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Chiang-Ni C, Huang JY, Hsu CY, Lo YC, Chen YYM, Lai CH, Chiu CH. Genetic diversity, biofilm formation, and Vancomycin resistance of clinical Clostridium innocuum isolates. BMC Microbiol 2024; 24:353. [PMID: 39294587 PMCID: PMC11409672 DOI: 10.1186/s12866-024-03503-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 09/05/2024] [Indexed: 09/20/2024] Open
Abstract
BACKGROUND Clostridium innocuum, previously considered a commensal microbe, is a spore-forming anaerobic bacterium. C. innocuum displays inherent resistance to vancomycin and is associated with extra-intestinal infections, antibiotic-associated diarrhea, and inflammatory bowel disease. This study seeks to establish a multilocus sequence typing (MLST) scheme to explore the correlation between C. innocuum genotyping and its potential pathogenic phenotypes. METHODS Fifty-two C. innocuum isolates from Linkou Chang Gung Memorial Hospital (CGMH) in Taiwan and 60 sequence-available C. innocuum isolates from the National Center for Biotechnolgy Information Genome Database were included. The concentrated sequence of housekeeping genes in C. innocuum was determined by amplicon sequencing and used for MLST and phylogenetic analyses. The biofilm production activity of the C. innocuum isolates was determined by crystal violet staining. RESULTS Of the 112 C. innocuum isolates, 58 sequence types were identified. Maximum likelihood estimation categorized 52 CGMH isolates into two phylogenetic clades. These isolates were found to be biofilm producers, with isolates in clade I exhibiting significantly higher biofilm production than isolates in clade II. The sub-inhibitory concentration of vancomycin seemed to minimally influence biofilm production by C. innocuum isolates. Nevertheless, C. innocuum embedded in the biofilm structure demonstrated resistance to vancomycin treatments at a concentration greater than 256 µg/mL. CONCLUSIONS This study suggests that a specific genetic clade of C. innocuum produces a substantial amount of biofilm. Furthermore, this phenotype assists C. innocuum in resisting high concentrations of vancomycin, which may potentially play undefined roles in C. innocuum pathogenesis.
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Affiliation(s)
- Chuan Chiang-Ni
- Department of Microbiology and Immunology, College of Medicine, Chang Gung University, No. 259 Wen-Hwa 1st Road, Kwei-Shan, Taoyuan, 333323, Taiwan.
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan.
| | - Jing-Yi Huang
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Chih-Yun Hsu
- Department of Microbiology and Immunology, College of Medicine, Chang Gung University, No. 259 Wen-Hwa 1st Road, Kwei-Shan, Taoyuan, 333323, Taiwan
| | - Yi-Chi Lo
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Yi-Ywan M Chen
- Department of Microbiology and Immunology, College of Medicine, Chang Gung University, No. 259 Wen-Hwa 1st Road, Kwei-Shan, Taoyuan, 333323, Taiwan
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan
| | - Chih-Ho Lai
- Department of Microbiology and Immunology, College of Medicine, Chang Gung University, No. 259 Wen-Hwa 1st Road, Kwei-Shan, Taoyuan, 333323, Taiwan
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan
| | - Cheng-Hsun Chiu
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan
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2
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Kochan TJ, Nozick SH, Valdes A, Mitra SD, Cheung BH, Lebrun-Corbin M, Medernach RL, Vessely MB, Mills JO, Axline CMR, Nelson JA, VanGosen EM, Ward TJ, Ozer EA, van Duin D, Chen L, Kreiswirth BN, Long SW, Musser JM, Bulman ZP, Wunderink RG, Hauser AR. Klebsiella pneumoniae clinical isolates with features of both multidrug-resistance and hypervirulence have unexpectedly low virulence. Nat Commun 2023; 14:7962. [PMID: 38042959 PMCID: PMC10693551 DOI: 10.1038/s41467-023-43802-1] [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: 07/07/2023] [Accepted: 11/21/2023] [Indexed: 12/04/2023] Open
Abstract
Klebsiella pneumoniae has been classified into two types, classical K. pneumoniae (cKP) and hypervirulent K. pneumoniae (hvKP). cKP isolates are highly diverse and important causes of nosocomial infections; they include globally disseminated antibiotic-resistant clones. hvKP isolates are sensitive to most antibiotics but are highly virulent, causing community-acquired infections in healthy individuals. The virulence phenotype of hvKP is associated with pathogenicity loci responsible for siderophore and hypermucoid capsule production. Recently, convergent strains of K. pneumoniae, which possess features of both cKP and hvKP, have emerged and are cause of much concern. Here, we screen the genomes of 2,608 multidrug-resistant K. pneumoniae isolates from the United States and identify 47 convergent isolates. We perform phenotypic and genomic characterization of 12 representative isolates. These 12 convergent isolates contain a variety of antimicrobial resistance plasmids and virulence plasmids. Most convergent isolates contain aerobactin biosynthesis genes and produce more siderophores than cKP isolates but not more capsule. Unexpectedly, only 1 of the 12 tested convergent isolates has a level of virulence consistent with hvKP isolates in a murine pneumonia model. These findings suggest that additional studies should be performed to clarify whether convergent strains are indeed more virulent than cKP in mouse and human infections.
