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Sauvat L, Verhoeven PO, Gagnaire J, Berthelot P, Paul S, Botelho-Nevers E, Gagneux-Brunon A. Vaccines and monoclonal antibodies to prevent healthcare-associated bacterial infections. Clin Microbiol Rev 2024:e0016022. [PMID: 39120140 DOI: 10.1128/cmr.00160-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2024] Open
Abstract
SUMMARYHealthcare-associated infections (HAIs) represent a burden for public health with a high prevalence and high death rates associated with them. Pathogens with a high potential for antimicrobial resistance, such as ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) and Clostridioides difficile, are responsible for most HAIs. Despite the implementation of infection prevention and control intervention, globally, HAIs prevalence is stable and they are mainly due to endogenous pathogens. It is undeniable that complementary to infection prevention and control measures, prophylactic approaches by active or passive immunization are needed. Specific groups at-risk (elderly people, chronic condition as immunocompromised) and also healthcare workers are key targets. Medical procedures and specific interventions are known to be at risk of HAIs, in addition to hospital environmental exposure. Vaccines or monoclonal antibodies can be seen as attractive preventive approaches for HAIs. In this review, we present an overview of the vaccines and monoclonal antibodies in clinical development for prevention of the major bacterial HAIs pathogens. Based on the current state of knowledge, we look at the challenges and future perspectives to improve prevention by these means.
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Affiliation(s)
- Léo Sauvat
- CIRI - Centre International de Recherche en Infectiologie, GIMAP team, Inserm, U1111, CNRS, UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Lyon, France
- Faculty of Medicine, Université Jean Monnet St-Etienne, St-Etienne, France
- Infection Control Unit, University Hospital of Saint-Etienne, Saint-Etienne, France
- Department of Infectious Diseases, University Hospital of Saint-Etienne, Saint-Etienne, France
| | - Paul O Verhoeven
- CIRI - Centre International de Recherche en Infectiologie, GIMAP team, Inserm, U1111, CNRS, UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Lyon, France
- Faculty of Medicine, Université Jean Monnet St-Etienne, St-Etienne, France
- Department of Infectious Agents and Hygiene, University-Hospital of Saint-Etienne, Saint-Etienne, France
| | - Julie Gagnaire
- Infection Control Unit, University Hospital of Saint-Etienne, Saint-Etienne, France
- Department of Infectious Diseases, University Hospital of Saint-Etienne, Saint-Etienne, France
| | - Philippe Berthelot
- CIRI - Centre International de Recherche en Infectiologie, GIMAP team, Inserm, U1111, CNRS, UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Lyon, France
- Faculty of Medicine, Université Jean Monnet St-Etienne, St-Etienne, France
- Infection Control Unit, University Hospital of Saint-Etienne, Saint-Etienne, France
- Department of Infectious Diseases, University Hospital of Saint-Etienne, Saint-Etienne, France
| | - Stéphane Paul
- CIRI - Centre International de Recherche en Infectiologie, GIMAP team, Inserm, U1111, CNRS, UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Lyon, France
- Faculty of Medicine, Université Jean Monnet St-Etienne, St-Etienne, France
- CIC 1408 Inserm, Axe vaccinologie, University Hospital of Saint-Etienne, Saint-Etienne, France
| | - Elisabeth Botelho-Nevers
- CIRI - Centre International de Recherche en Infectiologie, GIMAP team, Inserm, U1111, CNRS, UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Lyon, France
- Faculty of Medicine, Université Jean Monnet St-Etienne, St-Etienne, France
- Department of Infectious Diseases, University Hospital of Saint-Etienne, Saint-Etienne, France
- CIC 1408 Inserm, Axe vaccinologie, University Hospital of Saint-Etienne, Saint-Etienne, France
| | - Amandine Gagneux-Brunon
- CIRI - Centre International de Recherche en Infectiologie, GIMAP team, Inserm, U1111, CNRS, UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Lyon, France
- Faculty of Medicine, Université Jean Monnet St-Etienne, St-Etienne, France
- Department of Infectious Diseases, University Hospital of Saint-Etienne, Saint-Etienne, France
- CIC 1408 Inserm, Axe vaccinologie, University Hospital of Saint-Etienne, Saint-Etienne, France
