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Cersosimo LM, Worley JN, Bry L. Approaching toxigenic Clostridia from a one health perspective. Anaerobe 2024; 87:102839. [PMID: 38552896 DOI: 10.1016/j.anaerobe.2024.102839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 02/29/2024] [Accepted: 03/17/2024] [Indexed: 04/08/2024]
Abstract
Spore-forming pathogens have a unique capacity to thrive in diverse environments, and with temporal persistence afforded through their ability to sporulate. Their prevalence in diverse ecosystems requires a One Health approach to identify critical reservoirs and outbreak-associated transmission chains, given their capacity to freely move across soils, waterways, foodstuffs and as commensals or infecting pathogens in human and animal populations. Among anaerobic spore-formers, genomic resources for pathogens including C. botulinum, C. difficile, and C. perfringens enable our capacity to identify common and unique factors that support their persistence in diverse reservoirs and capacity to cause disease. Publicly available genomic resources for spore-forming pathogens at NCBI's Pathogen Detection program aid outbreak investigations and longitudinal monitoring in national and international programs in public health and food safety, as well as for local healthcare systems. These tools also enable research to derive new knowledge regarding disease pathogenesis, and to inform strategies in disease prevention and treatment. As global community resources, the continued sharing of strain genomic data and phenotypes further enhances international resources and means to develop impactful applications. We present examples showing use of these resources in surveillance, including capacity to assess linkages among clinical, environmental, and foodborne reservoirs and to further research investigations into factors promoting their persistence and virulence in different settings.
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Affiliation(s)
- Laura M Cersosimo
- Massachusetts Host-Microbiome Center, Dept. Pathology, Brigham & Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Jay N Worley
- Massachusetts Host-Microbiome Center, Dept. Pathology, Brigham & Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA; National Center for Biotechnology Information, NIH, Bethesda, MD, USA
| | - Lynn Bry
- Massachusetts Host-Microbiome Center, Dept. Pathology, Brigham & Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
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2
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Cersosimo LM, Worley JN, Bry L. Approaching pathogenic Clostridia from a One Health perspective. bioRxiv 2024:2024.01.08.574718. [PMID: 38260382 PMCID: PMC10802438 DOI: 10.1101/2024.01.08.574718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Spore-forming pathogens have a unique capacity to thrive in diverse environments, and with temporal persistence afforded through their ability to sporulate. These behaviors require a One Health approach to identify critical reservoirs and outbreak-associated transmission chains, given their capacity to freely move across soils, waterways, foodstuffs, and as commensals or infecting pathogens in human and veterinary populations. Among anaerobic spore-formers, genomic resources for pathogens including C. botulinum, C. difficile, and C. perfringens enable our capacity to identify common and unique factors that support their persistence in diverse reservoirs and capacity to cause disease. Publicly available genomic resources for spore-forming pathogens at NCBI's Pathogen Detection program aid outbreak investigations and longitudinal monitoring in national and international programs in public health and food safety, as well as for local healthcare systems. These tools also enable research to derive new knowledge regarding disease pathogenesis, and to inform strategies in disease prevention and treatment. As global community resources, the continued sharing of strain genomic data and phenotypes further enhances international resources and means to develop impactful applications. We present examples showing use of these resources in surveillance, including capacity to assess linkages among clinical, environmental, and foodborne reservoirs and to further research investigations into factors promoting their persistence and virulence in different settings.
