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Xie M, Ye L, Chen K, Xu Q, Yang C, Chen X, Chan EWC, Li F, Chen S. Clinical use of tigecycline may contribute to the widespread dissemination of carbapenem-resistant hypervirulent Klebsiella pneumoniae strains. Emerg Microbes Infect 2024; 13:2306957. [PMID: 38240375 PMCID: PMC10829843 DOI: 10.1080/22221751.2024.2306957] [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] [Received: 10/22/2023] [Accepted: 01/14/2024] [Indexed: 02/01/2024]
Abstract
The emergence of carbapenem-resistant hypervirulent Klebsiella pneumoniae (CR-hvKP) poses grave threats to human health. These strains increased dramatically in clinical settings in China in the past few years but not in other parts of the world. Four isogenic K. pneumoniae strains, including classical K. pneumoniae, carbapenem-resistant K. pneumoniae (CRKP), hypervirulent K. pneumoniae (hvKP) and CR-hvKP, were created and subjected to phenotypic characterization, competition assays, mouse sepsis model and rat colonization tests to investigate the mechanisms underlying the widespread nature of CR-hvKP in China. Acquisition of virulence plasmid led to reduced fitness and abolishment of colonization in the gastrointestinal tract, which may explain why hvKP is not clinically prevalent after its emergence for a long time. However, tigecycline treatment facilitated the colonization of hvKP and CR-hvKP and reduced the population of Lactobacillus spp. in animal gut microbiome. Feeding with Lactobacillus spp. could significantly reduce the colonization of hvKP and CR-hvKP in the animal gastrointestinal tract. Our data implied that the clinical use of tigecycline to treat carbapenem-resistant K. pneumoniae infections facilitated the high spread of CR-hvKP in clinical settings in China and demonstrated that Lactobacillus spp. was a potential candidate for anticolonization strategy against CR-hvKP.
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Affiliation(s)
- Miaomiao Xie
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong
- Department of Food Science and Nutrition, Faculty of Science, The Hong Kong Polytechnic University, Kowloon, Hong Kong
| | - Lianwei Ye
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong
| | - Kaichao Chen
- Department of Food Science and Nutrition, Faculty of Science, The Hong Kong Polytechnic University, Kowloon, Hong Kong
| | - Qi Xu
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong
| | - Chen Yang
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong
| | - Xiangnan Chen
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong
| | - Edward Wai-Chi Chan
- State Key Lab of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Kowloon, Hong Kong
| | - Fuyong Li
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong
| | - Sheng Chen
- Department of Food Science and Nutrition, Faculty of Science, The Hong Kong Polytechnic University, Kowloon, Hong Kong
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2
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Vornhagen J, Rao K, Bachman MA. Gut community structure as a risk factor for infection in Klebsiella pneumoniae-colonized patients. mSystems 2024; 9:e0078624. [PMID: 38975759 PMCID: PMC11334466 DOI: 10.1128/msystems.00786-24] [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: 06/10/2024] [Accepted: 06/11/2024] [Indexed: 07/09/2024] Open
Abstract
The primary risk factor for infection with members of the Klebsiella pneumoniae species complex is prior gut colonization, and infection is often caused by the colonizing strain. Despite the importance of the gut as a reservoir for infectious K. pneumoniae, little is known about the association between the gut microbiome and infection. To explore this relationship, we undertook a case-control study comparing the gut community structure of K. pneumoniae-colonized intensive care and hematology/oncology patients. Cases were K. pneumoniae-colonized patients infected by their colonizing strain (N = 83). Controls were K. pneumoniae-colonized patients who remained asymptomatic (N = 149). First, we characterized the gut community structure of K. pneumoniae-colonized patients agnostic to case status. Next, we determined that gut community data is useful for classifying cases and controls using machine learning models and that the gut community structure differed between cases and controls. K. pneumoniae relative abundance, a known risk factor for infection, had the greatest feature importance, but other gut microbes were also informative. Finally, we show that integration of gut community structure with bacterial genotype data enhanced the ability of machine learning models to discriminate cases and controls. Interestingly, inclusion of patient clinical variables failed to improve the ability of machine learning models to discriminate cases and controls. This study demonstrates that including gut community data with K. pneumoniae-derived biomarkers improves our ability to classify infection in K. pneumoniae-colonized patients.IMPORTANCEColonization is generally the first step in pathogenesis for bacteria with pathogenic potential. This step provides a unique window for intervention since a given potential pathogen has yet to cause damage to its host. Moreover, intervention during the colonization stage may help alleviate the burden of therapy failure as antimicrobial resistance rises. Yet, to understand the therapeutic potential of interventions that target colonization, we must first understand the biology of colonization and if biomarkers at the colonization stage can be used to stratify infection risk. The bacterial genus Klebsiella includes many species with varying degrees of pathogenic potential. Members of the K. pneumoniae species complex have the highest pathogenic potential. Patients colonized in their gut by these bacteria are at higher risk of subsequent infection with their colonizing strain. However, we do not understand if other members of the gut microbiota can be used as a biomarker to predict infection risk. In this study, we show that the gut microbiota differs between colonized patients who develop an infection versus those who do not. Additionally, we show that integrating gut microbiota data with bacterial factors improves the ability to classify infections. Surprisingly, patient clinical factors were not useful for classifying infections alone or when added to microbiota-based models. This indicates that the bacterial genotype and the microbial community in which it exists may determine the progression to infection. As we continue to explore colonization as an intervention point to prevent infections in individuals colonized by potential pathogens, we must develop effective means for predicting and stratifying infection risk.
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Affiliation(s)
- Jay Vornhagen
- Department of Microbiology & Immunology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Krishna Rao
- Department of Internal Medicine/Infectious Diseases Division, Michigan Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Michael A. Bachman
- Department of Pathology, Michigan Medicine, University of Michigan, Ann Arbor, Michigan, USA
- Department of Microbiology & Immunology, Michigan Medicine, University of Michigan, Ann Arbor, Michigan, USA
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Zhang SL, McGann CM, Duranova T, Strysko J, Steenhoff AP, Gezmu A, Nakstad B, Arscott-Mills T, Bayani O, Moorad B, Tlhako N, Richard-Greenblatt M, Planet PJ, Coffin SE, Silverman MA. Maternal and neonatal IgG against Klebsiella pneumoniae are associated with broad protection from neonatal sepsis: a case-control study of hospitalized neonates in Botswana. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.28.24308042. [PMID: 38854006 PMCID: PMC11160826 DOI: 10.1101/2024.05.28.24308042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Sepsis is the leading postnatal cause of neonatal mortality worldwide. Globally Klebsiella pneumoniae is the leading cause of sepsis in hospitalized neonates. This study reports development and evaluation of ELISA for anti-Klebsiella IgG using dried blood spot samples and evaluates the association of anti-Klebsiella IgG (anti-Kleb IgG) antibodies in maternal and neonatal samples and the risk of neonatal sepsis. Neonates and their mothers were enrolled at 0-96 hours of life in the neonatal unit of a tertiary referral hospital in Gaborone, Botswana and followed until death or discharge to assess for episodes of blood culture-confirmed neonatal sepsis. Neonates with sepsis had significantly lower levels of Kleb-IgG compared to neonates who did not develop sepsis (Mann-Whitney U, p=0.012). Similarly, samples from mothers of neonates who developed sepsis tended to have less Kleb-IgG compared to mothers of controls (p=0.06). The inverse correlation between Kleb-IgG levels and all-cause bacteremia suggests that maternal Kleb-IgG is broadly protective through cross-reactivity with common bacterial epitopes. These data support the continued use of immunoglobulin assays using DBS samples to explore the role of passive immunity on neonatal sepsis risk and reaffirm the critical need for research supporting the development of maternal vaccines for neonatal sepsis.