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Sulaiman JE, Thompson J, Cheung PLK, Qian Y, Mill J, James I, Vivas EI, Simcox J, Venturelli O. Human gut microbiota interactions shape the long-term growth dynamics and evolutionary adaptations of Clostridioides difficile. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.15.603560. [PMID: 39071283 PMCID: PMC11275832 DOI: 10.1101/2024.07.15.603560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Clostridioides difficile can transiently or persistently colonize the human gut, posing a risk factor for infections. This colonization is influenced by complex molecular and ecological interactions with human gut microbiota. By investigating C. difficile dynamics in human gut communities over hundreds of generations, we show patterns of stable coexistence, instability, or competitive exclusion. Lowering carbohydrate concentration shifted a community containing C. difficile and the prevalent human gut symbiont Phocaeicola vulgatus from competitive exclusion to coexistence, facilitated by increased cross-feeding. In this environment, C. difficile adapted via single-point mutations in key metabolic genes, altering its metabolic niche from proline to glucose utilization. These metabolic changes substantially impacted inter-species interactions and reduced disease severity in the mammalian gut. In sum, human gut microbiota interactions are crucial in shaping the long-term growth dynamics and evolutionary adaptations of C. difficile , offering key insights for developing anti- C. difficile strategies.
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3
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Fishbein SRS, DeVeaux AL, Khanna S, Ferreiro AL, Liao J, Agee W, Ning J, Mahmud B, Wallace MJ, Hink T, Reske KA, Guruge J, Leekha S, Dubberke ER, Dantas G. Commensal-pathogen dynamics structure disease outcomes during Clostridioides difficile colonization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.11.603094. [PMID: 39026847 PMCID: PMC11257545 DOI: 10.1101/2024.07.11.603094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Gastrointestinal colonization by Clostridioides difficile is common in healthcare settings and ranges in clinical presentation from asymptomatic carriage to lethal C. difficile infection (CDI). We used a systems biology approach to investigate why patients colonized with C. difficile have a range of outcomes. Microbiota-humanization of germ-free mice with fecal samples from toxigenic C. difficile carriers revealed a spectrum of virulence among clade 1 lineages and identified commensal Blautia associated with markers of non-pathogenic colonization. Using gnotobiotic mice engrafted with defined human microbiota, we observed strain-specific CDI severity across clade 1 strains. Yet, mice engrafted with a higher diversity community were protected from severe disease across all strains without suppression of C. difficile colonization. These results indicate that when colonization resistance has been breached without overt infection, commensals can attenuate a diversity of virulent strains without inhibiting pathogen colonization, providing insight into determinants of stable C. difficile carriage.
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Long DR, Cifu A, Salipante SJ, Sawyer RG, Machutta K, Alverdy JC. Preventing Surgical Site Infections in the Era of Escalating Antibiotic Resistance and Antibiotic Stewardship. JAMA Surg 2024:2820522. [PMID: 38922606 DOI: 10.1001/jamasurg.2024.0429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/27/2024]
Abstract
Importance According to the Centers for Disease Control and Prevention and governing bodies within the American College of Surgeons, the administration of antibiotics as prophylaxis against infection prior to a planned elective procedure is, with rare exception, routinely recommended. The goal of "getting to zero" infections remains a high priority for policymakers, practitioners, and certainly for patients. Observations Despite the many advances in surgical technique, skin decontamination, sterile procedure, and enhanced recovery programs, surgical site infections continue to adversely affect procedures as diverse as dental implant surgery, joint arthroplasty, and major abdominal surgery. Although surgical site infection rates are at historically low levels, progress has stalled in recent reporting periods and such infections remain disabling, costly, and occasionally lethal. Stakeholders in the field, including surgeons, infectious diseases specialists, and industry, advocate for strategies emphasizing greater levels of intraoperative sterility or broader-spectrum antibiotic coverage as the most appropriate path forward. Conclusions and Relevance The current emphasis on ever-increasing levels of intraoperative sterility and extended-spectrum antibiotic use are not sustainable long-term solutions. Continuing to escalate these approaches may contribute to unintended consequences including antimicrobial resistance. Principles of antimicrobial stewardship and microbiome sciences can be applied to inform a more effective and sustainable approach to infection prevention in the field of surgery.
