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Sansom SE, Shimasaki T, Dangana T, Lin MY, Schoeny ME, Fukuda C, Moore NM, Yelin RD, Bassis CM, Rhee Y, Cornejo Cisneros E, Bell P, Lolans K, Aboushaala K, Young VB, Hayden MK. Comparison of Daily versus Admission and Discharge Surveillance Cultures for Multidrug-Resistant Organism Detection in an Intensive Care Unit. J Infect Dis 2024:jiae162. [PMID: 38546721 DOI: 10.1093/infdis/jiae162] [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: 09/26/2023] [Revised: 03/19/2024] [Accepted: 03/26/2024] [Indexed: 05/24/2024] Open
Abstract
BACKGROUND Admission and discharge screening of patients for asymptomatic gut colonization with multidrug-resistant organisms (MDROs) is a traditional approach to active surveillance, but its sensitivity for detecting colonization is uncertain. METHODS Daily rectal or fecal swab samples and clinical data were collected over 12 months from patients in one 25-bed intensive care unit (ICU) in Chicago, IL USA and tested for the following multidrug-resistant organisms (MDROs): vancomycin-resistant enterococci (VRE); third-generation cephalosporin-resistant Enterobacterales, including extended-spectrum β-lactamase-producing Enterobacterales (ESBL); and carbapenem-resistant Enterobacterales (CRE). MDRO detection by (1) admission/discharge surveillance cultures or (2) clinical cultures were compared to daily surveillance cultures. Samples underwent 16S rRNA gene sequencing to measure the relative abundance of operational taxonomic units (OTUs) corresponding to each MDRO. RESULTS Compared with daily surveillance cultures, admission/discharge cultures detected 91% of prevalent MDRO colonization and 63% of incident MDRO colonization among medical ICU patients. Only a minority (7%) of MDRO carriers were identified by clinical cultures. Higher relative abundance of MDRO-associated OTUs and specific antibiotic exposures were independently associated with higher probability of MDRO detection by culture. CONCLUSION Admission and discharge surveillance cultures underestimated MDRO acquisitions in an ICU. These limitations should be considered when designing sampling strategies for epidemiologic studies that use culture-based surveillance.
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Affiliation(s)
- Sarah E Sansom
- Department of Internal Medicine/Division of Infectious Diseases, Rush University Medical Center, Chicago, IL USA
| | - Teppei Shimasaki
- Department of Internal Medicine/Division of Infectious Diseases, Rush University Medical Center, Chicago, IL USA
| | - Thelma Dangana
- Department of Internal Medicine/Division of Infectious Diseases, Rush University Medical Center, Chicago, IL USA
| | - Michael Y Lin
- Department of Internal Medicine/Division of Infectious Diseases, Rush University Medical Center, Chicago, IL USA
| | | | - Christine Fukuda
- Department of Internal Medicine/Division of Infectious Diseases, Rush University Medical Center, Chicago, IL USA
| | - Nicholas M Moore
- Department of Internal Medicine/Division of Infectious Diseases, Rush University Medical Center, Chicago, IL USA
| | - Rachel D Yelin
- Department of Internal Medicine/Division of Infectious Diseases, Rush University Medical Center, Chicago, IL USA
| | - Christine M Bassis
- Department of Internal Medicine/Division of Infectious Diseases, University of Michigan Medical School, Ann Arbor, MI USA
| | - Yoona Rhee
- Department of Internal Medicine/Division of Infectious Diseases, Rush University Medical Center, Chicago, IL USA
| | - Enrique Cornejo Cisneros
- Department of Internal Medicine/Division of Infectious Diseases, Rush University Medical Center, Chicago, IL USA
| | - Pamela Bell
- Department of Internal Medicine/Division of Infectious Diseases, Rush University Medical Center, Chicago, IL USA
| | - Karen Lolans
- Department of Internal Medicine/Division of Infectious Diseases, Rush University Medical Center, Chicago, IL USA
| | - Khaled Aboushaala
- Department of Internal Medicine/Division of Infectious Diseases, Rush University Medical Center, Chicago, IL USA
| | - Vincent B Young
- Department of Internal Medicine/Division of Infectious Diseases, University of Michigan Medical School, Ann Arbor, MI USA
- Department of Microbiology & Immunology, University of Michigan Medical School, Ann Arbor, MI USA
| | - Mary K Hayden
- Department of Internal Medicine/Division of Infectious Diseases, Rush University Medical Center, Chicago, IL USA
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Selvaraj Anand S, Wu CT, Bremer J, Bhatti M, Treangen TJ, Kalia A, Shelburne SA, Shropshire WC. Identification of a novel CG307 sub-clade in third-generation-cephalosporin-resistant Klebsiella pneumoniae causing invasive infections in the USA. Microb Genom 2024; 10:001201. [PMID: 38407244 PMCID: PMC10926705 DOI: 10.1099/mgen.0.001201] [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: 11/28/2023] [Accepted: 01/31/2024] [Indexed: 02/27/2024] Open
Abstract