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Affiliation(s)
- Siqi Linsey Zhang
- Division of Infectious Diseases, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Carolyn M McGann
- Division of Neonatology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Tereza Duranova
- Division of Infectious Diseases, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Jonathan Strysko
- Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Botswana-University of Pennsylvania Partnership, Gaborone, Botswana
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Andrew P Steenhoff
- Division of Infectious Diseases, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Botswana-University of Pennsylvania Partnership, Gaborone, Botswana
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Alemayehu Gezmu
- Faculties of Medicine & Health Sciences, Department of Paediatric & Adolescent Health, University of Botswana, Gaborone, Botswana
| | - Britt Nakstad
- Faculties of Medicine & Health Sciences, Department of Paediatric & Adolescent Health, University of Botswana, Gaborone, Botswana
| | - Tonya Arscott-Mills
- Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Botswana-University of Pennsylvania Partnership, Gaborone, Botswana
| | - One Bayani
- Faculties of Medicine & Health Sciences, Department of Paediatric & Adolescent Health, University of Botswana, Gaborone, Botswana
| | - Banno Moorad
- Botswana-University of Pennsylvania Partnership, Gaborone, Botswana
| | - Nametso Tlhako
- Botswana-University of Pennsylvania Partnership, Gaborone, Botswana
| | - Melissa Richard-Greenblatt
- Hospital for Sick Children, Toronto, Canada
- Department of Laboratory and Pathobiology, University of Toronto, Canada
| | - Paul J Planet
- Division of Infectious Diseases, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Susan E Coffin
- Division of Infectious Diseases, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Michael A Silverman
- Division of Infectious Diseases, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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4
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Wang Z, Shao C, Shao J, Hao Y, Jin Y. Risk factors of Carbapenem-resistant Enterobacterales intestinal colonization for subsequent infections in hematological patients: a retrospective case-control study. Front Microbiol 2024; 15:1355069. [PMID: 38680915 PMCID: PMC11045900 DOI: 10.3389/fmicb.2024.1355069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 04/01/2024] [Indexed: 05/01/2024] Open
Abstract
Objective Infections caused by Carbapenem-resistant Enterobacterales (CRE) have high treatment costs, high mortality and few effective therapeutic agents. This study aimed to determine the risk factors for progression from intestinal colonization to infection in hematological patients and the risk factors for 30-day mortality in infected patients. Methods A retrospective case-control study was conducted in the Department of Hematology at Shandong Provincial Hospital affiliated to Shandong First Medical University from April 2018 to April 2022. Patients who developed subsequent infections were identified as the case group by electronic medical record query of patients with a positive rectal screen for CRE colonization, and patients who did not develop subsequent infections were identified as the control group by stratified random sampling. Univariate analysis and logistic regression analysis determined risk factors for developing CRE infection and risk factors for mortality in CRE-infected patients. Results Eleven hematological patients in the study developed subsequent infections. The overall 30-day mortality rate for the 44 hematological patients in the case-control study was 11.4% (5/44). Mortality was higher in the case group than in the control group (36.5 vs. 3.0%, P = 0.0026), and septic shock was an independent risk factor for death (P = 0.024). Univariate analysis showed that risk factors for developing infections were non-steroidal immunosuppressants, serum albumin levels, and days of hospitalization. In multivariable logistic regression analysis, immunosuppressants [odds ratio (OR), 19.132; 95% confidence interval (CI), 1.349-271.420; P = 0.029] and serum albumin levels (OR, 0.817; 95% CI, 0.668-0.999; P = 0.049) were independent risk factors for developing infections. Conclusion Our findings suggest that septic shock increases mortality in CRE-infected hematological patients. Hematological patients with CRE colonization using immunosuppressive agents and reduced serum albumin are more likely to progress to CRE infection. This study may help clinicians prevent the onset of infection early and take measures to reduce mortality rates.
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Affiliation(s)
| | | | | | | | - Yan Jin
- Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
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5
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Kijineh B, Alemeyhu T, Mengistu M, Ali MM. Prevalence of phenotypic multi-drug resistant Klebsiella species recovered from different human specimens in Ethiopia: A systematic review and meta-analysis. PLoS One 2024; 19:e0297407. [PMID: 38335186 PMCID: PMC10857728 DOI: 10.1371/journal.pone.0297407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 01/04/2024] [Indexed: 02/12/2024] Open
Abstract
BACKGROUND Multidrug-resistant (MDR) Klebsiella species are among public health important bacteria that cause infections difficult to treat with available antimicrobial agents. Infections with Klebsiella lead to high morbidity and mortality in developing countries particularly in patients admitted to the intensive care unit. This systematic review and meta-analysis aimed to determine the pooled prevalence of MDR Klebsiella species from different human specimens using studies conducted in Ethiopia from 2018-2022. METHODS We have systematically searched online databases such as PubMed/Medline, Google Scholar, Hinari, African journals online, Web of Science, Cochrane, and grey literature (Addis Ababa University and Hawassa University) to identify studies reporting the proportion of MDR Klebsiella species in Ethiopia. Published articles were selected based on the Preferred Reporting Item of Systematic Review and Meta-analysis (PRISMA). R-Studio version 4.2.3 was used to conduct pooled prevalence, heterogeneity test, and publication bias. A binary random effect model was used to determine the pooled prevalence. Heterogeneity was checked with the inconsistency index (I2). Publication bias was checked with a funnel plot and Egger test. Sensitivity analysis was conducted with leave-one-out analysis. Joanna Briggs Institute's critical appraisal tool for prevalence studies was used to check the quality of each article. RESULTS In this systematic review and meta-analysis, 40 articles were included in which 12,239 human specimens were examined. Out of the total specimens examined, 721 Klebsiella species were isolated and 545 isolates were reported to be MDR Klebsiella species. The prevalence of MDR Klebsiella species ranged from 7.3%-100% whereas the pooled prevalence of MDR Klebsiella species was 72% (95% CI: 63 - 82%, I2 = 95%). Sub-group analysis based on region revealed the highest prevalence of MDR from Addis Ababa (97%) and the least from the Somali region (33%); whereas sub-group analysis based on the specimen type indicated the highest prevalence was from blood culture specimens 96% and the least was from other specimens (ear and vaginal discharge, and stool) (51%). CONCLUSION Our finding indicated a high prevalence of MDR Klebsiella species found in different human specimens. The prevalence of MDR Klebsiella varies across regions in Ethiopia, age, the type of specimens, source and site of infection. Therefore, integrated action should be taken to reduce the prevalence of MDR Klebsiella species in regional states and focus on clinical features. Effective infection and prevention control should be applied to reduce the transmission within and outside health care settings.
