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Miles-Jay A, Snitkin ES, Lin MY, Shimasaki T, Schoeny M, Fukuda C, Dangana T, Moore N, Sansom SE, Yelin RD, Bell P, Rao K, Keidan M, Standke A, Bassis C, Hayden MK, Young VB. Longitudinal genomic surveillance of carriage and transmission of Clostridioides difficile in an intensive care unit. Nat Med 2023; 29:2526-2534. [PMID: 37723252 PMCID: PMC10579090 DOI: 10.1038/s41591-023-02549-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 08/17/2023] [Indexed: 09/20/2023]
Abstract
Despite enhanced infection prevention efforts, Clostridioides difficile remains the leading cause of healthcare-associated infections in the United States. Current prevention strategies are limited by their failure to account for patients who carry C. difficile asymptomatically, who may act as hidden reservoirs transmitting infections to other patients. To improve the understanding of asymptomatic carriers' contribution to C. difficile spread, we conducted admission and daily longitudinal culture-based screening for C. difficile in a US-based intensive care unit over nine months and performed whole-genome sequencing on all recovered isolates. Despite a high burden of carriage, with 9.3% of admissions having toxigenic C. difficile detected in at least one sample, only 1% of patients culturing negative on admission to the unit acquired C. difficile via cross-transmission. While patients who carried toxigenic C. difficile on admission posed minimal risk to others, they themselves had a 24-times greater risk for developing a healthcare-onset C. difficile infection than noncarriers. Together, these findings suggest that current infection prevention practices can be effective in preventing nosocomial cross-transmission of C. difficile, and that decreasing C. difficile infections in hospitals further will require interventions targeting the transition from asymptomatic carriage to infection.
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Affiliation(s)
- Arianna Miles-Jay
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Evan S Snitkin
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA.
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA.
| | - Michael Y Lin
- Division of Infectious Diseases, Department of Medicine, Rush University Medical Center, Chicago, IL, USA
| | - Teppei Shimasaki
- Division of Infectious Diseases, Department of Medicine, Rush University Medical Center, Chicago, IL, USA
| | - Michael Schoeny
- Division of Infectious Diseases, Department of Medicine, Rush University Medical Center, Chicago, IL, USA
| | - Christine Fukuda
- Division of Infectious Diseases, Department of Medicine, Rush University Medical Center, Chicago, IL, USA
| | - Thelma Dangana
- Division of Infectious Diseases, Department of Medicine, Rush University Medical Center, Chicago, IL, USA
| | - Nicholas Moore
- Division of Infectious Diseases, Department of Medicine, Rush University Medical Center, Chicago, IL, USA
| | - Sarah E Sansom
- Division of Infectious Diseases, Department of Medicine, Rush University Medical Center, Chicago, IL, USA
| | - Rachel D Yelin
- Division of Infectious Diseases, Department of Medicine, Rush University Medical Center, Chicago, IL, USA
| | - Pamela Bell
- Division of Infectious Diseases, Department of Medicine, Rush University Medical Center, Chicago, IL, USA
| | - Krishna Rao
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Micah Keidan
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Alexandra Standke
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Christine Bassis
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Mary K Hayden
- Division of Infectious Diseases, Department of Medicine, Rush University Medical Center, Chicago, IL, USA
| | - Vincent B Young
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
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2
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Lapp Z, Octaria R, O’Malley SM, Nguyen TN, Wolford H, Crawford R, Moore C, Snippes Vagnone P, Noel D, Duffy N, Pirani A, Thomas LS, Pattee B, Pearson C, Bulens SN, Hoffman S, Kainer M, Anacker M, Meek J, See I, Gontjes KJ, Chan A, Lynfield R, Maloney M, Hayden MK, Snitkin E, Slayton RB. Distinct Origins and Transmission Pathways of blaKPC Enterobacterales across Three U.S. States. J Clin Microbiol 2023; 61:e0025923. [PMID: 37439675 PMCID: PMC10446861 DOI: 10.1128/jcm.00259-23] [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: 03/06/2023] [Accepted: 06/27/2023] [Indexed: 07/14/2023] Open
Abstract
Carbapenem-resistant Enterobacterales (CRE) are among the most concerning antibiotic resistance threats due to high rates of multidrug resistance, transmissibility in health care settings, and high mortality rates. We evaluated the potential for regional genomic surveillance to track the spread of blaKPC-carrying CRE (KPC-CRE) by using isolate collections from health care facilities in three U.S. states. Clinical isolates were collected from Connecticut (2017 to 2018), Minnesota (2012 to 2018), and Tennessee (2016 to 2017) through the U.S. Centers for Disease Control and Prevention's Multi-site Gram-negative Surveillance Initiative (MuGSI) and additional surveillance. KPC-CRE isolates were whole-genome sequenced, yielding 255 isolates from 214 patients across 96 facilities. Case report data on patient comorbidities, facility exposures, and interfacility patient transfer were extracted. We observed that in Connecticut, most KPC-CRE isolates showed evidence of importation from outside the state, with limited local transmission. In Minnesota, cases were mainly from sporadic importation and transmission of blaKPC-carrying Klebsiella pneumoniae ST258, and clonal expansion of blaKPC-carrying Enterobacter hormaechei ST171, primarily at a single focal facility and its satellite facilities. In Tennessee, we observed transmission of diverse strains of blaKPC-carrying Enterobacter and Klesbiella, with evidence that most derived from the local acquisition of blaKPC plasmids circulating in an interconnected regional health care network. Thus, the underlying processes driving KPC-CRE burden can differ substantially across regions and can be discerned through regional genomic surveillance. This study provides proof of concept that integrating genomic data with information on interfacility patient transfers can provide insights into locations and drivers of regional KPC-CRE burden that can enable targeted interventions.
