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Ferraris L, Delannoy J, Mazuet C, Diancourt L, Mesa-Schein V, Barbut F, Aires J. Clostridium neonatale antimicrobial susceptibility, genetic resistance determinants, and genotyping: a multicentre spatiotemporal retrospective analysis. J Antimicrob Chemother 2024; 79:271-279. [PMID: 38084883 PMCID: PMC10832599 DOI: 10.1093/jac/dkad369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 11/21/2023] [Indexed: 02/02/2024] Open
Abstract
BACKGROUND Clostridium neonatale was isolated during an outbreak of neonatal necrotizing enterocolitis (NEC) in 2002. C. neonatale was validated as a new species within the genus Clostridium sensu stricto in 2018. In the present study, we evaluated the antimicrobial susceptibility, genetic determinants of resistance, and phylogenetic relationships of a collection of clinical isolates of C. neonatale. METHODS C. neonatale strains (n = 68) were isolated from the stools of preterm neonates who either developed NEC or were asymptomatic carriers of C. neonatale in different periods and in different hospitals. Antimicrobial susceptibility was determined by the disc diffusion method. The MICs of clindamycin, cefotaxime and tetracycline were determined. Genetic determinants of resistance were screened by PCR (n = 68) and WGS (n = 35). Genotyping of the isolates was performed by MLST. RESULTS Antimicrobial resistance was found to clindamycin (n = 24; 35%), cefotaxime (n = 7; 10%) and tetracycline (n = 1; 1%). One clindamycin-resistant isolate carried erm(B) by PCR. In addition, one isolate carrying tet(M) was tetracycline resistant (MIC = 16 mg/L) and 44 isolates carrying either tet(O), tet(32) or tet(M) were tetracycline susceptible (MICs < 16 mg/L). MLST showed that ST2 and ST15 were significantly associated with tet(32) (P < 0.0001) and tet(O) (P < 0.0001), respectively. From WGS, we identified aph(3')-IIa and blaTEM-116 genes and a blaCBP-1-like gene. CONCLUSIONS C. neonatale is susceptible to anti-anaerobic molecules but resistant to clindamycin, cefotaxime and tetracycline. Genes encoding tetracycline ribosomal protection, macrolide-lincosamide-streptogramin B rRNA methyltransferase, aminoglycoside 3'-phosphotransferase and β-lactamases have been identified in genomic regions flanked by mobile genetic elements.
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Affiliation(s)
- Laurent Ferraris
- Faculté de Pharmacie de Paris, Université Paris Cité, INSERM, UMR-S 1139 (3PHM), Paris F-75006, France
| | - Johanne Delannoy
- Faculté de Pharmacie de Paris, Université Paris Cité, INSERM, UMR-S 1139 (3PHM), Paris F-75006, France
| | - Christelle Mazuet
- Institut Pasteur, Université Paris Cité, Centre National de Référence des Bactéries anaérobies et Botulisme, Paris F-75015, France
| | - Laure Diancourt
- Institut Pasteur, Université Paris Cité, Centre National de Référence des Bactéries anaérobies et Botulisme, Paris F-75015, France
| | - Victoria Mesa-Schein
- Faculté de Pharmacie de Paris, Université Paris Cité, INSERM, UMR-S 1139 (3PHM), Paris F-75006, France
| | - Frédéric Barbut
- Faculté de Pharmacie de Paris, Université Paris Cité, INSERM, UMR-S 1139 (3PHM), Paris F-75006, France
| | - Julio Aires
- Faculté de Pharmacie de Paris, Université Paris Cité, INSERM, UMR-S 1139 (3PHM), Paris F-75006, France
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Mesa V, Delannoy J, Ferraris L, Diancourt L, Mazuet C, Barbut F, Aires J. Core-genome multilocus sequence typing and core-SNP analysis of Clostridium neonatale strains isolated in different spatio-temporal settings. Microbiol Spectr 2023; 11:e0276623. [PMID: 37909758 PMCID: PMC10714970 DOI: 10.1128/spectrum.02766-23] [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: 07/06/2023] [Accepted: 09/25/2023] [Indexed: 11/03/2023] Open
Abstract
IMPORTANCE Clostridium neonatale has been isolated from the fecal samples of asymptomatic neonates and cases of necrotizing enterocolitis (NEC). Taking advantage of a large collection of independent strains isolated from different spatio-temporal settings, we developed and established a cgMLST scheme for the molecular typing of C. neonatale. Both the cgMLST and cgSNP methods demonstrate comparable discrimination power. Results indicate geographic- and temporal- independent clustering of C. neonatale NEC-associated strains. No specific cgMLST clade of C. neonatale was genetically associated with NEC.