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Affiliation(s)
- Travis J Kochan
- Laboratory of Respiratory and Special Pathogens, Division of Bacterial, Parasitic, and Allergenic Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA.
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
| | - Sophia H Nozick
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Aliki Valdes
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Sumitra D Mitra
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Bettina H Cheung
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Marine Lebrun-Corbin
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Rachel L Medernach
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Division of Infectious Diseases, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Madeleine B Vessely
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Jori O Mills
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Christopher M R Axline
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Julia A Nelson
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Ethan M VanGosen
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Timothy J Ward
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Egon A Ozer
- Division of Infectious Diseases, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - David van Duin
- Division of Infectious Diseases, University of North Carolina, Chapel Hill, NC, USA
| | - Liang Chen
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA
| | - Barry N Kreiswirth
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA
| | - S Wesley Long
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital Research Institute, Houston, TX, USA
| | - James M Musser
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital Research Institute, Houston, TX, USA
| | - Zackery P Bulman
- College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA
| | - Richard G Wunderink
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Simpson Querrey Institute for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Alan R Hauser
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Division of Infectious Diseases, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
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3
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Atassi G, Medernach R, Scheetz M, Nozick S, Rhodes NJ, Murphy-Belcaster M, Murphy KR, Alisoltani A, Ozer EA, Hauser AR. Genomics of Aminoglycoside Resistance in Pseudomonas aeruginosa Bloodstream Infections at a United States Academic Hospital. Microbiol Spectr 2023; 11:e0508722. [PMID: 37191517 PMCID: PMC10269721 DOI: 10.1128/spectrum.05087-22] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 04/22/2023] [Indexed: 05/17/2023] Open
Abstract
Pseudomonas aeruginosa frequently becomes resistant to aminoglycosides by the acquisition of aminoglycoside modifying enzyme (AME) genes and the occurrence of mutations in the mexZ, fusA1, parRS, and armZ genes. We examined resistance to aminoglycosides in a collection of 227 P. aeruginosa bloodstream isolates collected over 2 decades from a single United States academic medical institution. Resistance rates of tobramycin and amikacin were relatively stable over this time, while the resistance rates of gentamicin were somewhat more variable. For comparison, we examined resistance rates to piperacillin-tazobactam, cefepime, meropenem, ciprofloxacin, and colistin. Resistance rates to the first four antibiotics were also stable, although uniformly higher for ciprofloxacin. Colistin resistance rates were initially quite low, rose substantially, and then began to decrease at the end of the study. Clinically relevant AME genes were identified in 14% of isolates, and mutations predicted to cause resistance were relatively common in the mexZ and armZ genes. In a regression analysis, resistance to gentamicin was associated with the presence of at least one gentamicin-active AME gene and significant mutations in mexZ, parS, and fusA1. Resistance to tobramycin was associated with the presence of at least one tobramycin-active AME gene. An extensively drug-resistant strain, PS1871, was examined further and found to contain five AME genes, most of which were within clusters of antibiotic resistance genes embedded in transposable elements. These findings demonstrate the relative contributions of aminoglycoside resistance determinants to P. aeruginosa susceptibilities at a United States medical center. IMPORTANCE Pseudomonas aeruginosa is frequently resistant to multiple antibiotics, including aminoglycosides. The rates of resistance to aminoglycosides in bloodstream isolates collected over 2 decades at a United States hospital remained constant, suggesting that antibiotic stewardship programs may be effective in countering an increase in resistance. Mutations in the mexZ, fusA1, parR, pasS, and armZ genes were more common than acquisition of genes encoding aminoglycoside modifying enzymes. The whole-genome sequence of an extensively drug resistant isolate indicates that resistance mechanisms can accumulate in a single strain. Together, these results suggest that aminoglycoside resistance in P. aeruginosa remains problematic and confirm known resistance mechanisms that can be targeted for the development of novel therapeutics.