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Affiliation(s)
- Laura M. Cersosimo
- Massachusetts Host-Microbiome Center, Dept. Pathology, Brigham & Women's Hospital, Harvard Medical School, Boston, MA
| | - Jay N. Worley
- Massachusetts Host-Microbiome Center, Dept. Pathology, Brigham & Women's Hospital, Harvard Medical School, Boston, MA
- National Center for Biotechnology Information, NIH, Bethesda, MD
| | - Lynn Bry
- Massachusetts Host-Microbiome Center, Dept. Pathology, Brigham & Women's Hospital, Harvard Medical School, Boston, MA
- Clinical Microbiology Laboratory, Dept. Pathology, Brigham & Women's Hospital, Boston, MA
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3
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Couturier J, Davies K, Barbut F. Ribotypes and New Virulent Strains Across Europe. Adv Exp Med Biol 2024; 1435:151-168. [PMID: 38175475 DOI: 10.1007/978-3-031-42108-2_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Clostridioides (formerly Clostridium) difficile is a major bacterial cause of post-antibiotic diarrhoea. The epidemiology of C. difficile infections (CDIs) has dramatically changed since the early 2000s, with an increasing incidence and severity across Europe. This trend is partly due to the emergence and rapid worldwide spread of the hypervirulent and epidemic PCR ribotype 027. Profiles of patients with CDI have also evolved, with description of community-acquired (CA) infections in patients with no traditional risk factors for CDI. However, epidemiological studies indicated that some European countries have successfully controlled the dissemination of the 027 clone whereas other countries reported the emergence of other virulent or unusual strains. The aims of this review are to summarize the current European CDI epidemiology and to describe the new virulent C. difficile strains circulating in Europe, as well as other potential emerging strains described elsewhere. Standardized typing methods and surveillance programmes are mandatory for a better understanding and monitoring of CDI in Europe.
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Affiliation(s)
- Jeanne Couturier
- National Reference Laboratory for C. difficile, Hôpital Saint-Antoine, Paris, France.
- Université Paris Cité, UMR INSERM 1139, Paris, France.
| | - Kerrie Davies
- Healthcare Associated Infections Research Group, Leeds Teaching Hospitals NHS Trust and University of Leeds, Leeds, UK
- European Society of Clinical Microbiology and Infectious Diseases (ESCMID) study group for Clostridioides difficile (ESGCD), Basel, Switzerland
| | - Frédéric Barbut
- National Reference Laboratory for C. difficile, Hôpital Saint-Antoine, Paris, France
- Université Paris Cité, UMR INSERM 1139, Paris, France
- European Society of Clinical Microbiology and Infectious Diseases (ESCMID) study group for Clostridioides difficile (ESGCD), Basel, Switzerland
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Filippidis P, Senn L, Poncet F, Grandbastien B, Prod'hom G, Greub G, Guery B, Blanc DS. Core genome multilocus sequence typing of Clostridioides difficile to investigate transmission in the hospital setting. Eur J Clin Microbiol Infect Dis 2023; 42:1469-1476. [PMID: 37870711 PMCID: PMC10651541 DOI: 10.1007/s10096-023-04676-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 10/02/2023] [Indexed: 10/24/2023]
Abstract
PURPOSE Traditional epidemiological investigations of healthcare-associated Clostridioides difficile infection (HA-CDI) are often insufficient. This study aimed to evaluate a procedure that includes secondary isolation and genomic typing of single toxigenic colonies using core genome multilocus sequence typing (cgMLST) for the investigation of C. difficile transmission. METHODS We analyzed retrospectively all toxigenic C. difficile-positive stool samples stored at the Lausanne University Hospital over 6 consecutive months. All isolates were initially typed and classified using a modified double-locus sequence typing (DLST) method. Genome comparison of isolates with the same DLST and clustering were subsequently performed using cgMLST. The electronic administrative records of patients with CDI were investigated for spatiotemporal epidemiological links supporting hospital transmission. A comparative descriptive analysis between genomic and epidemiological data was then performed. RESULTS From January to June 2021, 86 C. difficile isolates were recovered from thawed samples of 71 patients. Thirteen different DLST types were shared by > 1 patient, and 13 were observed in single patients. A genomic cluster was defined as a set of isolates from different patients with ≤ 3 locus differences, determined by cgMLST. Seven genomic clusters were identified, among which plausible epidemiological links were identified in only 4/7 clusters. CONCLUSION Among clusters determined by cgMLST analysis, roughly 40% included unexplained HA-CDI acquisitions, which may be explained by unidentified epidemiological links, asymptomatic colonization, and/or shared common community reservoirs. The use of DLST, followed by whole genome sequencing analysis, is a promising and cost-effective stepwise approach for the investigation of CDI transmission in the hospital setting.