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Affiliation(s)
- Victoria Mesa
- Université Paris Cité, INSERM, UMR-S 1139 (3PHM), Faculté de Pharmacie de Paris, Paris, France
| | - Johanne Delannoy
- Université Paris Cité, INSERM, UMR-S 1139 (3PHM), Faculté de Pharmacie de Paris, Paris, France
| | - Laurent Ferraris
- Université Paris Cité, INSERM, UMR-S 1139 (3PHM), Faculté de Pharmacie de Paris, Paris, France
| | - Laure Diancourt
- Institut Pasteur, Université de Paris Cité, Centre National de Référence des Bactéries anaérobies et Botulisme, Paris, France
| | - Christelle Mazuet
- Institut Pasteur, Université de Paris Cité, Centre National de Référence des Bactéries anaérobies et Botulisme, Paris, France
| | - Frédéric Barbut
- Université Paris Cité, INSERM, UMR-S 1139 (3PHM), Faculté de Pharmacie de Paris, Paris, France
| | - Julio Aires
- Université Paris Cité, INSERM, UMR-S 1139 (3PHM), Faculté de Pharmacie de Paris, Paris, France
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Aires J, Ilhan ZE, Nicolas L, Ferraris L, Delannoy J, Bredel M, Chauvire-Drouard A, Barbut F, Rozé JC, Lepage P, Butel MJ. Occurrence of Neonatal Necrotizing Enterocolitis in Premature Neonates and Gut Microbiota: A Case-Control Prospective Multicenter Study. Microorganisms 2023; 11:2457. [PMID: 37894115 PMCID: PMC10609581 DOI: 10.3390/microorganisms11102457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 09/24/2023] [Accepted: 09/26/2023] [Indexed: 10/29/2023] Open
Abstract
BACKGROUND Necrotizing enterocolitis (NEC) is still one of the leading causes of neonatal death. The present study reports the data from a French case-control prospective multicenter study. METHODS A total of 146 preterm neonates (PNs) with or without NEC were included. Bacterial 16S rRNA gene sequencing was performed on stool samples (n = 103). Specific culture media were used to isolate Escherichia coli, Clostridium butyricum, and Clostridium neonatale, and strains were phenotypically characterized. RESULTS The gut microbiota of PNs was dominated by Firmicutes and Proteobacteria, and five enterotypes were identified. The microbiota composition was similar between NEC cases and PN controls. However, differences were observed in the relative abundance of Lactobacillus genus, which was significantly lower in the NEC group, whereas that of the Clostridium cluster III was significantly higher (p < 0.05). Within enterotypes, several phylotypes were significantly more abundant in NEC cases (p < 0.05). Regarding perinatal factors, a statistical association was found between the gut microbiota and cesarean delivery and antifungal therapy. In NEC cases and PN controls, the carriage rates and virulence genes of uropathogenic E. coli were equivalent based on culture. No correlation was found between E. coli, C. butyricum, and C. neonatale carriages, beta-lactam resistance, and antibiotic treatment. CONCLUSIONS At disease onset, our data support a microbiota dysbiosis between NEC and control infants at the genus level. In addition, it provides valuable information on bacterial antimicrobial susceptibility.
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Affiliation(s)
- Julio Aires
- Faculté de Pharmacie de Paris, Université Paris Cité, INSERM, UMR-S 1139 (3PHM), 75006 Paris, France (F.B.)
