and Control, Beijing, China
| | - Yuan Wu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Prevention and Control, Beijing, China. .,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China.
| | - Jin-Xing Lu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Prevention and Control, Beijing, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
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Modelling diverse sources of Clostridium difficile in the community: importance of animals, infants and asymptomatic carriers. Epidemiol Infect 2020; 147:e152. [PMID: 31063089 PMCID: PMC6518831 DOI: 10.1017/s0950268819000384] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Clostridium difficile infections (CDIs) affect patients in hospitals and in the community, but the relative importance of transmission in each setting is unknown. We developed a mathematical model of C. difficile transmission in a hospital and surrounding community that included infants, adults and transmission from animal reservoirs. We assessed the role of these transmission routes in maintaining disease and evaluated the recommended classification system for hospital- and community-acquired CDIs. The reproduction number in the hospital was <1 (range: 0.16–0.46) for all scenarios. Outside the hospital, the reproduction number was >1 for nearly all scenarios without transmission from animal reservoirs (range: 1.0–1.34). However, the reproduction number for the human population was <1 if a minority (>3.5–26.0%) of human exposures originated from animal reservoirs. Symptomatic adults accounted for <10% transmission in the community. Under conservative assumptions, infants accounted for 17% of community transmission. An estimated 33–40% of community-acquired cases were reported but 28–39% of these reported cases were misclassified as hospital-acquired by recommended definitions. Transmission could be plausibly sustained by asymptomatically colonised adults and infants in the community or exposure to animal reservoirs, but not hospital transmission alone. Under-reporting of community-onset cases and systematic misclassification underplays the role of community transmission.
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