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Affiliation(s)
- Paraskevas Filippidis
- Infection Prevention and Control Unit, Infectious Diseases Service, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
- Infectious Diseases Service, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Laurence Senn
- Infection Prevention and Control Unit, Infectious Diseases Service, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Fabrice Poncet
- Infection Prevention and Control Unit, Infectious Diseases Service, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
- Swiss National Reference Center for Emerging Antibiotic Resistance (NARA), University of Fribourg, Fribourg, Switzerland
| | - Bruno Grandbastien
- Infection Prevention and Control Unit, Infectious Diseases Service, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Guy Prod'hom
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Gilbert Greub
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Benoit Guery
- Infection Prevention and Control Unit, Infectious Diseases Service, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Dominique S Blanc
- Infection Prevention and Control Unit, Infectious Diseases Service, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland.
- Swiss National Reference Center for Emerging Antibiotic Resistance (NARA), University of Fribourg, Fribourg, Switzerland.
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Magnusson C, Mernelius S, Bengnér M, Norén T, Serrander L, Forshell S, Matussek A. Characterization of a Clostridioides difficile outbreak caused by PCR ribotype 046, associated with increased mortality. Emerg Microbes Infect 2022; 11:850-859. [PMID: 35240942 PMCID: PMC8942542 DOI: 10.1080/22221751.2022.2049981] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
This study describes a large nosocomial outbreak of Clostridioides difficile infections (CDI) dominated by ribotype (RT) 046 in a Swedish hospital. The present study aimed to examine the pathogenicity of this RT, explore epidemiological links by whole genome sequencing (WGS), and evaluate different interventions implemented to stop the outbreak. Clinical isolates (n = 366) collected during and after the outbreak were ribotyped and 246 isolates were subjected to WGS. Medical records of patients infected with the seven most common RTs were evaluated. RT046 was spread effectively throughout the hospital and was the most common among the 44 different RTs found (114/366 isolates). Infection with RT046 was associated with higher mortality compared to other strains (20.2% to 7.8%), although there were no differences in concomitant disease, age or antibiotic treatment. To control the outbreak, several measures were successfully implemented.
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Affiliation(s)
- Cecilia Magnusson
- Department of Infectious Diseases, Region Jönköping County, Jönköping and Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Sara Mernelius
- Laboratory Medicine, Region Jönköping County, Jönköping and Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Malin Bengnér
- Office for control of Communicable Diseases, Region Jönköping County, Jönköping, Sweden
| | - Torbjörn Norén
- Faculty of Medicine and Health, Department of Laboratory Medicine, National Reference Laboratory for Clostridioides difficile, Clinical Microbiology, Örebro University, Örebro, Sweden
| | - Lena Serrander
- Division of Clinical Microbiology, Department of Clinical and Experimental Medicine, Faculty of Health Sciences, Linköping University, Linköping, Sweden
| | - Sophie Forshell
- Department of Infectious Diseases, Region Jönköping County, Jönköping and Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Andreas Matussek
- Laboratory Medicine, Region Jönköping County, Jönköping and Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden.,Division of Laboratory Medicine, Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Division of Laboratory Medicine, Oslo University Hospital, Oslo, Norway
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6
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Courbin V, Le Neindre K, Couturier J, Gateau C, Zaidi RS, Youssouf A, Barbut F. Transmission Patterns of Clostridioides difficile in a Non-Epidemic Setting Based on WGS Analysis. Microbiology Research 2022; 13:530-8. [DOI: 10.3390/microbiolres13030037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Clostridioides difficile is a major nosocomial pathogen and has a considerable burden on healthcare systems. Our objective was to determine the transmission patterns of C. difficile in a non-epidemic setting using whole-genome multi-locus sequence typing (wgMLST) and core-genome single-nucleotide polymorphism (cgSNP) analyses. A retrospective study was conducted in a 650-bed university hospital between January 2016 and February 2017. In total, 191 strains isolated from 169 symptomatic C. difficile infection (CDI) patients were analyzed by WGS. Sequences were compared using wgMLST and cgSNP analyses. Genetic data and ward movements were then combined to identify the transmission rate and the type of transmission. The transmission rate varied from 55/169 (19.5%) (wgMLST) to 33/169 (32.5%) (cgSNP). Most transmission was considered cryptic, irrespective of the genetic analysis (38/55 [69.1%] by wgMLST to 25/33 [75.8%] by cgSNP). No transmission within the same ward was observed. In a non-epidemic setting, most C. difficile transmission occurs from sources other than symptomatic CDI patients.