- FHU PREMA, Fighting Prematurity, 75014 Paris, France
| | - Zehra Esra Ilhan
- Micalis Institute, INRA, AgroParisTech, University Paris-Saclay, 91190 Paris, France; (Z.E.I.); (M.B.)
| | - Lancelot Nicolas
- Faculté de Pharmacie de Paris, Université Paris Cité, INSERM, UMR-S 1139 (3PHM), 75006 Paris, France (F.B.)
- FHU PREMA, Fighting Prematurity, 75014 Paris, France
| | - Laurent Ferraris
- Faculté de Pharmacie de Paris, Université Paris Cité, INSERM, UMR-S 1139 (3PHM), 75006 Paris, France (F.B.)
- FHU PREMA, Fighting Prematurity, 75014 Paris, France
| | - Johanne Delannoy
- Faculté de Pharmacie de Paris, Université Paris Cité, INSERM, UMR-S 1139 (3PHM), 75006 Paris, France (F.B.)
- FHU PREMA, Fighting Prematurity, 75014 Paris, France
| | - Maxime Bredel
- Micalis Institute, INRA, AgroParisTech, University Paris-Saclay, 91190 Paris, France; (Z.E.I.); (M.B.)
| | - Anne Chauvire-Drouard
- Centre d’Investigation Clinique CIC 1413, INSERM, CHU de Nantes, 44093 Nantes, France;
| | - Frédéric Barbut
- Faculté de Pharmacie de Paris, Université Paris Cité, INSERM, UMR-S 1139 (3PHM), 75006 Paris, France (F.B.)
- FHU PREMA, Fighting Prematurity, 75014 Paris, France
| | - Jean-Christophe Rozé
- Department of Neonatal Medicine, University Hospital of Nantes, 44093 Nantes, France;
| | - Patricia Lepage
- Micalis Institute, INRA, AgroParisTech, University Paris-Saclay, 91190 Paris, France; (Z.E.I.); (M.B.)
| | - Marie-José Butel
- Faculté de Pharmacie de Paris, Université Paris Cité, INSERM, UMR-S 1139 (3PHM), 75006 Paris, France (F.B.)
- FHU PREMA, Fighting Prematurity, 75014 Paris, France
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Carroll KC, Munson E, Butler-Wu SM, Patrick S. Point-Counterpoint: What's in a Name? Clinical Microbiology Laboratories Should Use Nomenclature Based on Current Taxonomy. J Clin Microbiol 2023; 61:e0173222. [PMID: 36625570 PMCID: PMC9879091 DOI: 10.1128/jcm.01732-22] [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: 01/11/2023] Open
Abstract
INTRODUCTION The mnemonic SPICE (Serratia, Pseudomonas, indole-positive Proteus, Citrobacter, and Enterobacter) has served as a reminder to consider when a Gram-negative organism may carry a chromosomal copy of blaampC, with the associated risk of developing resistance to first-, second-, and third-generation cephalosporins. However, in 2017, there was a well-founded proposal to rename Enterobacter aerogenes to Klebsiella aerogenes, based on whole-genome sequencing (WGS), and the SPICE mnemonic lost its relevance. With the increased use of WGS for taxonomy, it seems like bacteria and fungi are undergoing constant name changes. These changes create unique challenges for clinical microbiology laboratories, who would like to issue reports that are readily understood and that help clinicians determine empirical antibiotic therapy, interpret antimicrobial resistance, and understand clinical significance. In this Point-Counterpoint, Drs. Karen Carroll and Erik Munson discuss the pros of updating bacterial taxonomy and why clinical labs must continue to update reporting, while Drs. Susan Butler-Wu and Sheila Patrick argue for caution in adopting new names for microorganisms.