Despite the notable clinical impact, recent molecular epidemiology regarding third-generation-cephalosporin-resistant (3GC-R) Klebsiella pneumoniae in the USA remains limited. We performed whole-genome sequencing of 3GC-R K. pneumoniae bacteraemia isolates collected from March 2016 to May 2022 at a tertiary care cancer centre in Houston, TX, USA, using Illumina and Oxford Nanopore Technologies platforms. A comprehensive comparative genomic analysis was performed to dissect population structure, transmission dynamics and pan-genomic signatures of our 3GC-R K. pneumoniae population. Of the 178 3GC-R K. pneumoniae bacteraemias that occurred during our study time frame, we were able to analyse 153 (86 %) bacteraemia isolates, 126 initial and 27 recurrent isolates. While isolates belonging to the widely prevalent clonal group (CG) 258 were rarely observed, the predominant CG, 307, accounted for 37 (29 %) index isolates and displayed a significant correlation (Pearson correlation test P value=0.03) with the annual frequency of 3GC-R K. pneumoniae bacteraemia. Interestingly, only 11 % (4/37) of CG307 isolates belonged to the commonly detected 'Texas-specific' clade that has been observed in previous Texas-based K. pneumoniae antimicrobial-resistance surveillance studies. We identified nearly half of our CG307 isolates (n=18) belonged to a novel, monophyletic CG307 sub-clade characterized by the chromosomally encoded bla SHV-205 and unique accessory genome content. This CG307 sub-clade was detected in various regions of the USA, with genome sequences from 24 additional strains becoming recently available in the National Center for Biotechnology Information (NCBI) SRA database. Collectively, this study underscores the emergence and dissemination of a distinct CG307 sub-clade that is a prevalent cause of 3GC-R K. pneumoniae bacteraemia among cancer patients seen in Houston, TX, and has recently been isolated throughout the USA.
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Affiliation(s)
- Selvalakshmi Selvaraj Anand
- Graduate Program in Diagnostic Genetics and Genomics, School of Health Professions, MD Anderson Cancer Center, University of Texas, Houston, TX, USA
| | - Chin-Ting Wu
- Graduate Program in Diagnostic Genetics and Genomics, School of Health Professions, MD Anderson Cancer Center, University of Texas, Houston, TX, USA
| | - Jordan Bremer
- Department of Infectious Diseases, Infection Control, and Employee Health, MD Anderson Cancer Center, University of Texas, Houston, TX, USA
| | - Micah Bhatti
- Department of Laboratory Medicine, MD Anderson Cancer Center, University of Texas, Houston, TX, USA
| | - Todd J. Treangen
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Awdhesh Kalia
- Graduate Program in Diagnostic Genetics and Genomics, School of Health Professions, MD Anderson Cancer Center, University of Texas, Houston, TX, USA
| | - Samuel A. Shelburne
- Department of Infectious Diseases, Infection Control, and Employee Health, MD Anderson Cancer Center, University of Texas, Houston, TX, USA
- Department of Genomic Medicine, MD Anderson Cancer Center, University of Texas, Houston, TX, USA
| | - William C. Shropshire
- Department of Infectious Diseases, Infection Control, and Employee Health, MD Anderson Cancer Center, University of Texas, Houston, TX, USA
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Schluter J, Djukovic A, Taylor BP, Yan J, Duan C, Hussey GA, Liao C, Sharma S, Fontana E, Amoretti LA, Wright RJ, Dai A, Peled JU, Taur Y, Perales MA, Siranosian BA, Bhatt AS, van den Brink MRM, Pamer EG, Xavier JB. The TaxUMAP atlas: Efficient display of large clinical microbiome data reveals ecological competition in protection against bacteremia. Cell Host Microbe 2023; 31:1126-1139.e6. [PMID: 37329880 PMCID: PMC10527165 DOI: 10.1016/j.chom.2023.05.027] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 09/28/2022] [Accepted: 05/24/2023] [Indexed: 06/19/2023]
Abstract
Longitudinal microbiome data provide valuable insight into disease states and clinical responses, but they are challenging to mine and view collectively. To address these limitations, we present TaxUMAP, a taxonomically informed visualization for displaying microbiome states in large clinical microbiome datasets. We used TaxUMAP to chart a microbiome atlas of 1,870 patients with cancer during therapy-induced perturbations. Bacterial density and diversity were positively associated, but the trend was reversed in liquid stool. Low-diversity states (dominations) remained stable after antibiotic treatment, and diverse communities had a broader range of antimicrobial resistance genes than dominations. When examining microbiome states associated with risk for bacteremia, TaxUMAP revealed that certain Klebsiella species were associated with lower risk for bacteremia localize in a region of the atlas that is depleted in high-risk enterobacteria. This indicated a competitive interaction that was validated experimentally. Thus, TaxUMAP can chart comprehensive longitudinal microbiome datasets, enabling insights into microbiome effects on human health.