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Goyal M, Pelegrin AC, Jaillard M, Saharman YR, Klaassen CHW, Verbrugh HA, Severin JA, van Belkum A. Whole Genome Multi-Locus Sequence Typing and Genomic Single Nucleotide Polymorphism Analysis for Epidemiological Typing of Pseudomonas aeruginosa From Indonesian Intensive Care Units. Front Microbiol 2022; 13:861222. [PMID: 35910643 PMCID: PMC9329958 DOI: 10.3389/fmicb.2022.861222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 06/17/2022] [Indexed: 11/13/2022] Open
Abstract
We have previously studied carbapenem non-susceptible Pseudomonas aeruginosa (CNPA) strains from intensive care units (ICUs) in a referral hospital in Jakarta, Indonesia (Pelegrin et al., 2019). We documented that CNPA transmissions and acquisitions among patients were variable over time and that these were not significantly reduced by a set of infection control measures. Three high risk international CNPA clones (sequence type (ST)235, ST823, ST357) dominated, and carbapenem resistance was due to carbapenemase-encoding genes and mutations in the porin OprD. Pelegrin et al. (2019) reported core genome analysis of these strains. We present a more refined and detailed whole genome-based analysis of major clones represented in the same dataset. As per our knowledge, this is the first study reporting Single Nucleotide Polymorphisms (wgSNP) analysis of Pseudomonas strains. With whole genome-based Multi Locus Sequence Typing (wgMLST) of the 3 CNPA clones (ST235, ST357 and ST823), three to eleven subgroups with up to 200 allelic variants were observed for each of the CNPA clones. Furthermore, we analyzed these CNPA clone clusters for the presence of wgSNP to redefine CNPA transmission events during hospitalization. A maximum number 35350 SNPs (including non-informative wgSNPs) and 398 SNPs (ST-specific_informative-wgSNPs) were found in ST235, 34,570 SNPs (including non-informative wgSNPs) and 111 SNPs (ST-specific_informative-wgSNPs) in ST357 and 26,443 SNPs (including non-informative SNPs) and 61 SNPs (ST-specific_informative-wgSNPs) in ST823. ST-specific_Informative-wgSNPs were commonly noticed in sensor-response regulator genes. However, the majority of non-informative wgSNPs was found in conserved hypothetical proteins or in uncharacterized proteins. Of note, antibiotic resistance and virulence genes segregated according to the wgSNP analyses. A total of 8 transmission chains for ST235 strains followed by 9 and 4 possible transmission chains for ST357 and ST823 were traceable on the basis of pairwise distances of informative-wgSNPs (0 to 4 SNPs) among the strains. The present study demonstrates the value of detailed whole genome sequence analysis for highly refined epidemiological analysis of P. aeruginosa.
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Affiliation(s)
- Manisha Goyal
- bioMérieux Open Innovation and Partnerships, Macry-LÉtoile, France
| | | | | | - Yulia Rosa Saharman
- Department of Clinical Microbiology, Faculty of Medicine, Dr. Cipto Mangunkusumo General Hospital, Universitas Indonesia, Jakarta, Indonesia
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - Corné H. W. Klaassen
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - Henri A. Verbrugh
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - Juliëtte A. Severin
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - Alex van Belkum
- bioMérieux Open Innovation and Partnerships, Macry-LÉtoile, France
- *Correspondence: Alex van Belkum,
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Abdrabou AMM, Bischoff M, Mellmann A, von Müller L, Margardt L, Gärtner BC, Berger FK, Haase G, Häfner H, Hoffmann R, Simon V, Stappmanns H, Hischebeth GT, Büchler C, Rößler S, Hochauf-Stange K, Pfeffer K, MacKenzie C, Kunz C, Alsalameh R, Dziobaka J, le Chapot VS, Sanabria E, Hogardt M, Komp J, Imirzalioglu C, Schmiedel J, Pararas M, Sommer F, Groß U, Bohne W, Kekulé AS, Dagwadordsch U, Löffler B, Rödel J, Walker SV, Tobys D, Weikert-Asbeck S, Hauswaldt S, Kaasch AJ, Zautner AE, Joß N, Siegel E, Kehr K, Schaumburg F, Schoeler S, Hamprecht A, Hellkamp J, Hagemann JB, Kubis J, Hering S, Warnke P. Implementation of a Clostridioides difficile sentinel surveillance system in Germany: First insights for 2019–2021. Anaerobe 2022; 77:102548. [DOI: 10.1016/j.anaerobe.2022.102548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 03/08/2022] [Accepted: 03/14/2022] [Indexed: 11/01/2022]