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Affiliation(s)
- Karen C. Carroll
- Division of Medical Microbiology, Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Erik Munson
- Department of Medical Laboratory Science, Marquette University, Milwaukee, Wisconsin, USA
| | - Susan M. Butler-Wu
- Department of Pathology and Laboratory Medicine, Keck School of Medicine of USC, Los Angeles, California, USA
| | - Sheila Patrick
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen’s University Belfast, Belfast, United Kingdom
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Rocha Martin VN, Del’Homme C, Chassard C, Schwab C, Braegger C, Bernalier-Donadille A, Lacroix C. A proof of concept infant-microbiota associated rat model for studying the role of gut microbiota and alleviation potential of Cutibacterium avidum in infant colic. Front Nutr 2022; 9:902159. [PMID: 36071938 PMCID: PMC9441890 DOI: 10.3389/fnut.2022.902159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 07/28/2022] [Indexed: 11/20/2022] Open
Abstract
Establishing the relationship between gut microbiota and host health has become a main target of research in the last decade. Human gut microbiota-associated animal models represent one alternative to human research, allowing for intervention studies to investigate causality. Recent cohort and in vitro studies proposed an altered gut microbiota and lactate metabolism with excessive H2 production as the main causes of infant colic. To evaluate H2 production by infant gut microbiota and to test modulation of gut colonizer lactose- and lactate-utilizer non-H2-producer, Cutibacterium avidum P279, we established and validated a gnotobiotic model using young germ-free rats inoculated with fecal slurries from infants younger than 3 months. Here, we show that infant microbiota-associated (IMA) rats inoculated with fresh feces from healthy (n = 2) and colic infants (n = 2) and fed infant formula acquired and maintained similar quantitative and qualitative fecal microbiota composition compared to the individual donor’s profile. We observed that IMA rats excreted high levels of H2, which were linked to a high abundance of lactate-utilizer H2-producer Veillonella. Supplementation of C. avidum P279 to colic IMA rats reduced H2 levels compared to animals receiving a placebo. Taken together, we report high H2 production by infant gut microbiota, which might be a contributing factor for infant colic, and suggest the potential of C. avidum P279 in reducing the abdominal H2 production, bloating, and pain associated with excessive crying in colic infants.
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Affiliation(s)
- Vanesa Natalin Rocha Martin
- Laboratory of Food Biotechnology, Department of Health Sciences and Technology, Institute of Food, Nutrition and Health, ETH-Zurich, Zurich, Switzerland
- Division of Gastroenterology and Nutrition, University Children’s Hospital Zurich, Zurich, Switzerland
| | - Christophe Del’Homme
- INRAE UMR 454, MEDIS Unit, Clermont-Ferrand Research Centre, Saint Genes-Champanelle, France
| | | | - Clarissa Schwab
- Laboratory of Food Biotechnology, Department of Health Sciences and Technology, Institute of Food, Nutrition and Health, ETH-Zurich, Zurich, Switzerland
| | - Christian Braegger
- Division of Gastroenterology and Nutrition, University Children’s Hospital Zurich, Zurich, Switzerland
| | | | - Christophe Lacroix
- Laboratory of Food Biotechnology, Department of Health Sciences and Technology, Institute of Food, Nutrition and Health, ETH-Zurich, Zurich, Switzerland
- *Correspondence: Christophe Lacroix,
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Mesa V, Monot M, Ferraris L, Popoff M, Mazuet C, Barbut F, Delannoy J, Dupuy B, Butel MJ, Aires J. Core-, pan- and accessory genome analyses of Clostridium neonatale: insights into genetic diversity. Microb Genom 2022; 8. [PMID: 35550024 PMCID: PMC9465065 DOI: 10.1099/mgen.0.000813] [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] [Indexed: 11/24/2022] Open
Abstract
Clostridium neonatale is a potential opportunistic pathogen recovered from faecal samples in cases of necrotizing enterocolitis (NEC), a gastrointestinal disease affecting preterm neonates. Although the C. neonatale species description and name validation were published in 2018, comparative genomics are lacking. In the present study, we provide the closed genome assembly of the C. neonatale ATCC BAA-265T (=250.09) reference strain with a manually curated functional annotation of the coding sequences. Pan-, core- and accessory genome analyses were performed using the complete 250.09 genome (4.7 Mb), three new assemblies (4.6–5.6 Mb), and five publicly available draft genome assemblies (4.6–4.7 Mb). The C. neonatale pan-genome contains 6840 genes, while the core-genome has 3387 genes. Pan-genome analysis revealed an ‘open’ state and genomic diversity. The strain-specific gene families ranged from five to 742 genes. Multiple mobile genetic elements were predicted, including a total of 201 genomic islands, 13 insertion sequence families, one CRISPR-Cas type I-B system and 15 predicted intact prophage signatures. Primary virulence classes including offensive, defensive, regulation of virulence-associated genes and non-specific virulence factors were identified. The presence of a tet(W/N/W) gene encoding a tetracycline resistance ribosomal protection protein and a 23S rRNA methyltransferase ermQ gene were identified in two different strains. Together, our results revealed a genetic diversity and plasticity of C. neonatale genomes and provide a comprehensive view of this species genomic features, paving the way for the characterization of its biological capabilities.