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Affiliation(s)
- Zena Lapp
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Rany Octaria
- Department of Medicine, Division of Epidemiology, Vanderbilt University, Nashville, Tennessee, USA
- Tennessee Department of Health, Nashville, Tennessee, USA
| | | | - Tu Ngoc Nguyen
- Connecticut Department of Public Health, Hartford, Connecticut, USA
| | - Hannah Wolford
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Ryan Crawford
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | | | | | - Diane Noel
- Connecticut Department of Public Health, Hartford, Connecticut, USA
| | - Nadezhda Duffy
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Ali Pirani
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | | | | | - Claire Pearson
- Connecticut Department of Public Health, Hartford, Connecticut, USA
| | - Sandra N. Bulens
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Sophie Hoffman
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Marion Kainer
- Tennessee Department of Health, Nashville, Tennessee, USA
| | | | - James Meek
- Connecticut Emerging Infections Program, Yale School of Public Health, New Haven, Connecticut, USA
| | - Isaac See
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Kyle J. Gontjes
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | - Allison Chan
- Tennessee Department of Health, Nashville, Tennessee, USA
| | - Ruth Lynfield
- Minnesota Department of Health, Saint Paul, Minnesota, USA
| | - Meghan Maloney
- Connecticut Department of Public Health, Hartford, Connecticut, USA
| | - Mary K. Hayden
- Department of Medicine, Division of Infectious Diseases, Rush University Medical Center, Chicago, Illinois, USA
- Department of Pathology, Rush University Medical Center, Chicago, Illinois, USA
| | - Evan Snitkin
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
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3
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Koch M, Noonan AJC, Qiu Y, Dofher K, Kieft B, Mottahedeh S, Shastri M, Hallam SJ. The survivor strain: isolation and characterization of Phormidium yuhuli AB48, a filamentous phototactic cyanobacterium with biotechnological potential. Front Bioeng Biotechnol 2022; 10:932695. [PMID: 36046667 PMCID: PMC9420970 DOI: 10.3389/fbioe.2022.932695] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 06/27/2022] [Indexed: 11/13/2022] Open
Abstract
Despite their recognized potential, current applications of cyanobacteria as microbial cell factories remain in early stages of development. This is partly due to the fact that engineered strains are often difficult to grow at scale. This technical challenge contrasts with the dense and highly productive cyanobacteria populations thriving in many natural environments. It has been proposed that the selection of strains pre-adapted for growth in industrial photobioreactors could enable more productive cultivation outcomes. Here, we described the initial morphological, physiological, and genomic characterization of Phormidium yuhuli AB48 isolated from an industrial photobioreactor environment. P. yuhuli AB48 is a filamentous phototactic cyanobacterium with a growth rate comparable to Synechocystis sp. PCC 6803. The isolate forms dense biofilms under high salinity and alkaline conditions and manifests a similar nutrient profile to Arthrospira platensis (Spirulina). We sequenced, assembled, and analyzed the P. yuhuli AB48 genome, the first closed circular isolate reference genome for a member of the Phormidium genus. We then used cultivation experiments in combination with proteomics and metabolomics to investigate growth characteristics and phenotypes related to industrial scale cultivation, including nitrogen and carbon utilization, salinity, and pH acclimation, as well as antibiotic resistance. These analyses provide insight into the biological mechanisms behind the desirable growth properties manifested by P. yuhuli AB48 and position it as a promising microbial cell factory for industrial-scale bioproduction[221, 1631].