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Affiliation(s)
- Biniyam Kijineh
- Department of Medical Laboratory Science, Wachemo University College of Medicine and Health Sciences, Hossana, Ethiopia
| | - Tsegaye Alemeyhu
- School of Medical Laboratory Science, Hawassa University College of Medicine and Health Sciences, Hawassa, Ethiopia
| | - Mulugeta Mengistu
- School of Medical Laboratory Science, Hawassa University College of Medicine and Health Sciences, Hawassa, Ethiopia
| | - Musa Mohammed Ali
- School of Medical Laboratory Science, Hawassa University College of Medicine and Health Sciences, Hawassa, Ethiopia
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Raffelsberger N, Buczek DJ, Svendsen K, Småbrekke L, Pöntinen AK, Löhr IH, Andreassen LLE, Simonsen GS, Sundsfjord A, Gravningen K, Samuelsen Ø. Community carriage of ESBL-producing Escherichia coli and Klebsiella pneumoniae: a cross-sectional study of risk factors and comparative genomics of carriage and clinical isolates. mSphere 2023; 8:e0002523. [PMID: 37306968 PMCID: PMC10470604 DOI: 10.1128/msphere.00025-23] [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: 01/17/2023] [Accepted: 04/05/2023] [Indexed: 06/13/2023] Open
Abstract
The global prevalence of infections caused by extended-spectrum β-lactamase-producing Enterobacterales (ESBL-E) is increasing, and for Escherichia coli, observations indicate that this is partly driven by community-onset cases. The ESBL-E population structure in the community is scarcely described, and data on risk factors for carriage are conflicting. Here, we report the prevalence and population structure of fecal ESBL-producing E. coli and Klebsiella pneumoniae (ESBL-Ec/Kp) in a general adult population, examine risk factors, and compare carriage isolates with contemporary clinical isolates. Fecal samples obtained from 4,999 participants (54% women) ≥40 years in the seventh survey of the population-based Tromsø Study, Norway (2015, 2016), were screened for ESBL-Ec/Kp. In addition, we included 118 ESBL-Ec clinical isolates from the Norwegian surveillance program in 2014. All isolates were whole-genome sequenced. Risk factors associated with carriage were analyzed using multivariable logistic regression. ESBL-Ec gastrointestinal carriage prevalence was 3.3% [95% confidence interval (CI) 2.8%-3.9%, no sex difference] and 0.08% (0.02%-0.20%) for ESBL-Kp. For ESBL-Ec, travel to Asia was the only independent risk factor (adjusted odds ratio 3.46, 95% CI 2.18-5.49). E. coli ST131 was most prevalent in both collections. However, the ST131 proportion was significantly lower in carriage (24%) versus clinical isolates (58%, P < 0.001). Carriage isolates were genetically more diverse with a higher proportion of phylogroup A (26%) than clinical isolates (5%, P < 0.001), indicating that ESBL gene acquisition occurs in a variety of E. coli lineages colonizing the gut. STs commonly related to extraintestinal infections were more frequent in clinical isolates also carrying a higher prevalence of antimicrobial resistance, which could indicate clone-associated pathogenicity.IMPORTANCEESBL-Ec and ESBL-Kp are major pathogens in the global burden of antimicrobial resistance. However, there is a gap in knowledge concerning the bacterial population structure of human ESBL-Ec/Kp carriage isolates in the community. We have examined ESBL-Ec/Kp isolates from a population-based study and compared these to contemporary clinical isolates. The large genetic diversity of carriage isolates indicates frequent ESBL gene acquisition, while those causing invasive infections are more clone dependent and associated with a higher prevalence of antibiotic resistance. The knowledge of factors associated with ESBL carriage helps to identify patients at risk to combat the spread of resistant bacteria within the healthcare system. Particularly, previous travel to Asia stands out as a major risk factor for carriage and should be considered in selecting empirical antibiotic treatment in critically ill patients.
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Affiliation(s)
- Niclas Raffelsberger
- Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
- Department of Medical Biology, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Dorota Julia Buczek
- Department of Medical Biology, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Kristian Svendsen
- Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Lars Småbrekke
- Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Anna Kaarina Pöntinen
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
- Department of Biostatistics, University of Oslo, Oslo, Norway
| | - Iren H. Löhr
- Department of Medical Microbiology, Stavanger University Hospital, Stavanger, Norway
| | | | - Gunnar Skov Simonsen
- Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
- Department of Medical Biology, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Norwegian E. coli ESBL Study Group
- Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
- Department of Medical Biology, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
- Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
- Department of Biostatistics, University of Oslo, Oslo, Norway
- Department of Medical Microbiology, Stavanger University Hospital, Stavanger, Norway
- Department of Microbiology and Infection Control, Akershus University Hospital, Nordbyhagen, Norway
- Division of Medicine and Laboratory Sciences, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Arnfinn Sundsfjord
- Department of Medical Biology, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - Kirsten Gravningen
- Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
- Department of Microbiology and Infection Control, Akershus University Hospital, Nordbyhagen, Norway
- Division of Medicine and Laboratory Sciences, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Ørjan Samuelsen
- Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
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Coleman S, Unterhauser K, Rezaul K, Ledala N, Lesmes S, Caimano MJ, Zhou Y, Jackson E, Gratalo D, Driscoll MD, Matson AP. High-resolution microbiome analysis reveals exclusionary Klebsiella species competition in preterm infants at risk for necrotizing enterocolitis. Sci Rep 2023; 13:7893. [PMID: 37193703 DOI: 10.1038/s41598-023-34735-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 05/06/2023] [Indexed: 05/18/2023] Open
Abstract
Intestinal colonization with Klebsiella has been linked to necrotizing enterocolitis (NEC), but methods of analysis usually failed to discriminate Klebsiella species or strains. A novel ~ 2500-base amplicon (StrainID) that spans the 16S and 23S rRNA genes was used to generate amplicon sequence variant (ASV) fingerprints for Klebsiella oxytoca and Klebsiella pneumoniae species complexes (KoSC and KpSC, respectively) and co-occurring fecal bacterial strains from 10 preterm infants with NEC and 20 matched controls. Complementary approaches were used to identify cytotoxin-producing isolates of KoSC. Klebsiella species colonized most preterm infants, were more prevalent in NEC subjects versus controls, and replaced Escherichia in NEC subjects. Single KoSC or KpSC ASV fingerprinted strains dominated the gut microbiota, suggesting exclusionary Klebsiella competition for luminal resources. Enterococcus faecalis was co-dominant with KoSC but present infrequently with KpSC. Cytotoxin-producing KoSC members were identified in most NEC subjects and were less frequent in controls. Few Klebsiella strains were shared between subjects. We conclude that inter-species Klebsiella competition, within an environment of KoSC and E. faecalis cooperation, appears to be an important factor for the development of NEC. Preterm infants seem to acquire Klebsiella primarily through routes other than patient-to-patient transmission.