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Affiliation(s)
- Victoria Mesa
- Université de Paris, UMR-S1139, F-75006, Paris, France
| | - Marc Monot
- Plate-forme Technologique Biomics - Centre de Ressources et Recherches Technologiques, Institut Pasteur, F-75015, Paris, France.,Institut Pasteur, Université de Paris, UMR-CNRS 2001, Laboratoire Pathogenèse des Bactéries Anaérobies, F-75015, Paris, France
| | | | - Michel Popoff
- Institut Pasteur, Université de Paris, Centre National de Référence des Bactéries anaérobies et Botulisme, F-75015, Paris, France
| | - Christelle Mazuet
- Institut Pasteur, Université de Paris, Centre National de Référence des Bactéries anaérobies et Botulisme, F-75015, Paris, France
| | - Frederic Barbut
- Université de Paris, UMR-S1139, F-75006, Paris, France.,Assistance Publique-Hôpitaux de Paris, Hôpital saint Antoine, Infection Control Unit, F-75012, Paris, France
| | | | - Bruno Dupuy
- Institut Pasteur, Université de Paris, UMR-CNRS 2001, Laboratoire Pathogenèse des Bactéries Anaérobies, F-75015, Paris, France
| | | | - Julio Aires
- Université de Paris, UMR-S1139, F-75006, Paris, France
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Munson E, Carroll KC. Summary of Novel Bacterial Isolates Derived from Human Clinical Specimens and Nomenclature Revisions Published in 2018 and 2019. J Clin Microbiol 2021; 59:e01309-20. [PMID: 32967902 PMCID: PMC8111135 DOI: 10.1128/jcm.01309-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Knowledge of novel prokaryotic taxon discovery and nomenclature revisions is of importance to clinical microbiology laboratory practice, infectious disease epidemiology, and studies of microbial pathogenesis. Relative to bacterial isolates derived from human clinical specimens, we present an in-depth summary of novel taxonomic designations and revisions to prokaryotic taxonomy that were published in 2018 and 2019. Included are several changes pertinent to former designations of or within Propionibacterium spp., Corynebacterium spp., Clostridium spp., Mycoplasma spp., Methylobacterium spp., and Enterobacteriaceae Future efforts to ascertain clinical relevance for many of these changes may be augmented by a document development committee that has been appointed by the Clinical and Laboratory Standards Institute.
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Affiliation(s)
- Erik Munson
- College of Health Sciences, Marquette University, Milwaukee, Wisconsin, USA
| | - Karen C Carroll
- Division of Medical Microbiology, Department of Pathology, the Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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Wei HC, Xing SJ, Chen P, Wu XF, Gu X, Luo L, Liang XF, Xue M. Plant protein diet-induced hypoimmunity by affecting the spiral valve intestinal microbiota and bile acid enterohepatic circulation in Amur sturgeon (Acipenser schrenckii). FISH & SHELLFISH IMMUNOLOGY 2020; 106:421-430. [PMID: 32798694 DOI: 10.1016/j.fsi.2020.08.025] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 08/10/2020] [Accepted: 08/11/2020] [Indexed: 06/11/2023]
Abstract
An 8-week growth trial was conducted to study enterohepatic recirculation of bile acid metabolism and the intestinal microbiota of Amur sturgeon (Acipenser schrenckii) fed with three diets, including 540 g/kg, 270 g/kg or 0 g/kg fishmeal, which was correspondingly replaced by a plant protein blend (named P0, P50 and P100, respectively). The diets were designed to be isonitrogenous, isoenergetic and essential nutrients balanced. With rising levels of dietary plant protein, disruption of the spiral valve intestinal microbiota and more morbidity with liver disease were observed in the P100 group, although there were no haematological abnormalities observed. An obvious bile acids enterohepatic circulation disorder was found with phenotypes of increased liver bile acids compensatory synthesis, and reduced expression of bile acid receptors (FXR and TGR5), which induced BA accumulative toxicity. Accompanied by increased oxidative stress, it further induced hepatic lesions and hypoimmunity, which were non-negligible reasons for the high mortality and low utilization ability of plant protein by Amur sturgeon.