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Affiliation(s)
- Giancarlo Atassi
- Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Rachel Medernach
- Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Marc Scheetz
- Department of Pharmacy Practice, Pharmacometrics Center of Excellence, Chicago College of Pharmacy, Midwestern University, Downers Grove, Illinois, USA
| | - Sophia Nozick
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Nathaniel J. Rhodes
- Pharmacometrics Center of Excellence, College of Graduate Studies, Department of Pharmacology, Midwestern University, Downers Grove, Illinois, USA
| | - Megan Murphy-Belcaster
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Katherine R. Murphy
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Arghavan Alisoltani
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Egon A. Ozer
- Department of Medicine (Division of Infectious Diseases), Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Alan R. Hauser
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Department of Medicine (Division of Infectious Diseases), Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
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4
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Bhattacharjee D, Flores C, Woelfel-Monsivais C, Seekatz AM. Diversity and Prevalence of Clostridium innocuum in the Human Gut Microbiota. mSphere 2023; 8:e0056922. [PMID: 36541771 PMCID: PMC9942572 DOI: 10.1128/msphere.00569-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 11/22/2022] [Indexed: 12/24/2022] Open
Abstract
Clostridia are a polyphyletic group of Gram-positive, spore-forming anaerobes in the Firmicutes phylum that significantly impact metabolism and functioning of the human gastrointestinal tract. Recently, Clostridia were divided into two separate classes, Clostridia and Erysipelotrichia, based on phenotypic and 16S rRNA gene-based differences. While Clostridia include many well-known pathogenic bacteria, Erysipelotrichia remain relatively uncharacterized, particularly regarding their role as a pathogen versus commensal. Despite wide recognition as a commensal, the erysipelotrichial species Clostridium innocuum has recently been associated with various disease states. To further understand the ecological and potential virulent role of C. innocuum, we conducted a genomic comparison across 38 C. innocuum isolates and 194 publicly available genomes. Based on colony morphology, we isolated multiple C. innocuum cultivars from the feces of healthy human volunteers (n = 5). Comparison of the 16S rRNA gene of our isolates against publicly available microbiota data sets in healthy individuals suggests a high prevalence of C. innocuum across the human population (>80%). Analysis of single nucleotide polymorphisms (SNPs) across core genes and average nucleotide identify (ANI) revealed the presence of four clades among all available genomes (n = 232 total). Investigation of carbohydrate and protein utilization pathways, including comparison against the carbohydrate-activating enzyme (CAZyme) database, demonstrated inter- and intraclade differences that were further substantiated in vitro. Collectively, these data indicate genetic variance within the C. innocuum species that may help clarify its role in human disease and health. IMPORTANCE Clostridia are a group of medically important anaerobes as both commensals and pathogens. Recently, a new class of Erysipelotrichia containing a number of reassigned clostridial species has emerged, including Clostridium innocuum. Recent studies have implicated C. innocuum as a potential causative agent of diarrhea in patients from whom Clostridioides difficile could not be isolated. Using genomic and in vitro comparison, this study sought to characterize C. innocuum in the healthy human gut. Our analyses suggest that C. innocuum is a highly prevalent and diverse species, demonstrating clade-specific differences in metabolism and potential virulence. Collectively, this study is the first investigation into a broader description of C. innocuum as a human gut inhabitant.