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Affiliation(s)
- Jonas Schluter
- Institute for Systems Genetics, Department of Microbiology, New York University Grossman School of Medicine, New York, NY, USA.
| | - Ana Djukovic
- Program for Computational and Systems Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Bradford P Taylor
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jinyuan Yan
- Program for Computational and Systems Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Caichen Duan
- Institute for Systems Genetics, Department of Microbiology, New York University Grossman School of Medicine, New York, NY, USA
| | - Grant A Hussey
- Institute for Systems Genetics, Department of Microbiology, New York University Grossman School of Medicine, New York, NY, USA
| | - Chen Liao
- Program for Computational and Systems Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Sneh Sharma
- Program for Computational and Systems Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Emily Fontana
- Department of Immunology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Luigi A Amoretti
- Department of Immunology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Roberta J Wright
- Department of Immunology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Anqi Dai
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jonathan U Peled
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Weill Cornell Medical College, New York, NY, USA
| | - Ying Taur
- Department of Immunology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Miguel-Angel Perales
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Weill Cornell Medical College, New York, NY, USA
| | | | - Ami S Bhatt
- Department of Genetics, Stanford University, Stanford, CA, USA; Department of Medicine, Division of Hematology, Stanford University, Stanford, CA, USA; Department of Medicine, Division of Blood and Marrow Transplantation and Cellular Therapy, Stanford University School of Medicine, Stanford, CA, USA
| | - Marcel R M van den Brink
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Weill Cornell Medical College, New York, NY, USA
| | - Eric G Pamer
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
| | - Joao B Xavier
- Program for Computational and Systems Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA.
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Lactobacillus supports Clostridiales to restrict gut colonization by multidrug-resistant Enterobacteriaceae. Nat Commun 2022; 13:5617. [PMID: 36153315 PMCID: PMC9509339 DOI: 10.1038/s41467-022-33313-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 09/09/2022] [Indexed: 11/10/2022] Open
Abstract
Infections by multidrug-resistant Enterobacteriaceae (MRE) are life-threatening to patients. The intestinal microbiome protects against MRE colonization, but antibiotics cause collateral damage to commensals and open the way to colonization and subsequent infection. Despite the significance of this problem, the specific commensals and mechanisms that restrict MRE colonization remain largely unknown. Here, by performing a multi-omic prospective study of hospitalized patients combined with mice experiments, we find that Lactobacillus is key, though not sufficient, to restrict MRE gut colonization. Lactobacillus rhamnosus and murinus increase the levels of Clostridiales bacteria, which induces a hostile environment for MRE growth through increased butyrate levels and reduced nutrient sources. This mechanism of colonization resistance, an interaction between Lactobacillus spp. and Clostridiales involving cooperation between microbiota members, is conserved in mice and patients. These results stress the importance of exploiting microbiome interactions for developing effective probiotics that prevent infections in hospitalized patients. Multidrug-resistant Enterobacteriaceae (MRE) represent a major threat for patients’ health. Here, the authors describe how cooperation between gut commensal bacteria (Lactobacillus spp. And Clostridiales) restrict MRE colonization in mice and patients
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