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Affiliation(s)
- H C Wei
- National Aquafeed Safety Assessment Center, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - S J Xing
- National Aquafeed Safety Assessment Center, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - P Chen
- National Aquafeed Safety Assessment Center, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - X F Wu
- National Aquafeed Safety Assessment Center, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - X Gu
- National Aquafeed Safety Assessment Center, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - L Luo
- Beijing Fisheries Research Institute, Beijing, 100068, China
| | - X F Liang
- National Aquafeed Safety Assessment Center, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - M Xue
- National Aquafeed Safety Assessment Center, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China; Agriculture and Rural Ministry Quality and Safety Risk Evaluation Laboratory of Feed and Feed Additives for Animal Husbandry, Beijing, 100081, China.
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Tindall BJ. The names Hungateiclostridium Zhang et al. 2018, Hungateiclostridium thermocellum (Viljoen et al. 1926) Zhang et al. 2018, Hungateiclostridium cellulolyticum (Patel et al. 1980) Zhang et al. 2018, Hungateiclostridium aldrichii (Yang et al. 1990) Zhang et al. 2018, Hungateiclostridium alkalicellulosi (Zhilina et al. 2006) Zhang et al. 2018, Hungateiclostridium clariflavum (Shiratori et al. 2009) Zhang et al. 2018, Hungateiclostridium straminisolvens (Kato et al. 2004) Zhang et al. 2018 and Hungateiclostridium saccincola (Koeck et al. 2016) Zhang et al. 2018 contravene Rule 51b of the International Code of Nomenclature of Prokaryotes and require replacement names in the genus Acetivibrio Patel et al. 1980. Int J Syst Evol Microbiol 2019; 69:3927-3932. [PMID: 31526446 DOI: 10.1099/ijsem.0.003685] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
A recent publication has created the genus name HungateiclostridiumZhang et al. 2018 and the new combinations Hungateiclostridium cellulolyticum (Patel et al. 1980) Zhang et al. 2018, Hungateiclostridium aldrichii (Yang et al. 1990.) Zhang et al. 2018, Hungateiclostridium alkalicellulosi (Zhilina et al. 2006) Zhang et al. 2018, Hungateiclostridium clariflavum (Shiratori et al. 2009) Zhang et al. 2018, Hungateiclostridium straminisolvens (Kato et al. 2004) Zhang et al. 2018 and Hungateiclostridium saccincola (Koeck et al. 2016) Zhang et al. 2018 for names at the rank of species that were previously either included in the genus ClostridiumPrazmowski 1880, Acetivibrio Patel et al. 1980 or HerbivoraxKoeck et al. 2016. Rules 23a, 38, 39b, 41a, 42 and 44 have not been followed and an illegitimate name at the rank of genus or illegitimate combinations at the rank of species as defined in Rule 51b(1) and (2) have been created. Another aspect is recognising the fact that an instance of heterotypic synonym has been created between Acetivibrio Patel et al. 1980, HerbivoraxKoeck et al. 2016 and HungateiclostridiumZhang et al. 2018, where the earliest validly published genus name is Acetivibrio Patel et al. 1980, of which the nomenclatural type is Acetivibrio cellulolyticus Patel et al. 1980. It follows from Rules 23a, 38, 39a, 39b, 41a, 42 and 44 that the genus name to be used is Acetivibrio Patel et al. 1980, with new combinations in that genus replacing those published in the genus HungateiclostridiumZhang et al. 2018, which together with the genus name are illegitimate according to Rule 51b of the International Code of Nomenclature of Prokaryotes. Additional issues are also addressed with regards to the names Pseudoclostridium thermosuccinogenes (Drent et al. 1995) Zhang et al. 2018, PseudoclostridiumZhang et al. 2018 OscillospiraceaePeshkoff 1940 (Approved Lists 1980), RuminococcaceaeRainey 2010, Eubacteriales Buchanan 1917 (Approved Lists 1980) and ClostridialesPrévot 1953 (Approved Lists 1980).