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9
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Senoh M, Kato H. Molecular epidemiology of endemic Clostridioides difficile infection in Japan. Anaerobe 2022; 74:102510. [DOI: 10.1016/j.anaerobe.2021.102510] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 12/26/2021] [Accepted: 12/30/2021] [Indexed: 02/08/2023]
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Baktash A, Corver J, Harmanus C, Smits WK, Fawley W, Wilcox MH, Kumar N, Eyre DW, Indra A, Mellmann A, Kuijper EJ. COMPARISON OF WHOLE GENOME SEQUENCE-BASED METHODS AND PCR RIBOTYPING FOR SUBTYPING OF Clostridioides difficile. J Clin Microbiol 2021;:JCM0173721. [PMID: 34911367 DOI: 10.1128/JCM.01737-21] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Clostridioides difficile is the most common cause of antibiotic-associated gastrointestinal infections. Capillary-electrophoresis (CE)-PCR ribotyping is currently the gold standard for C. difficile typing but lacks discriminatory power to study transmission and outbreaks in detail. New molecular methods have the capacity to differentiate better and provide standardized and interlaboratory exchangeable data. Using a well-characterized collection of diverse strains (N=630; 100 unique ribotypes (RTs)), we compared the discriminatory power of core genome multilocus sequence typing (cgMLST) (SeqSphere & EnteroBase), whole genome MLST (wgMLST) (EnteroBase) and single nucleotide polymorphism (SNP) analysis. A unique cgMLST profile (>6 allele differences) was observed in 82/100 RTs, indicating that cgMLST could distinguish most, but not all, RTs. Application of cgMLST in two outbreak settings with RT078 and RT181 (known with a low intra-RT allele difference) showed no distinction between outbreak- and non-outbreak strains, in contrast to wgMLST and SNP analysis. We conclude that cgMLST has the potential to be an alternative to CE-PCR ribotyping. The method is reproducible, easy to standardize and offers higher discrimination. However, adjusted cut-off thresholds and epidemiological data are necessary to recognize outbreaks of some specific RTs. We propose to use an allelic threshold 3 alleles to identify outbreaks.
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Abdrabou AMM, Ul Habib Bajwa Z, Halfmann A, Mellmann A, Nimmesgern A, Margardt L, Bischoff M, von Müller L, Gärtner B, Berger FK. Molecular epidemiology and antimicrobial resistance of Clostridioides difficile in Germany, 2014-2019. Int J Med Microbiol 2021; 311:151507. [PMID: 33915347 DOI: 10.1016/j.ijmm.2021.151507] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 03/12/2021] [Accepted: 04/15/2021] [Indexed: 01/05/2023] Open
Abstract
Clostridioides difficile is a Gram positive spore-forming rod and mainly responsible for nosocomial diarrhea in developed nations. Molecular and antimicrobial surveillance is important for monitoring the strain composition including genotypes of high epidemiological importance such as ribotype 027 (RT027) and corresponding resistance patterns. 1535 isolates obtained from samples sent between 2014 and 2019 to the German National Reference Center (NRC) for diagnostic reasons (NRC strain set), and 1143 isolates from a Tertiary Care University Center in Saarland, Germany (non-NRC strain set), were evaluated using antibiotic susceptibility testing and ribotyping. In the NRC strain set, RT027 overtook RT001, the main RT found in the preceding studies, and dominated with 36.2%, followed by RT001 (13.3%), and RT014 (8.5%). Of note, since 2016 a constant decrease of RT027 could be noticed. In the non-NRC strain set a large strain diversity was present with RT014 (18%) and RT001 (8.9%) being most prevalent. In NRC samples, resistance towards metronidazole, vancomycin, moxifloxacin, clarithromycin and rifampicin was 2.7%, 0%, 57.1%, 53.2% and 19.2%, respectively. Metronidazole resistance was almost exclusively found in RT027 isolates. Rifampicin resistance was also observed predominantly in isolates of RT027, constituting an almost four-fold increase, when compared to preceeding studies in this region. In conclusion these data demonstrate that RT027 is a driver for rifampicin and metronidazole resistance, underlining the importance of continuous surveillance efforts.