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Affiliation(s)
- Moritz Koch
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Avery J. C. Noonan
- Genome Science and Technology Program, University of British Columbia, Vancouver, BC, Canada
- ECOSCOPE Training Program, University of British Columbia, Vancouver, BC, Canada
| | - Yilin Qiu
- Genome Science and Technology Program, University of British Columbia, Vancouver, BC, Canada
| | - Kalen Dofher
- Genome Science and Technology Program, University of British Columbia, Vancouver, BC, Canada
| | - Brandon Kieft
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | | | | | - Steven J. Hallam
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
- Genome Science and Technology Program, University of British Columbia, Vancouver, BC, Canada
- ECOSCOPE Training Program, University of British Columbia, Vancouver, BC, Canada
- Graduate Program in Bioinformatics, University of British Columbia, Vancouver, BC, Canada
- Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
- *Correspondence: Steven J. Hallam,
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Vornhagen J, Roberts EK, Unverdorben L, Mason S, Patel A, Crawford R, Holmes CL, Sun Y, Teodorescu A, Snitkin ES, Zhao L, Simner PJ, Tamma PD, Rao K, Kaye KS, Bachman MA. Combined comparative genomics and clinical modeling reveals plasmid-encoded genes are independently associated with Klebsiella infection. Nat Commun 2022; 13:4459. [PMID: 35915063 PMCID: PMC9343666 DOI: 10.1038/s41467-022-31990-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 07/12/2022] [Indexed: 11/28/2022] Open
Abstract
Members of the Klebsiella pneumoniae species complex frequently colonize the gut and colonization is associated with subsequent infection. To identify genes associated with progression from colonization to infection, we undertook a case-control comparative genomics study. Concordant cases (N = 85), where colonizing and invasive isolates were identical strain types, were matched to asymptomatically colonizing controls (N = 160). Thirty-seven genes are associated with infection, 27 of which remain significant following adjustment for patient variables and bacterial phylogeny. Infection-associated genes are not previously characterized virulence factors, but instead a diverse group of stress resistance, regulatory and antibiotic resistance genes, despite careful adjustment for antibiotic exposure. Many genes are plasmid borne, and for some, the relationship with infection is mediated by gut dominance. Five genes were validated in a geographically-independent cohort of colonized patients. This study identifies several genes reproducibly associated with progression to infection in patients colonized by diverse Klebsiella.
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Affiliation(s)
- Jay Vornhagen
- Department of Pathology, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
- Department of Microbiology & Immunology, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Emily K Roberts
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Lavinia Unverdorben
- Department of Microbiology & Immunology, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Sophia Mason
- Department of Pathology, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Alieysa Patel
- Department of Pathology, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Ryan Crawford
- Department of Computational Medicine and Bioinformatics, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Caitlyn L Holmes
- Department of Pathology, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
- Department of Microbiology & Immunology, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Yuang Sun
- Department of Pathology, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Alexandra Teodorescu
- Department of Pathology, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Evan S Snitkin
- Department of Microbiology & Immunology, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
- Department of Internal Medicine/Infectious Diseases Division, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Lili Zhao
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Patricia J Simner
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MI, USA
| | - Pranita D Tamma
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MI, USA
| | - Krishna Rao
- Department of Internal Medicine/Infectious Diseases Division, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Keith S Kaye
- Department of Internal Medicine/Infectious Diseases Division, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Michael A Bachman
- Department of Pathology, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA.
- Department of Microbiology & Immunology, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA.