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Affiliation(s)
- Disha Bhattacharjee
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, USA
| | - Clara Flores
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, USA
| | | | - Anna M. Seekatz
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, USA
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5
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Cherny KE, Muscat EB, Balaji A, Mukherjee J, Ozer EA, Angarone MP, Hauser AR, Sichel JS, Amponsah E, Kociolek LK. Association Between Clostridium innocuum and Antibiotic-Associated Diarrhea in Adults and Children: A Cross-sectional Study and Comparative Genomics Analysis. Clin Infect Dis 2023; 76:e1244-e1251. [PMID: 35724319 PMCID: PMC10169446 DOI: 10.1093/cid/ciac483] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 06/03/2022] [Accepted: 06/09/2022] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND A recent study from Taiwan suggested that Clostridium innocuum may be an unrecognized cause of antibiotic-associated diarrhea (AAD) and clinically indistinguishable from Clostridioides difficile infection. Our objective was to compare C. innocuum prevalence and strain between those with AAD and asymptomatic controls. METHODS In this cross-sectional study, we collected stool from 200 individuals with AAD and 100 asymptomatic controls. We evaluated the association between AAD and C. innocuum in stool using anaerobic culture and quantitative polymerase chain reaction (qPCR). To identify strain-specific associations with AAD, we performed whole-genome sequencing of C. innocuum isolates using Illumina MiSeq and constructed comparative genomics analyses. RESULTS C. innocuum was isolated from stool of 126/300 (42%) subjects and more frequently from asymptomatic controls than AAD subjects (50/100 [50%] vs 76/200 [38%], respectively; P = .047). C. innocuum isolation frequency was not associated with AAD in either the adult or pediatric subgroups. C. innocuum and C. difficile were frequently co-prevalent in individuals with and without diarrhea. There were no phylogenetic differences or accessory genome associations between C. innocuum isolates from AAD subjects and asymptomatic controls. CONCLUSIONS C. innocuum was frequently isolated and at a greater frequency in asymptomatic controls than those with AAD. We did not identify strain lineages or accessory genomic elements associated with AAD. These data highlight that differentiating C. innocuum-associated diarrhea from asymptomatic colonization, and differentiating diarrhea caused by C. difficile from C. innocuum, are clinical microbiology challenges that require additional investigation to identify host-specific factors and/or biomarkers that distinguish these conditions.
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Affiliation(s)
- Kathryn E Cherny
- Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - Emily B Muscat
- Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
| | - Aakash Balaji
- Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
| | - Jayabrata Mukherjee
- Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
| | - Egon A Ozer
- Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - Michael P Angarone
- Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - Alan R Hauser
- Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - Joseph S Sichel
- Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - Emmanuel Amponsah
- Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
| | - Larry K Kociolek
- Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA.,Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
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6
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Kochan TJ, Nozick SH, Medernach RL, Cheung BH, Gatesy SWM, Lebrun-Corbin M, Mitra SD, Khalatyan N, Krapp F, Qi C, Ozer EA, Hauser AR. Genomic surveillance for multidrug-resistant or hypervirulent Klebsiella pneumoniae among United States bloodstream isolates. BMC Infect Dis 2022; 22:603. [PMID: 35799130 PMCID: PMC9263067 DOI: 10.1186/s12879-022-07558-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 06/21/2022] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Klebsiella pneumoniae strains have been divided into two major categories: classical K. pneumoniae, which are frequently multidrug-resistant and cause hospital-acquired infections in patients with impaired defenses, and hypervirulent K. pneumoniae, which cause severe community-acquired and disseminated infections in normal hosts. Both types of infections may lead to bacteremia and are associated with significant morbidity and mortality. The relative burden of these two types of K. pneumoniae among bloodstream isolates within the United States is not well understood. METHODS We evaluated consecutive K. pneumoniae isolates cultured from the blood of hospitalized patients at Northwestern Memorial Hospital (NMH) in Chicago, Illinois between April 2015 and April 2017. Bloodstream isolates underwent whole genome sequencing, and sequence types (STs), capsule loci (KLs), virulence genes, and antimicrobial resistance genes were identified in the genomes using the bioinformatic tools Kleborate and Kaptive. Patient demographic, comorbidity, and infection information, as well as the phenotypic antimicrobial resistance of the isolates were extracted from the electronic health record. Candidate hypervirulent isolates were tested in a murine model of pneumonia, and their plasmids were characterized using long-read