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Affiliation(s)
- Dustin R Long
- Division of Critical Care Medicine, Department of Anesthesiology & Pain Medicine, University of Washington, Seattle
| | - Adam Cifu
- Department of Internal Medicine, University of Chicago, Chicago, Illinois
| | - Stephen J Salipante
- Department of Laboratory Medicine & Pathology, University of Washington, Seattle
| | - Robert G Sawyer
- Department of Surgery, Western Michigan University Homer Stryker School of Medicine, Kalamazoo
| | | | - John C Alverdy
- Department of Surgery, University of Chicago, Chicago, Illinois
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5
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Di Bella S, Sanson G, Monticelli J, Zerbato V, Principe L, Giuffrè M, Pipitone G, Luzzati R. Clostridioides difficile infection: history, epidemiology, risk factors, prevention, clinical manifestations, treatment, and future options. Clin Microbiol Rev 2024; 37:e0013523. [PMID: 38421181 PMCID: PMC11324037 DOI: 10.1128/cmr.00135-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024] Open
Abstract
SUMMARYClostridioides difficile infection (CDI) is one of the major issues in nosocomial infections. This bacterium is constantly evolving and poses complex challenges for clinicians, often encountered in real-life scenarios. In the face of CDI, we are increasingly equipped with new therapeutic strategies, such as monoclonal antibodies and live biotherapeutic products, which need to be thoroughly understood to fully harness their benefits. Moreover, interesting options are currently under study for the future, including bacteriophages, vaccines, and antibiotic inhibitors. Surveillance and prevention strategies continue to play a pivotal role in limiting the spread of the infection. In this review, we aim to provide the reader with a comprehensive overview of epidemiological aspects, predisposing factors, clinical manifestations, diagnostic tools, and current and future prophylactic and therapeutic options for C. difficile infection.
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Affiliation(s)
- Stefano Di Bella
- Clinical Department of
Medical, Surgical and Health Sciences, Trieste
University, Trieste,
Italy
| | - Gianfranco Sanson
- Clinical Department of
Medical, Surgical and Health Sciences, Trieste
University, Trieste,
Italy
| | - Jacopo Monticelli
- Infectious Diseases
Unit, Trieste University Hospital
(ASUGI), Trieste,
Italy
| | - Verena Zerbato
- Infectious Diseases
Unit, Trieste University Hospital
(ASUGI), Trieste,
Italy
| | - Luigi Principe
- Microbiology and
Virology Unit, Great Metropolitan Hospital
“Bianchi-Melacrino-Morelli”,
Reggio Calabria, Italy
| | - Mauro Giuffrè
- Clinical Department of
Medical, Surgical and Health Sciences, Trieste
University, Trieste,
Italy
- Department of Internal
Medicine (Digestive Diseases), Yale School of Medicine, Yale
University, New Haven,
Connecticut, USA
| | - Giuseppe Pipitone
- Infectious Diseases
Unit, ARNAS Civico-Di Cristina
Hospital, Palermo,
Italy
| | - Roberto Luzzati
- Clinical Department of
Medical, Surgical and Health Sciences, Trieste
University, Trieste,
Italy
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6
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Cersosimo LM, Worley JN, Bry L. Approaching toxigenic Clostridia from a One Health perspective. Anaerobe 2024; 87:102839. [PMID: 38552896 PMCID: PMC11180571 DOI: 10.1016/j.anaerobe.2024.102839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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7
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Bloomfield M, Hutton S, Burton M, Tarring C, Velasco C, Clissold C, Balm M, Kelly M, Macartney-Coxson D, White R. Early identification of a ward-based outbreak of Clostridioides difficile using prospective multilocus sequence type-based Oxford Nanopore genomic surveillance. Infect Control Hosp Epidemiol 2024:1-7. [PMID: 38706217 DOI: 10.1017/ice.2024.77] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2024]
Abstract
OBJECTIVE To describe an outbreak of sequence type (ST)2 Clostridioides difficile infection (CDI) detected by a recently implemented multilocus sequence type (MLST)-based prospective genomic surveillance system using Oxford Nanopore Technologies (ONT) sequencing. SETTING Hemato-oncology ward of a public tertiary referral centre. METHODS From February 2022, we began prospectively sequencing all C. difficile isolated from inpatients at our institution on the ONT MinION device, with the output being an MLST. Bed-movement data are used to construct real-time ST-specific incidence charts based on ward exposures over the preceding three months. RESULTS Between February and October 2022, 76 of 118 (64.4%) CDI cases were successfully sequenced. There was wide ST variation across cases and the hospital, with only four different STs being seen in >4 patients. A clear predominance of ST2 CDI cases emerged among patients with exposure to our hemato-oncology ward between May and October 2022, which totalled ten patients. There was no detectable rise in overall CDI incidence for the ward or hospital due to the outbreak. Following a change in cleaning product to an accelerated hydrogen peroxide wipe and several other interventions, no further outbreak-associated ST2 cases were detected. A retrospective phylogenetic analysis using original sequence data showed clustering of the suspected outbreak cases, with the exception of two cases that were retrospectively excluded from the outbreak. CONCLUSIONS Prospective genomic surveillance of C. difficile using ONT sequencing permitted the identification of an outbreak of ST2 CDI that would have otherwise gone undetected.