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5
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Pudlo NA, Urs K, Crawford R, Pirani A, Atherly T, Jimenez R, Terrapon N, Henrissat B, Peterson D, Ziemer C, Snitkin E, Martens EC. Phenotypic and Genomic Diversification in Complex Carbohydrate-Degrading Human Gut Bacteria. mSystems 2022; 7:e0094721. [PMID: 35166563 PMCID: PMC8845570 DOI: 10.1128/msystems.00947-21] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 01/04/2022] [Indexed: 12/20/2022] Open
Abstract
Symbiotic bacteria are responsible for the majority of complex carbohydrate digestion in the human colon. Since the identities and amounts of dietary polysaccharides directly impact the gut microbiota, determining which microorganisms consume specific nutrients is central for defining the relationship between diet and gut microbial ecology. Using a custom phenotyping array, we determined carbohydrate utilization profiles for 354 members of the Bacteroidetes, a dominant saccharolytic phylum. There was wide variation in the numbers and types of substrates degraded by individual bacteria, but phenotype-based clustering grouped members of the same species indicating that each species performs characteristic roles. The ability to utilize dietary polysaccharides and endogenous mucin glycans was negatively correlated, suggesting exclusion between these niches. By analyzing related Bacteroides ovatus/Bacteroides xylanisolvens strains that vary in their ability to utilize mucin glycans, we addressed whether gene clusters that confer this complex, multilocus trait are being gained or lost in individual strains. Pangenome reconstruction of these strains revealed a remarkably mosaic architecture in which genes involved in polysaccharide metabolism are highly variable and bioinformatics data provide evidence of interspecies gene transfer that might explain this genomic heterogeneity. Global transcriptomic analyses suggest that the ability to utilize mucin has been lost in some lineages of B. ovatus and B. xylanisolvens, which harbor residual gene clusters that are involved in mucin utilization by strains that still actively express this phenotype. Our data provide insight into the breadth and complexity of carbohydrate metabolism in the microbiome and the underlying genomic events that shape these behaviors. IMPORTANCE Nonharmful bacteria are the primary microbial symbionts that inhabit the human gastrointestinal tract. These bacteria play many beneficial roles and in some cases can modify disease states, making it important to understand which nutrients sustain specific lineages. This knowledge will in turn lead to strategies to intentionally manipulate the gut microbial ecosystem. We designed a scalable, high-throughput platform for measuring the ability of gut bacteria to utilize polysaccharides, of which many are derived from dietary fiber sources that can be manipulated easily. Our results provide paths to expand phenotypic surveys of more diverse gut bacteria to understand their functions and also to leverage dietary fibers to alter the physiology of the gut microbial community.
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Affiliation(s)
- Nicholas A. Pudlo
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Karthik Urs
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Ryan Crawford
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Ali Pirani
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Todd Atherly
- Iowa State University, Department of Animal Science, Ames, Iowa, USA
- United States Department of Agriculture Agricultural Research Station, Ames, Iowa, USA
| | - Roberto Jimenez
- University of Nebraska, Department of Food Sciences, Lincoln, Nebraska, USA
| | - Nicolas Terrapon
- Aix Marseille Univ, CNRS, UMR7257 AFMB, Marseille, France
- INRAE, USC1408 AFMB, Marseille, France
| | - Bernard Henrissat
- Aix Marseille Univ, CNRS, UMR7257 AFMB, Marseille, France
- INRAE, USC1408 AFMB, Marseille, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Daniel Peterson
- University of Nebraska, Department of Food Sciences, Lincoln, Nebraska, USA
- Johns Hopkins University, Department of Pathology, Baltimore, Maryland, USA
| | - Cherie Ziemer
- Iowa State University, Department of Animal Science, Ames, Iowa, USA
- United States Department of Agriculture Agricultural Research Station, Ames, Iowa, USA
| | - Evan Snitkin
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Eric C. Martens
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
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Genomic Update of Phenotypic Prediction Rule for Methicillin-Resistant Staphylococcus aureus (MRSA) USA300 Discloses Jail Transmission Networks with Increased Resistance. Microbiol Spectr 2021; 9:e0037621. [PMID: 34287060 PMCID: PMC8552710 DOI: 10.1128/spectrum.00376-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is a leading cause of health care-associated (HA) and community-associated (CA) infections. USA300 strains are historically CA-MRSA, while USA100 strains are HA-MRSA. Here, we update an antibiotic prediction rule to distinguish these two genotypes based on antibiotic resistance phenotype using whole-genome sequencing (WGS), a more discriminatory methodology than pulsed-field gel electrophoresis (PFGE). MRSA clinical isolates collected from 2007 to 2017 underwent WGS; associated epidemiologic data were ascertained. In developing the rule, we examined MRSA isolates that included a population with a history of incarceration. Performance characteristics of antibiotic susceptibility for predicting USA300 compared to USA100, as