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Affiliation(s)
- Spencer Coleman
- Department of Pediatrics, UConn Health, Farmington, CT, USA
- University of Connecticut School of Medicine, 263 Farmington Avenue, Farmington, CT, 06030, USA
| | | | - Karim Rezaul
- Department of Pediatrics, UConn Health, Farmington, CT, USA
| | | | - Stephanie Lesmes
- Department of Research, Connecticut Children's Medical Center, Hartford, CT, USA
| | - Melissa J Caimano
- Department of Pediatrics, UConn Health, Farmington, CT, USA
- Department of Medicine, UConn Health, Farmington, CT, USA
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, USA
| | - Yanjiao Zhou
- Department of Medicine, UConn Health, Farmington, CT, USA
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | | | | | - Adam P Matson
- Department of Pediatrics, UConn Health, Farmington, CT, USA.
- Division of Neonatology, Connecticut Children's Medical Center, Hartford, CT, USA.
- Department of Immunology, UConn Health, Farmington, CT, USA.
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8
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Vornhagen J, Rao K, Bachman MA. Gut community structure as a risk factor for infection in Klebsiella -colonized patients. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.04.18.23288742. [PMID: 37131824 PMCID: PMC10153327 DOI: 10.1101/2023.04.18.23288742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The primary risk factor for infection with members of the Klebsiella pneumoniae species complex is prior gut colonization, and infection is often caused by the colonizing strain. Despite the importance of the gut as a reservoir for infectious Klebsiella , little is known about the association between the gut microbiome and infection. To explore this relationship, we undertook a case-control study comparing the gut community structure of Klebsiella -colonized intensive care and hematology/oncology patients. Cases were Klebsiella -colonized patients infected by their colonizing strain (N = 83). Controls were Klebsiella -colonized patients that remained asymptomatic (N = 149). First, we characterized the gut community structure of Klebsiella -colonized patients agnostic to case status. Next, we determined that gut community data is useful for classifying cases and controls using machine learning models and that the gut community structure differed between cases and controls. Klebsiella relative abundance, a known risk factor for infection, had the greatest feature importance but other gut microbes were also informative. Finally, we show that integration of gut community structure with bacterial genotype or clinical variable data enhanced the ability of machine learning models to discriminate cases and controls. This study demonstrates that including gut community data with patient- and Klebsiella -derived biomarkers improves our ability to predict infection in Klebsiella -colonized patients. Importance Colonization is generally the first step in pathogenesis for bacteria with pathogenic potential. This step provides a unique window for intervention since a given potential pathogen has yet to cause damage to its host. Moreover, intervention during the colonization stage may help alleviate the burden of therapy failure as antimicrobial resistance rises. Yet, to understand the therapeutic potential of interventions that target colonization, we must first understand the biology of colonization and if biomarkers at the colonization stage can be used to stratify infection risk. The bacterial genus Klebsiella includes many species with varying degrees of pathogenic potential. Members of the K. pneumoniae species complex have the highest pathogenic potential. Patients colonized in their gut by these bacteria are at higher risk of subsequent infection with their colonizing strain. However, we do not understand if other members of the gut microbiota can be used as a biomarker to predict infection risk. In this study, we show that the gut microbiota differs between colonized patients that develop an infection versus those that do not. Additionally, we show that integrating gut microbiota data with patient and bacterial factors improves the ability to predict infections. As we continue to explore colonization as an intervention point to prevent infections in individuals colonized by potential pathogens, we must develop effective means for predicting and stratifying infection risk.
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9
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Mason S, Vornhagen J, Smith SN, Mike LA, Mobley HLT, Bachman MA. The Klebsiella pneumoniae ter Operon Enhances Stress Tolerance. Infect Immun 2023; 91:e0055922. [PMID: 36651775 PMCID: PMC9933665 DOI: 10.1128/iai.00559-22] [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: 12/19/2022] [Accepted: 12/21/2022] [Indexed: 01/19/2023] Open
Abstract
Healthcare-acquired infections are a leading cause of disease in patients that are hospitalized or in long-term-care facilities. Klebsiella pneumoniae (Kp) is a leading cause of bacteremia, pneumonia, and urinary tract infections in these settings. Previous studies have established that the ter operon, a genetic locus that confers tellurite oxide (K2TeO3) resistance, is associated with infection in colonized patients. Rather than enhancing fitness during infection, the ter operon increases Kp fitness during gut colonization; however, the biologically relevant function of this operon is unknown. First, using a murine model of urinary tract infection, we demonstrate a novel role for the ter operon protein TerC as a bladder fitness factor. To further characterize TerC, we explored a variety of functions, including resistance to metal-induced stress, resistance to radical oxygen species-induced stress, and growth on specific sugars, all of which were independent of TerC. Then, using well-defined experimental guidelines, we determined that TerC is necessary for tolerance to ofloxacin, polymyxin B, and cetylpyridinium chloride. We used an ordered transposon library constructed in a Kp strain lacking the ter operon to identify the genes that are required to resist K2TeO3-induced and polymyxin B-induced stress, which suggested that K2TeO3-induced stress is experienced at the bacterial cell envelope. Finally, we confirmed that K2TeO3 disrupts the Kp cell envelope, though these effects are independent of ter. Collectively, the results from these studies indicate a novel role for the ter operon as a stress tolerance factor, thereby explaining its role in enhancing fitness in the gut and bladder.
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Affiliation(s)
- Sophia Mason
- Department of Pathology, Michigan Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Jay Vornhagen
- Department of Pathology, Michigan Medicine, University of Michigan, Ann Arbor, Michigan, USA
- Department of Microbiology & Immunology, Michigan Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Sara N. Smith
- Department of Microbiology & Immunology, Michigan Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Laura A. Mike
- Department of Medical Microbiology & Immunology, University of Toledo, Toledo, Ohio, USA
| | - Harry L. T. Mobley
- Department of Microbiology & Immunology, Michigan Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Michael A. Bachman
- Department of Pathology, Michigan Medicine, University of Michigan, Ann Arbor, Michigan, USA
- Department of Microbiology & Immunology, Michigan Medicine, University of Michigan, Ann Arbor, Michigan, USA
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10
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Evans T, Ali U, Anderton R, Raby E, Manning L, Litton E. Lower gut dysbiosis and mortality in acute critical illness: a systematic review and meta-analysis. Intensive Care Med Exp 2023; 11:6. [PMID: 36732439 PMCID: PMC9895325 DOI: 10.1186/s40635-022-00486-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 12/17/2022] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND The human gastrointestinal tract harbours a complex multi-kingdom community known as the microbiome. Dysbiosis refers to its disruption and is reportedly extreme in acute critical illness yet its clinical implications are unresolved. The review systematically evaluates the association between gut dysbiosis and clinical outcomes of patients early in critical illness. METHODS Following PRISMA guidelines, a prospectively registered search was undertaken of MEDLINE and Cochrane databases for observational studies undertaking metagenomic sequencing of the lower gastrointestinal tract of critically ill adults and children within 72 h of admission. Eligible studies reported an alpha diversity metric and one or more of the primary outcome, in-hospital mortality, or secondary clinical outcomes. After aggregate data were requested, meta-analysis was performed for four studies with in-hospital mortality stratified to high or low Shannon index. RESULTS The search identified 26 studies for systematic review and 4 had suitable data for meta-analysis. No effect of alpha diversity was seen on in-hospital mortality after binary transformation of Shannon index (odds ratio 0.52, CI 0.12-4.98, I2 = 0.64) however certainty of evidence is low. Pathogen dominance and commensal depletion were each more frequently associated with in-hospital mortality, adverse clinical and ecological sequelae, particularly overabundance of Enterococcus. CONCLUSIONS There is a paucity of large, rigorous observational studies in this population. Globally, alpha diversity was dynamically reduced in early ICU admission in adults and children and was not associated with in-hospital mortality. The abundance of taxa such as Enterococcus spp. appears to offer greater predictive capacity for important clinical and ecological outcomes.