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Affiliation(s)
- B J Tindall
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstraße 7B 38124, Braunschweig, Germany
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Hosny M, Baptiste E, Levasseur A, La Scola B. Molecular epidemiology of Clostridium neonatale and its relationship with the occurrence of necrotizing enterocolitis in preterm neonates. New Microbes New Infect 2019; 32:100612. [PMID: 31737279 PMCID: PMC6849425 DOI: 10.1016/j.nmni.2019.100612] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 10/02/2019] [Accepted: 10/07/2019] [Indexed: 12/15/2022] Open
Abstract
Clostridia-especially Clostridium butyricum-are among the taxa most frequently identified from stool samples of preterm neonates with necrotizing enterocolitis (NEC). Recently, Clostridium neonatale has also been detected from epidemic cases, but using a culture-based approach we were unable to confirm this discovery in a local cohort. In order to investigate this link by a molecular approach, a specific rpoB-based quantitative real-time PCR was developed to detect C. neonatale directly from patients' stool specimens. Design of this rpoB-based quantitative real-time PCR was based on the genomic analysis of seven clinical isolates of C. neonatale. It was tested on stool samples from 88 preterm neonates with necrotizing enterocolitis and 71 matched controls. C. neonatale was significantly more prevalent in stools from preterm neonates with necrotizing enterocolitis than in controls (respectively 30/88 (34%) versus 9/71 (13%); p 0.003). Whole-genome analysis also allowed the identification of three genomic clusters of C. neonatale. This clustering was associated with a geographical location regardless of isolation from the NEC or control, suggesting asymptomatic carriage. Although less prevalent than C. butyricum in our cohort, C. neonatale is significantly associated with the occurrence of necrotizing enterocolitis.
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Affiliation(s)
| | | | | | - B. La Scola
- Aix-Marseille Université UM63, Institut de Recherche pour le Développement IRD 198, Assistance Publique, Hôpitaux de Marseille (AP-HM), Microbes, Evolution, Phylogeny and Infection (MEΦI), Institut Hospitalo-Universitaire (IHU), Méditerranée Infection, France
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Yu HY, Meade A, Liu SJ. Phylogeny of Clostridium spp. Based on Conservative Genes and Comparisons with Other Trees. Microbiology (Reading) 2019. [DOI: 10.1134/s002626171904012x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Schönherr-Hellec S, Aires J. Clostridia and necrotizing enterocolitis in preterm neonates. Anaerobe 2019; 58:6-12. [PMID: 30980889 DOI: 10.1016/j.anaerobe.2019.04.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 03/26/2019] [Accepted: 04/09/2019] [Indexed: 02/08/2023]
Abstract
Necrotizing enterocolitis (NEC) is the most severe life threatening gastrointestinal disease among preterm neonates. NEC continues to account for substantial morbidity and mortality in neonatal intensive care units worldwide. Although its pathogenesis remains incompletely elucidated, NEC is recognized as a multifactorial disease involving intestinal unbalanced inflammatory response, feeding strategies, and bacterial colonization. Epidemiological studies, clinical signs, and animal models support the participation of anaerobic bacteria, particularly clostridia species, in NEC development. Colonization by clostridia seems particularly deleterious. The present review is the opportunity to propose an update on the role of clostridia and NEC.
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Affiliation(s)
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- EA 4065, Faculty of Pharmacy, Paris Descartes University, Paris, France.
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