defined by WGS, were examined. Phylogenetic analysis was performed to examine resistant USA300 clades. We identified 275 isolates (221 USA300, 54 USA100). Combination susceptibility to clindamycin or levofloxacin performed the best overall (sensitivity 80.7%, specificity 75.9%) to identify USA300. The average number of antibiotic classes with resistance was higher for USA100 (3 versus 2, P < 0.001). Resistance to ≤2 classes was predictive for USA300 (area under the curve (AUC) 0.84, 95% confidence interval 0.78 to 0.90). Phylogenetic analysis identified a cluster of USA300 strains characterized by increased resistance among incarcerated individuals. Using a combination of clindamycin or levofloxacin susceptibility, or resistance to ≤2 antibiotic classes, was predictive of USA300 as defined by WGS. Increased resistance was observed among individuals with incarceration exposure, suggesting circulation of a more resistant USA300 clade among at-risk community networks. Our phenotypic prediction rule could be used as an epidemiologic tool to describe community and nosocomial shifts in USA300 MRSA and quickly identify emergence of lineages with increased resistance. IMPORTANCE Methicillin-resistant Staphylococcus aureus (MRSA) is an important cause of health care-associated (HA) and community-associated (CA) infections, but the epidemiology of these strains (USA100 and USA300, respectively) now overlaps in health care settings. Although sequencing technology has become more available, many health care facilities still lack the capabilities to perform these analyses. In this study, we update a simple prediction rule based on antibiotic resistance phenotype with integration of whole-genome sequencing (WGS) to predict strain type based on antibiotic resistance profiles that can be used in settings without access to molecular strain typing methods. This prediction rule has many potential epidemiologic applications, such as analysis of retrospective data sets, regional monitoring, and ongoing surveillance of CA-MRSA infection trends. We demonstrate application of this rule to identify an emerging USA300 strain with increased antibiotic resistance among incarcerated individuals that deviates from the rule.
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7
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Lapp Z, Crawford R, Miles-Jay A, Pirani A, Trick WE, Weinstein RA, Hayden MK, Snitkin ES, Lin MY. Regional Spread of blaNDM-1-Containing Klebsiella pneumoniae ST147 in Post-Acute Care Facilities. Clin Infect Dis 2021; 73:1431-1439. [PMID: 33999991 PMCID: PMC8528401 DOI: 10.1093/cid/ciab457] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND Carbapenem-resistant Enterobacterales (CRE) harboring blaKPC have been endemic in Chicago-area healthcare networks for more than a decade. During 2016-2019, a series of regional point-prevalence surveys identified increasing prevalence of blaNDM-containing CRE in multiple long-term acute care hospitals (LTACHs) and ventilator-capable skilled nursing facilities (vSNFs). We performed a genomic epidemiology investigation of blaNDM-producing CRE to understand their regional emergence and spread. METHODS We performed whole-genome sequencing on New Delhi metallo-beta-lactamase (NDM)+ CRE isolates from 4 point-prevalence surveys across 35 facilities (LTACHs, vSNFs, and acute care hospital medical intensive care units) in the Chicago area and investigated the genomic relatedness and transmission dynamics of these isolates over time. RESULTS Genomic analyses revealed that the rise of NDM+ CRE was due to the clonal dissemination of an sequence type (ST) 147 Klebsiella pneumoniae strain harboring blaNDM-1 on an IncF plasmid. Dated phylogenetic reconstructions indicated that ST147 was introduced into the region around 2013 and likely acquired NDM around 2015. Analyzing the relatedness of strains within and between facilities supported initial increases in prevalence due to intrafacility transmission in certain vSNFs, with evidence of subsequent interfacility spread among LTACHs and vSNFs connected by patient transfer. CONCLUSIONS We identified a regional outbreak of blaNDM-1 ST147 that began in and disseminated across Chicago area post-acute care facilities. Our findings highlight the importance of performing genomic surveillance at post-acute care facilities to identify emerging threats.
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Affiliation(s)
- Zena Lapp
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Ryan Crawford
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Arianna Miles-Jay
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | - Ali Pirani
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | - William E Trick
- Department of Medicine, Rush University Medical Center, Chicago, Illinois, USA,Department of Medicine, Cook County Health, 4Chicago, Illinois, USA
| | - Robert A Weinstein
- Department of Medicine, Rush University Medical Center, Chicago, Illinois, USA,Department of Medicine, Cook County Health, 4Chicago, Illinois, USA
| | - Mary K Hayden
- Department of Medicine, Rush University Medical Center, Chicago, Illinois, USA,Department of Pathology, Rush University Medical Center, Chicago, Illinois, USA
| | - Evan S Snitkin
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | - Michael Y Lin
- Department of Medicine, Rush University Medical Center, Chicago, Illinois, USA,Correspondence: M. Y. Lin, Department of Medicine, Division of Infectious Diseases, Rush University Medical Center, 600 S Paulina St, Ste 143, Chicago, IL 60612 ()
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