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Affiliation(s)
- Tess Evans
- grid.459958.c0000 0004 4680 1997Intensive Care Unit, Fiona Stanley Hospital, South Metropolitan Health Service, WA Health, Perth, Australia ,grid.1012.20000 0004 1936 7910School of Medicine, University of Western Australia, Nedlands, Australia
| | - Umar Ali
- grid.1012.20000 0004 1936 7910School of Medicine, University of Western Australia, Nedlands, Australia
| | - Ryan Anderton
- grid.266886.40000 0004 0402 6494School of Health Sciences, University of Notre Dame Australia (Fremantle), Fremantle, Australia
| | - Edward Raby
- grid.459958.c0000 0004 4680 1997Department of Infectious Diseases, Fiona Stanley Hospital, South Metropolitan Health Service, WA Health, Perth, Australia ,grid.1012.20000 0004 1936 7910School of Medicine, University of Western Australia, Nedlands, Australia
| | - Laurens Manning
- grid.459958.c0000 0004 4680 1997Department of Infectious Diseases, Fiona Stanley Hospital, South Metropolitan Health Service, WA Health, Perth, Australia ,grid.1012.20000 0004 1936 7910School of Medicine, University of Western Australia, Nedlands, Australia
| | - Edward Litton
- grid.459958.c0000 0004 4680 1997Intensive Care Unit, Fiona Stanley Hospital, South Metropolitan Health Service, WA Health, Perth, Australia ,grid.1012.20000 0004 1936 7910School of Medicine, University of Western Australia, Nedlands, Australia
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11
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Herrera G, Arboleda JC, Pérez-Jaramillo JE, Patarroyo MA, Ramírez JD, Muñoz M. Microbial Interdomain Interactions Delineate the Disruptive Intestinal Homeostasis in Clostridioides difficile Infection. Microbiol Spectr 2022; 10:e0050222. [PMID: 36154277 PMCID: PMC9602525 DOI: 10.1128/spectrum.00502-22] [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: 02/08/2022] [Accepted: 09/06/2022] [Indexed: 11/20/2022] Open
Abstract
Clostridioides difficile infection (CDI) creates an imbalance in the intestinal microbiota due to the interaction of the components making up this ecosystem, but little is known about the impact of this disease on other microbial members. This work has thus been aimed at evaluating the taxonomic composition, potential gene-associated functions, virulence factors, and antimicrobial resistance profiles of gut microbiomes. A total of 48 DNA samples obtained from patients with health care facility-acquired (HCFO) and community-onset (CO) diarrhea were distributed in the following four groups according to CDI status: HCFO/+ (n = 13), HCFO/- (n = 8), CO/+ (n = 13), and CO/- (n = 14). These samples were subjected to shotgun metagenomics sequencing. Although the CDI groups' microbiota had microbiome alterations, the greatest imbalance was observed in the in the HCFO+/- groups, with an increase in common pathogens and phage populations, as well as a decrease in beneficial microorganisms that leads to a negative impact on some intestinal homeostasis-related metabolic processes. A reduction in the relative abundance of butyrate metabolism-associated genes was also detected in the HCFO groups (P < 0.01), with an increase in some virulence factors and antibiotic-resistance markers. A set of 51 differentially abundant species in the groups with potential association to CDI enabled its characterization, leading to their spatial separation by onset. Strong correlations between phages and some archaeal and bacterial phyla were identified. This highlighted the need to study the microbiota's various components since their imbalance is multifactorial, with some pathogens contributing to a greater or lesser extent because of their interaction with the ecosystem they inhabit. IMPORTANCE Clostridioides difficile infection represents a serious public health problem in different countries due to its high morbi-mortality and the high costs it represents for health care systems. Studies have shown the impact of this infection on intestinal microbiome homeostasis, mainly on bacterial populations. Our research provides evidence of the impact of CDI at both the compositional (bacteria, archaea, and viruses), and functional levels, allowing us to understand that the alterations of the microbiota occur systemically and are caused by multiple perturbations generated by different members of the microbiota as well as by some pathogens that take advantage of the imbalance to proliferate. Likewise, the 51 differentially abundant species in the study groups with potential association to CDI found in this study could help us envisage future treatments against this and other inflammatory diseases, improving future therapeutic options for patients.