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Affiliation(s)
- Max Bloomfield
- Awanui Labs Wellington, Department of Microbiology and Molecular Pathology, Wellington, New Zealand
- Te Whatu Ora/Health New Zealand, Infection Prevention and Control, Capital, Coast and Hutt Valley, Wellington, New Zealand
| | - Samantha Hutton
- Awanui Labs Wellington, Department of Microbiology and Molecular Pathology, Wellington, New Zealand
| | - Megan Burton
- Awanui Labs Wellington, Department of Microbiology and Molecular Pathology, Wellington, New Zealand
| | - Claire Tarring
- Awanui Labs Wellington, Department of Microbiology and Molecular Pathology, Wellington, New Zealand
| | - Charles Velasco
- Awanui Labs Wellington, Department of Microbiology and Molecular Pathology, Wellington, New Zealand
| | - Carolyn Clissold
- Te Whatu Ora/Health New Zealand, Infection Prevention and Control, Capital, Coast and Hutt Valley, Wellington, New Zealand
| | - Michelle Balm
- Awanui Labs Wellington, Department of Microbiology and Molecular Pathology, Wellington, New Zealand
- Te Whatu Ora/Health New Zealand, Infection Prevention and Control, Capital, Coast and Hutt Valley, Wellington, New Zealand
| | - Matthew Kelly
- Te Whatu Ora/Health New Zealand, Infection Prevention and Control, Capital, Coast and Hutt Valley, Wellington, New Zealand
| | | | - Rhys White
- Institute of Environmental Science and Research, Health Group, Porirua, New Zealand
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8
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Newcomer EP, Fishbein SRS, Zhang K, Hink T, Reske KA, Cass C, Iqbal ZH, Struttmann EL, Burnham CAD, Dubberke ER, Dantas G. Genomic surveillance of Clostridioides difficile transmission and virulence in a healthcare setting. mBio 2024; 15:e0330023. [PMID: 38329369 PMCID: PMC10936198 DOI: 10.1128/mbio.03300-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 01/16/2024] [Indexed: 02/09/2024] Open
Abstract
Clostridioides difficile infection (CDI) is a major cause of healthcare-associated diarrhea, despite the widespread implementation of contact precautions for patients with CDI. Here, we investigate strain contamination in a hospital setting and the genomic determinants of disease outcomes. Across two wards over 6 months, we selectively cultured C. difficile from patients (n = 384) and their environments. Whole-genome sequencing (WGS) of 146 isolates revealed that most C. difficile isolates were from clade 1 (131/146, 89.7%), while only one isolate of the hypervirulent ST1 was recovered. Of culture-positive admissions (n = 79), 19 (24%) patients were colonized with toxigenic C. difficile on admission to the hospital. We defined 25 strain networks at ≤2 core gene single nucleotide polymorphisms; two of these networks contain strains from different patients. Strain networks were temporally linked (P < 0.0001). To understand the genomic correlates of the disease, we conducted WGS on an additional cohort of C. difficile (n = 102 isolates) from the same hospital and confirmed that clade 1 isolates are responsible for most CDI cases. We found that while toxigenic C. difficile isolates are associated with the presence of cdtR, nontoxigenic isolates have an increased abundance of prophages. Our pangenomic analysis of clade 1 isolates suggests that while toxin genes (tcdABER and cdtR) were associated with CDI symptoms, they are dispensable for patient colonization. These data indicate that toxigenic and nontoxigenic C. difficile contamination persist in a hospital setting and highlight further investigation into how accessory genomic repertoires contribute to C. difficile colonization and disease. IMPORTANCE Clostridioides difficile infection remains a leading cause of hospital-associated diarrhea, despite increased antibiotic stewardship and transmission prevention strategies. This suggests a changing genomic landscape of C. difficile. Our study provides insight into the nature of prevalent C. difficile strains in a hospital setting and transmission patterns among carriers. Longitudinal sampling of surfaces and patient stool revealed that both toxigenic and nontoxigenic strains of C. difficile clade 1 dominate these two wards. Moreover, quantification of transmission in carriers of these clade 1 isolates underscores the need to revisit infection prevention measures in this patient group. We identified unique genetic signatures associated with virulence in this clade. Our data highlight the complexities of preventing transmission of this pathogen in a hospital setting and the need to investigate the mechanisms of in vivo persistence and virulence of prevalent lineages in the host gut microbiome.