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12
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Szarvas J, Bartels MD, Westh H, Lund O. Rapid Open-Source SNP-Based Clustering Offers an Alternative to Core Genome MLST for Outbreak Tracing in a Hospital Setting. Front Microbiol 2021; 12:636608. [PMID: 33868194 PMCID: PMC8047125 DOI: 10.3389/fmicb.2021.636608] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 03/09/2021] [Indexed: 11/13/2022] Open
Abstract
Traditional genotyping methods for infection control of antimicrobial-resistant bacteria in healthcare settings have been supplemented by whole-genome sequencing (WGS), often relying on a gene-based approach, e.g., core genome multilocus sequence typing (cgMLST), to cluster-related samples. In this study, we compared clusters of methicillin-resistant Staphylococcus aureus (MRSA) and Enterococcus faecium analyzed with the commercial cgMLST software Ridom SeqSphere+ and with an open-source single-nucleotide polymorphism (SNP)-based phylogenetic analysis pipeline (PAPABAC). A total of 5,655 MRSA and 2,572 E. faecium patient isolates, collected between 2013 and 2018, were processed. Clusters of 1,844 MRSA and 1,355 E. faecium isolates were compared to cgMLST results, and epidemiological data were included when available. The phylogenies inferred by the two different technologies were highly concordant, and the MRSA SNP tree re-captured known hospital-related outbreaks and epidemiologically linked samples. PAPABAC has the advantage over Ridom SeqSphere+ to generate stable, referable clusters without the need for sequence assembly, and it is a free-of-charge, open-source alternative to the commercial software.
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Affiliation(s)
- Judit Szarvas
- Research Group for Genomic Epidemiology, Division for Global Surveillance, National Food Institute, Technical University of Denmark, Lyngby, Denmark
| | - Mette Damkjaer Bartels
- MRSA Knowledge Center, Copenhagen University Hospital Hvidovre, Hvidovre, Denmark.,Department of Clinical Microbiology, Copenhagen University Hospital Hvidovre, Hvidovre, Denmark
| | - Henrik Westh
- Department of Clinical Microbiology, Copenhagen University Hospital Hvidovre, Hvidovre, Denmark.,Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ole Lund
- Research Group for Genomic Epidemiology, Division for Global Surveillance, National Food Institute, Technical University of Denmark, Lyngby, Denmark
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Kamboj M, McMillen T, Syed M, Chow HY, Jani K, Aslam A, Brite J, Fanelli B, Hasan NA, Dadlani M, Westblade L, Zehir A, Simon M, Babady NE. Evaluation of a Combined Multilocus Sequence Typing and Whole-Genome Sequencing Two-Step Algorithm for Routine Typing of Clostridioides difficile. J Clin Microbiol 2021; 59:e01955-20. [PMID: 33177119 DOI: 10.1128/JCM.01955-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 10/21/2020] [Indexed: 01/05/2023] Open
Abstract
Multilocus sequence typing (MLST) is a low-resolution but rapid genotyping method for Clostridioides difficile Whole-genome sequencing (WGS) has emerged as the new gold standard for C. difficile typing, but cost and lack of standardization still limit broad utilization. In this study, we evaluated the potential to combine the portability of MLST with the increased resolution of WGS for a cost-saving approach to routine C. difficile typing. C. difficile strains from two New York City hospitals (hospital A and hospital B) were selected. WGS single-nucleotide polymorphism (wgSNP) was performed using established methods. Sequence types (ST) were determined using PubMLST, while wgSNP analysis was performed using the Bionumerics software. An additional analysis of a subset of data (hospital A) was made comparing the Bionumerics software to the CosmosID pipeline. Cost and turnaround time to results were compared for the algorithmic approach of MLST followed by wgSNP versus direct wgSNP. Among the 202 C. difficile isolates typed, 91% (n = 185/203) clustered within the representative ST, showing a high agreement between MLST and wgSNP. While clustering was similar between the Bionumerics and CosmosID pipelines, large differences in the overall number of SNPs were noted. A two-step algorithm for routine typing results in significantly lower cost than routine use of WGS. Our results suggest that using MLST as a first step in routine typing of C. difficile followed by WGS for MLST concordant strains is a less technically demanding, cost-saving approach for performing C. difficile typing than WGS alone without loss of discriminatory power.