sequencing. We also extracted STs, KLs, and virulence and antimicrobial resistance genes from the genomes of bloodstream isolates submitted from 33 United States institutions between 2007 and 2021 to the National Center for Biotechnology Information (NCBI) database. RESULTS Consecutive K. pneumoniae bloodstream isolates (n = 104, one per patient) from NMH consisted of 75 distinct STs and 51 unique capsule loci. The majority of these isolates (n = 58, 55.8%) were susceptible to all tested antibiotics except ampicillin, but 17 (16.3%) were multidrug-resistant. A total of 32 (30.8%) of these isolates were STs of known high-risk clones, including ST258 and ST45. In particular, 18 (17.3%) were resistant to ceftriaxone (of which 17 harbored extended-spectrum beta-lactamase genes) and 9 (8.7%) were resistant to meropenem (all of which harbored a carbapenemase genes). Four (3.8%) of the 104 isolates were hypervirulent K. pneumoniae, as evidenced by hypermucoviscous phenotypes, high levels of virulence in a murine model of pneumonia, and the presence of large plasmids similar to characterized hypervirulence plasmids. These isolates were cultured from patients who had not recently traveled to Asia. Two of these hypervirulent isolates belonged to the well characterized ST23 lineage and one to the re-emerging ST66 lineage. Of particular concern, two of these isolates contained plasmids with tra conjugation loci suggesting the potential for transmission. We also analyzed 963 publicly available genomes of K. pneumoniae bloodstream isolates from locations within the United States. Of these, 465 (48.3%) and 760 (78.9%) contained extended-spectrum beta-lactamase genes or carbapenemase genes, respectively, suggesting a bias towards submission of antibiotic-resistant isolates. The known multidrug-resistant high-risk clones ST258 and ST307 were the predominant sequence types. A total of 32 (3.3%) of these isolates contained aerobactin biosynthesis genes and 26 (2.7%) contained at least two genetic features of hvKP strains, suggesting elevated levels of virulence. We identified 6 (0.6%) isolates that were STs associated with hvKP: ST23 (n = 4), ST380 (n = 1), and ST65 (n = 1). CONCLUSIONS Examination of consecutive isolates from a single center demonstrated that multidrug-resistant high-risk clones are indeed common, but a small number of hypervirulent K. pneumoniae isolates were also observed in patients with no recent travel history to Asia, suggesting that these isolates are undergoing community spread in the United States. A larger collection of publicly available bloodstream isolate genomes also suggested that hypervirulent K. pneumoniae strains are present but rare in the USA; however, this collection appears to be heavily biased towards highly antibiotic-resistant isolates (and correspondingly away from hypervirulent isolates).
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Affiliation(s)
- Travis J Kochan
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA.
| | - Sophia H Nozick
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Rachel L Medernach
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
- Division of Infectious Diseases, Department of Medicine, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Bettina H Cheung
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Samuel W M Gatesy
- Division of Infectious Diseases, Department of Medicine, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Marine Lebrun-Corbin
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Sumitra D Mitra
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Natalia Khalatyan
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Fiorella Krapp
- Division of Infectious Diseases, Department of Medicine, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Chao Qi
- Department of Pathology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Egon A Ozer
- Division of Infectious Diseases, Department of Medicine, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
- Center for Pathogen Genomics and Microbial Evolution, Havey Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Alan R Hauser
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
- Division of Infectious Diseases, Department of Medicine, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
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7
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Skinner AM, Petrella L, Spandoni S, Serna-Perez F, Johnson S. Can Clostridium innocuum masquerade as Clostridioides difficile? Clin Infect Dis 2022; 75:1268-1269. [PMID: 35579505 DOI: 10.1093/cid/ciac377] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Andrew M Skinner
- Department of Research and Medicine, Edward Hines Jr Veterans Administration Hospital, Hines, Illinois, USA.,Loyola University Medical Center, Department of Medicine, Maywood, Illinois, USA
| | - Laurica Petrella
- Department of Research and Medicine, Edward Hines Jr Veterans Administration Hospital, Hines, Illinois, USA
| | - Stacey Spandoni
- Department of Research and Medicine, Edward Hines Jr Veterans Administration Hospital, Hines, Illinois, USA
| | - Fidel Serna-Perez
- Department of Research and Medicine, Edward Hines Jr Veterans Administration Hospital, Hines, Illinois, USA
| | - Stuart Johnson
- Department of Research and Medicine, Edward Hines Jr Veterans Administration Hospital, Hines, Illinois, USA.,Loyola University Medical Center, Department of Medicine, Maywood, Illinois, USA
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