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Affiliation(s)
- Giovanny Herrera
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Juan Camilo Arboleda
- Unidad de Bioprospección and Estudio de Microbiomas, Programa de Estudio y Control de Enfermedades Tropicales (PECET), Sede de Investigación Universitaria, Universidad de Antioquia, Medellín, Colombia
- Semillero de Investigación en Bioinformática-GenomeSeq, Seccional Oriente, Universidad de Antioquia, Medellín, Colombia
- Grupo de Fundamentos y Enseñanza de la Física y los Sistemas Dinámicos, Instituto de Biología, Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia, Medellín, Colombia
| | - Juan E. Pérez-Jaramillo
- Semillero de Investigación en Bioinformática-GenomeSeq, Seccional Oriente, Universidad de Antioquia, Medellín, Colombia
- Grupo de Fundamentos y Enseñanza de la Física y los Sistemas Dinámicos, Instituto de Biología, Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia, Medellín, Colombia
| | - Manuel Alfonso Patarroyo
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
- Microbiology Department, Faculty of Medicine, Universidad Nacional de Colombia, Bogotá, Colombia
- Health Sciences Division, Universidad Santo Tomás, Bogotá, Colombia
| | - Juan David Ramírez
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
- Molecular Microbiology Laboratory, Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Marina Muñoz
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
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12
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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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13
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Zhu R, Xu X, Lian S, Cai M, Zhang H, Chen X, Cao Y. Intestinal Colonization with Carbapenem-Resistant Enterobacteriaceae in Acute Leukemia Patients: Risk Factors and Molecular Characteristics. Infect Drug Resist 2022; 15:4275-4283. [PMID: 35965853 PMCID: PMC9365016 DOI: 10.2147/idr.s376413] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 07/29/2022] [Indexed: 11/23/2022] Open
Abstract
Background Carbapenem-resistant Enterobacteriaceae (CRE) colonization is associated with bacterial translocation, which can result in subsequent endogenous CRE infection. In the present study, we aim to investigate the colonization-related risk factors and molecular epidemiological characteristics of CRE in patients with acute leukemia. Methods From January 2021 to December 2021, acute leukemia patients were screened for CRE by fecal/perianal swabs. We identified the species, carbapenemase-encoding genes, and virulence genes of the colonizing strains and performed antimicrobial susceptibility tests and ERIC-PCR typing. Risk factors for CRE colonization were identified by univariate and multivariate analysis. Results We collected a total of 21 colonizing strains from 320 patients. All strains were resistant to meropenem. Klebsiella pneumoniae was the most abundant species, and ERIC-PCR typing showed low diversity. Univariate analysis showed that age, cephalosporins, penicillins, tigecyclines, and hematopoietic stem cell transplantation status were risk factors for CRE colonization; simultaneously discovered CRE strains played a dominant role in invasive infection of colonized patients. Logistic multivariate regression analysis showed that age, cephalosporins, and tigecyclines were independent risk factors for CRE intestinal colonization. Conclusion CRE colonization can increase the incidence of CRE infection in patients with acute leukemia. Early detection of CRE colonization through CRE screening is an important measure to control the spread of CRE.
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Affiliation(s)
- Rongping Zhu
- Department of Clinical Laboratory, Fujian Medical University Union Hospital, Fuzhou, 350001, People’s Republic of China
| | - Xiaohong Xu
- Department of Clinical Laboratory, Fujian Medical University Union Hospital, Fuzhou, 350001, People’s Republic of China
| | - Siyan Lian
- Department of Clinical Laboratory, Fujian Medical University Union Hospital, Fuzhou, 350001, People’s Republic of China
| | - Meili Cai
- Department of Clinical Laboratory, Fujian Medical University Union Hospital, Fuzhou, 350001, People’s Republic of China
| | - Hui Zhang
- Fujian Medical University, Fuzhou, 350001, People’s Republic of China
| | - Xin Chen
- Fujian Medical University, Fuzhou, 350001, People’s Republic of China
| | - Yingping Cao
- Department of Clinical Laboratory, Fujian Medical University Union Hospital, Fuzhou, 350001, People’s Republic of China
- Correspondence: Yingping Cao, Department of Clinical Laboratory, Fujian Medical University Union Hospital, Fuzhou, 350001, People’s Republic of China, Tel +86 13365910806, Email
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14
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The importance of active surveillance of carbapenem-resistant Enterobacterales (CRE) in colonization rates in critically ill patients. PLoS One 2022; 17:e0262554. [PMID: 35051212 PMCID: PMC8775193 DOI: 10.1371/journal.pone.0262554] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 12/28/2021] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVE This study aimed to demonstrate the importance of active carbapenem-resistant Enterobacterales (CRE) surveillance and evaluate the prevalence of invasive infections, risk factors, and mortality risk in CRE-colonized patients. METHODS Retrospective cohort study analyzing 1,920 patients identified using an active CRE surveillance protocol, admitted to an adult intensive care unit in southeastern Brazil from January 2014 to December 2018. RESULTS There were 297 (15.47%) CRE colonized patients, with one colonized for every six control patients. CRE-colonized patients demonstrated an increased chance of infection (odds ratio [OR] 7.967, p < 0.001). Overall, 20.54% of the colonized patients presented invasive infection (81.96% due to Klebsiella pneumoniae). The colonization and infection ratio demonstrated the important role of the active CRE surveillance protocol. There were identified multiple risk factors for CRE colonization, including long-term mechanical ventilation (OR 1.624, p = 0.019) and previous exposure to aminopenicillins (OR 5.204, p < 0.001), carbapenems (OR 3.703, p = 0.017), cephalosporins (OR 12.036, p < 0.001), and fluoroquinolones (OR 5.238, p = 0.012). The mortality risk was significantly higher among colonized (OR 2.356, p < 0.001) and colonized-infected (OR 2.000, p = 0.009) patients and in those with Enterobacter cloacae colonization (OR 5.173, p < 0,001) and previous aminopenicillins exposure (OR 3.452, p = 0.007). CONCLUSIONS Early detection of CRE colonization through screening testing proved to be an important tool to control CRE spread. However, observation over the years has shown no effective control of colonization and infection. The prevalence rates of CRE colonization and colonization-infection were high, as were the mortality rates. In conclusion, an active CRE surveillance protocol is essential, but its impact depends on the effective implementation of preventive measures and feedback between team members.
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15
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Jia T, Chang WS, Marcelino VR, Zhao S, Liu X, You Y, Holmes EC, Shi M, Zhang C. Characterization of the Gut Microbiome and Resistomes of Wild and Zoo-Captive Macaques. Front Vet Sci 2022; 8:778556. [PMID: 35141306 PMCID: PMC8819141 DOI: 10.3389/fvets.2021.778556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 12/21/2021] [Indexed: 11/13/2022] Open
Abstract
Rhesus macaques (Macaca mulatta) are the most widely distributed species of Old World monkey and are frequently used as animal models to study human health and disease. Their gastrointestinal microbial community likely plays a major role in their physiology, ecology and evolution. Herein, we compared the fecal microbiome and antibiotic resistance genes in 15 free-ranging and 81 zoo-captive rhesus macaques sampled from two zoos in China, using both 16S amplicon sequencing and whole genome shotgun DNA sequencing approaches. Our data revealed similar levels of microbial diversity/richness among the three groups, although the composition of each group differed significantly and were particularly marked between the two zoo-captive and one wild groups. Zoo-captive animals also demonstrated a greater abundance and diversity of antibiotic genes. Through whole genome shotgun sequencing we also identified a mammalian (simian) associated adenovirus. Overall, this study provides a comprehensive analysis of resistomes and microbiomes in zoo-captive and free-ranging monkeys, revealing that semi-captive wildlife might harbor a higher diversity of antimicrobial resistant genes.