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Affiliation(s)
- Erin P. Newcomer
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Skye R. S. Fishbein
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
- Division of Laboratory and Genomic Medicine, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Kailun Zhang
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
- Division of Laboratory and Genomic Medicine, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Tiffany Hink
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Kimberly A. Reske
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Candice Cass
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Zainab H. Iqbal
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Emily L. Struttmann
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Carey-Ann D. Burnham
- Division of Laboratory and Genomic Medicine, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Erik R. Dubberke
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
- Division of Laboratory and Genomic Medicine, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
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9
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Cersosimo LM, Worley JN, Bry L. Approaching pathogenic Clostridia from a One Health perspective. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 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] [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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10
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Newcomer EP, Fishbein SRS, Zhang K, Hink T, Reske KA, Cass C, Iqbal ZH, Struttmann EL, Dubberke ER, Dantas G. Genomic surveillance of Clostridioides difficile transmission and virulence in a healthcare setting. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.09.26.23295023. [PMID: 38105952 PMCID: PMC10723495 DOI: 10.1101/2023.09.26.23295023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Clostridioides difficile infection (CDI) is a major cause of healthcare-associated diarrhea, despite the widespread implementation of contact precautions for patients with CDI. Here, we investigate strain contamination in a hospital setting and genomic determinants of disease outcomes. Across two wards over six months, we selectively cultured C. difficile from patients (n=384) and their environments. Whole-genome sequencing (WGS) of 146 isolates revealed that most C. difficile isolates were from clade 1 (131/146, 89.7%), while only one isolate of the hypervirulent ST1 was recovered. Of culture-positive admissions (n=79), 19 (24%) of patients were colonized with toxigenic C. difficile on admission to the hospital. We defined 25 strain networks at ≤ 2 core gene SNPs; 2 of these networks contain strains from different patients. Strain networks were temporally linked (p<0.0001). To understand genomic correlates of disease, we conducted WGS on an additional cohort of C. difficile (n=102 isolates) from the same hospital and confirmed that clade 1 isolates are responsible for most CDI cases. We found that while toxigenic C. difficile isolates are associated with the presence of cdtR , nontoxigenic isolates have an increased abundance of prophages. Our pangenomic analysis of clade 1 isolates suggests that while toxin genes ( tcdABER and cdtR ) were associated with CDI symptoms, they are dispensable for patient colonization. These data indicate toxigenic and nontoxigenic C. difficile contamination persists in a hospital setting and highlight further investigation into how accessory genomic repertoires contribute to C. difficile colonization and disease.
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11
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Barranco C. Spotlight on infection control. Nat Rev Gastroenterol Hepatol 2023; 20:759. [PMID: 37864093 DOI: 10.1038/s41575-023-00861-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/22/2023]
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