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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] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 02/20/2020] [Indexed: 02/08/2023]
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Novakova E, Stefkovicova M, Kopilec MG, Novak M, Kotlebova N, Kuijper E, Krutova M. The emergence of Clostridium difficile ribotypes 027 and 176 with a predominance of the Clostridium difficile ribotype 001 recognized in Slovakia following the European standardized Clostridium difficile infection surveillance of 2016. Int J Infect Dis 2020; 90:111-115. [PMID: 31707136 PMCID: PMC6912155 DOI: 10.1016/j.ijid.2019.10.038] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 10/25/2019] [Accepted: 10/29/2019] [Indexed: 12/26/2022] Open
Abstract
AIM To obtain standardized epidemiological data for Clostridium difficile infection (CDI) in Slovakia. METHODS Between October and December 2016, 36 hospitals in Slovakia used the European Centre for Disease Prevention and Control (ECDC) Clostridium difficile infection (CDI) surveillance protocol. RESULTS The overall mean CDI incidence density was 2.8 (95% confidence interval 1.9-3.9) cases per 10 000 patient-days. Of 332 CDI cases, 273 (84.9%) were healthcare-associated, 45 (15.1%) were community-associated, and 14 (4.2%) were cases of recurrent CDI. A complicated course of CDI was reported in 14.8% of cases (n=51). CDI outcome data were available for 95.5% of cases (n=317). Of the 35 patients (11.1%) who died, 34 did so within 30 days after their CDI diagnosis. Of the 78 isolates obtained from 12 hospitals, 46 belonged to PCR ribotype 001 (59.0%; 11 hospitals) and 23 belonged to ribotype 176 (29.5%; six hospitals). A total of 73 isolates (93.6%) showed reduced susceptibility to moxifloxacin (ribotypes 001 and 176; p< 0.01). A reduced susceptibility to metronidazole was observed in 13 isolates that subsequently proved to be metronidazole-susceptible when, after thawing, they were retested using the agar dilution method. No reduced susceptibility to vancomycin was found. CONCLUSIONS These results show the emergence of C. difficile ribotypes 027 and 176 with a predominance of ribotype 001 in Slovakia in 2016. Given that an almost homogeneous reduced susceptibility to moxifloxacin was detected in C. difficile isolates, this stresses the importance of reducing fluoroquinolone prescriptions in Slovak healthcare settings.
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Affiliation(s)
- Elena Novakova
- Department of Microbiology and Immunology, Comenius University, Jessenius Faculty of Medicine in Martin, Slovakia
| | - Maria Stefkovicova
- Department of Epidemiology, Regional Public Health Authority, Trenčín, Slovakia; Department of Laboratory Medicine and Public Health, Faculty of Health Care, Alexander Dubcek University, Trenčín, Slovakia
| | | | - Martin Novak
- Department of Public Health, Comenius University, Jessenius Faculty of Medicine in Martin, Slovakia
| | - Nina Kotlebova
- Department of Microbiology and Immunology, Comenius University, Jessenius Faculty of Medicine in Martin, Slovakia
| | - Ed Kuijper
- Department of Medical Microbiology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Marcela Krutova
- Department of Medical Microbiology, Charles University in Prague, 2nd Faculty of Medicine and Motol University Hospital, Prague, Czech Republic.
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Rupnik M, Janezic S. Clostridioides (Clostridium) difficile - Interesting and difficult. Anaerobe 2019; 60:102124. [PMID: 31839124 DOI: 10.1016/j.anaerobe.2019.102124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Maja Rupnik
- National laboratory for Health, Environment and Food (NLZOH), Maribor, Slovenia; University of Maribor, Faculty of Medicine, Maribor, Slovenia
| | - Sandra Janezic
- National laboratory for Health, Environment and Food (NLZOH), Maribor, Slovenia; University of Maribor, Faculty of Medicine, Maribor, Slovenia
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