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Affiliation(s)
- Ting Jia
- Beijing Key Laboratory of Captive Wildlife Technologies, Beijing Zoo, Beijing, China
| | - Wei-Shan Chang
- Sydney Institute for Infectious Diseases, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW, Australia
- *Correspondence: Wei-Shan Chang
| | - Vanessa R. Marcelino
- Sydney Institute for Infectious Diseases, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW, Australia
- Department of Molecular and Translational Sciences, Monash University, Clayton, VIC, Australia
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia
| | - Sufen Zhao
- Beijing Key Laboratory of Captive Wildlife Technologies, Beijing Zoo, Beijing, China
| | - Xuefeng Liu
- Beijing Key Laboratory of Captive Wildlife Technologies, Beijing Zoo, Beijing, China
| | - Yuyan You
- Beijing Key Laboratory of Captive Wildlife Technologies, Beijing Zoo, Beijing, China
| | - Edward C. Holmes
- Sydney Institute for Infectious Diseases, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Mang Shi
- School of Medicine, Sun Yat-sen University, Guangzhou, China
- Mang Shi
| | - Chenglin Zhang
- Beijing Key Laboratory of Captive Wildlife Technologies, Beijing Zoo, Beijing, China
- Chenglin Zhang
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16
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Lephart P, LeBar W, Newton D. Behind Every Great Infection Prevention Program is a Great Microbiology Laboratory: Key Components and Strategies for an Effective Partnership. Infect Dis Clin North Am 2021; 35:789-802. [PMID: 34362544 DOI: 10.1016/j.idc.2021.04.012] [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: 11/18/2022]
Abstract
A great clinical microbiology laboratory supporting a great infection prevention program requires focusing on the following services: rapid and accurate identification of pathogens associated with health care-associated infections; asymptomatic surveillance for health care-acquired pathogens before infections arise; routine use of broad and flexible antimicrobial susceptibility testing to direct optimal therapy; implementation of epidemiologic tracking tools to identify outbreaks; development of clear result communication with interpretative comments for clinicians. These goals are best realized in a collaborative relationship with the infection prevention program so that both can benefit from the shared priorities of providing the best patient care.
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Affiliation(s)
- Paul Lephart
- Clinical Microbiology Laboratory, Department of Pathology, University of Michigan Medical School, 2800 Plymouth Road Building 36-1221-52, Ann Arbor, MI 48109-2800, USA.
| | - William LeBar
- Clinical Microbiology Laboratory, Department of Pathology, University of Michigan Medical School, 2800 Plymouth Road Building 36-1221-52, Ann Arbor, MI 48109-2800, USA
| | - Duane Newton
- NaviDx Consulting, Department of Pathology, University of Michigan Medical School, 2800 Plymouth Road Building 36-1221-52, Ann Arbor, MI 48109-2800, USA
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17
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Abstract
Klebsiella commonly colonizes the intestinal tract of hospitalized patients and is a leading cause of health care-associated infections. Colonization is associated with subsequent infection, but the factors determining this progression are unclear. A cohort study was performed, in which intensive care and hematology/oncology patients with Klebsiella colonization based on rectal swab culture were enrolled and monitored for infection for 90 days after a positive swab. Electronic medical records were analyzed for patient factors associated with subsequent infection, and variables of potential significance in a bivariable analysis were used to build a final multivariable model. Concordance between colonizing and infecting isolates was assessed by wzi capsular gene sequencing. Among 2,087 hospitalizations from 1,978 colonized patients, 90 cases of infection (4.3%) were identified. The mean time to infection was 20.6 ± 24.69 (range, 0 to 91; median, 11.5) days. Of 86 typed cases, 68 unique wzi types were identified, and 69 cases (80.2%) were colonized with an isolate of the same type prior to infection. Based on multivariable modeling, overall comorbidities, depression, and low albumin levels at the time of rectal swab collection were independently associated with subsequent Klebsiella infection (i.e., cases). Despite the high diversity of colonizing strains of Klebsiella, there is high concordance with subsequent infecting isolates, and progression to infection is relatively quick. Readily accessible data from the medical record could be used by clinicians to identify colonized patients at an increased risk of subsequent Klebsiella infection. IMPORTANCEKlebsiella is a leading cause of health care-associated infections. Patients who are intestinally colonized with Klebsiella are at a significantly increased risk of subsequent infection, but only a subset of colonized patients progress to disease. Colonization offers a potential window of opportunity to intervene and prevent these infections, if the patients at greatest risk could be identified. To identify patient factors associated with infection in colonized patients, we studied 1,978 colonized patients. We found that patients with a higher burden of underlying disease in general, depression in particular, and low albumin levels in a blood test were more likely to develop infection. However, these variables did not completely predict infection, suggesting that other host and microbial factors may also be important. The clinical variables associated with infection are readily available in the medical record and could serve as the foundation for developing an integrated risk assessment of Klebsiella infection in hospitalized patients.
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Golob JL, Rao K. Signal Versus Noise: How to Analyze the Microbiome and Make Progress on Antimicrobial Resistance. J Infect Dis 2021; 223:S214-S221. [PMID: 33880565 PMCID: PMC8206798 DOI: 10.1093/infdis/jiab184] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Antimicrobial resistance has become a worldwide medical challenge [1], so impactful that vancomycin-resistant Enterococcus (VRE) and methicillin-resistant Staphylococcus aureus (MRSA) have entered the common vernacular. We have attempted to reduce the selective pressure through antimicrobial stewardship, curtail the spread by identifying and isolating carriers and individuals with symptomatic infection, and treat antibiotic-resistant organisms (AROs) by developing novel antimicrobials. Despite these extraordinary measures, the challenge of AROs continues to grow. The gut microbiome, the ecosystem of microbes (ie, the microbiota) and metabolites present upon and within all humans, is an emerging target for both the risk for colonization and defense against infection with AROs. Here, informed from experiences and successes with understanding the role of the microbiome in mediating risk of Clostridioides difficile infection (CDI), we (1) review our understanding of the risk from ARO acquisition; (2) review our current understanding of the gut microbiome's ability to resist colonization with AROs; (3) describe how experimental model systems can test these initial, global insights to arrive at more granular, mechanistic ones; and (4) suggest a path forward to make further progress in the field.
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Affiliation(s)
- Jonathan L Golob
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan, Ann Arbor, Michigan, USA
| | - Krishna Rao
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan, Ann Arbor, Michigan, USA
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19
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Shirvani F, Behzad A, Abdollahi N, Mohkam M, Sharifian M, Esfandiar N, Fallah F. Frequency and co-colonization of vancomycin-resistant Enterococci and Candida in ICU-hospitalized children. New Microbes New Infect 2021; 41:100881. [PMID: 34026230 PMCID: PMC8121691 DOI: 10.1016/j.nmni.2021.100881] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 04/03/2021] [Accepted: 04/07/2021] [Indexed: 02/03/2023] Open
Abstract
In the time span between January 2018 and September 2020, 205 patients were enrolled in a prospective cohort study at Mofid Children's Hospital. Demographic information and clinical data on all the participating children were collected and rectal swabs were performed for the sampling method. All samples were analysed so as to identify the presence of Enterococcus and Candida colonization by the use of conventional biochemical tests. Resistance to vancomycin in Enterococcus isolates was phenotypically identified using an E-test kit and MIC value, interpreted according to the CLSI criteria. The presence of vanA and vanB genes, which encode the resistance to vancomycin, was screened by PCR assay. Candida species were detected in 21.5% of rectal swab samples. Candida glabrata (56.8%) and Candida albicans (43.2%) were the only Candida species detected. Enterococcus species were detected in 29.3% of rectal swab samples. Out of 60 Enterococcus isolates, 33 (55%) were resistant to vancomycin. Moreover, vanA was detected in 84.8% and vanB was detected in 3% of the 33 vancomycin-resistant Enterococcus isolates. Enterococcus and Candida species were frequently detected in the <1 year and 1–3 years age groups, respectively. Central venous access catheter and brain tumour were the main reasons for hospital admissions, 32.2% and 20.1% of total admissions, respectively. Furthermore, it must be noted that the most frequent underlying medical conditions in participating patients were esophageal atresia and hydrocephalus. The results of the present study demonstrated the necessity of determining the susceptibility of Enterococcus isolates to vancomycin before prescribing antibiotics.
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Affiliation(s)
- F Shirvani
- Paediatric Infections Research Centre, Research Institute for Children's Health, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - A Behzad
- Paediatric Intensive Care Department, Mofid Children Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - N Abdollahi
- Paediatric Infections Research Centre, Research Institute for Children's Health, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - M Mohkam
- Paediatric Nephrology Research Centre, Research Institute for Children's Health, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - M Sharifian
- Paediatric Nephrology Research Centre, Research Institute for Children's Health, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - N Esfandiar
- Paediatric Nephrology Research Centre, Research Institute for Children's Health, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - F Fallah
- Paediatric Infections Research Centre, Research Institute for Children's Health, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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20
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Vornhagen J, Bassis CM, Ramakrishnan S, Hein R, Mason S, Bergman Y, Sunshine N, Fan Y, Holmes CL, Timp W, Schatz MC, Young VB, Simner PJ, Bachman MA. A plasmid locus associated with Klebsiella clinical infections encodes a microbiome-dependent gut fitness factor. PLoS Pathog 2021; 17:e1009537. [PMID: 33930099 PMCID: PMC8115787 DOI: 10.1371/journal.ppat.1009537] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 05/12/2021] [Accepted: 04/07/2021] [Indexed: 02/07/2023] Open
Abstract
Klebsiella pneumoniae (Kp) is an important cause of healthcare-associated infections, which increases patient morbidity, mortality, and hospitalization costs. Gut colonization by Kp is consistently associated with subsequent Kp disease, and patients are predominantly infected with their colonizing strain. Our previous comparative genomics study, between disease-causing and asymptomatically colonizing Kp isolates, identified a plasmid-encoded tellurite (TeO3-2)-resistance (ter) operon as strongly associated with infection. However, TeO3-2 is extremely rare and toxic to humans. Thus, we used a multidisciplinary approach to determine the biological link between ter and Kp infection. First, we used a genomic and bioinformatic approach to extensively characterize Kp plasmids encoding the ter locus. These plasmids displayed substantial variation in plasmid incompatibility type and gene content. Moreover, the ter operon was genetically independent of other plasmid-encoded virulence and antibiotic resistance loci, both in our original patient cohort and in a large set (n = 88) of publicly available ter operon-encoding Kp plasmids, indicating that the ter operon is likely playing a direct, but yet undescribed role in Kp disease. Next, we employed multiple mouse models of infection and colonization to show that 1) the ter operon is dispensable during bacteremia, 2) the ter operon enhances fitness in the gut, 3) this phenotype is dependent on the colony of origin of mice, and 4) antibiotic disruption of the gut microbiota eliminates the requirement for ter. Furthermore, using 16S rRNA gene sequencing, we show that the ter operon enhances Kp fitness in the gut in the presence of specific indigenous microbiota, including those predicted to produce short chain fatty acids. Finally, administration of exogenous short-chain fatty acids in our mouse model of colonization was sufficient to reduce fitness of a ter mutant. These findings indicate that the ter operon, strongly associated with human infection, encodes factors that resist stress induced by the indigenous gut microbiota during colonization. This work represents a substantial advancement in our molecular understanding of Kp pathogenesis and gut colonization, directly relevant to Kp disease in healthcare settings.
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Affiliation(s)
- Jay Vornhagen
- Department of Pathology, University of Michigan, Ann Arbor, MI, United States of America
- Department of Microbiology & Immunology, University of Michigan, Ann Arbor, MI, United States of America
| | - Christine M. Bassis
- Department of Internal Medicine/Infectious Diseases Division, University of Michigan, Ann Arbor, MI, United States of America
| | - Srividya Ramakrishnan
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, United States of America
| | - Robert Hein
- Department of Internal Medicine/Infectious Diseases Division, University of Michigan, Ann Arbor, MI, United States of America
| | - Sophia Mason
- Department of Pathology, University of Michigan, Ann Arbor, MI, United States of America
| | - Yehudit Bergman
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - Nicole Sunshine
- Department of Pathology, University of Michigan, Ann Arbor, MI, United States of America
| | - Yunfan Fan
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, United States of America
| | - Caitlyn L. Holmes
- Department of Pathology, University of Michigan, Ann Arbor, MI, United States of America
- Department of Microbiology & Immunology, University of Michigan, Ann Arbor, MI, United States of America
| | - Winston Timp
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, United States of America
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
- Department of Medicine, Division of Infectious Disease, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - Michael C. Schatz
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, United States of America
- Department of Biology, Johns Hopkins University, Baltimore, MD, United States of America
- Simons Center for Quantitative Biology, Cold Spring Harbor, NY, United States of America
| | - Vincent B. Young
- Department of Microbiology & Immunology, University of Michigan, Ann Arbor, MI, United States of America
- Department of Internal Medicine/Infectious Diseases Division, University of Michigan, Ann Arbor, MI, United States of America
| | - Patricia J. Simner
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - Michael A. Bachman
- Department of Pathology, University of Michigan, Ann Arbor, MI, United States of America
- Department of Microbiology & Immunology, University of Michigan, Ann Arbor, MI, United States of America
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21
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Colonization Dynamics of Multidrug-Resistant Klebsiella pneumoniae Are Dictated by Microbiota-Cluster Group Behavior over Individual Antibiotic Susceptibility: A Metataxonomic Analysis. Antibiotics (Basel) 2021; 10:antibiotics10030268. [PMID: 33800048 PMCID: PMC8001907 DOI: 10.3390/antibiotics10030268] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 02/25/2021] [Accepted: 03/04/2021] [Indexed: 12/17/2022] Open
Abstract
Gastrointestinal carriage of multidrug-resistant (MDR) bacteria is one of the main risk factors for developing serious, difficult-to-treat infections. Given that there is currently no all-round solution to eliminate colonization with MDR bacteria, it is particularly important to understand the dynamic process of colonization to aid the development of novel decolonization strategies. The aim of our present study was to perform metataxonomic analyses of gut microbiota dynamics during colonization with an extended-spectrum β-lactamase (ESBL)- and carbapenemase-producing Klebsiella pneumoniae (ECKP) strain in mice; additionally, to ascertain the effects of antibiotic administration (ampicillin, ceftazidime, and ciprofloxacin) on the establishment and elimination of ECKP intestinal colonization. We have found that the phyla Bacteroidetes and Firmicutes were most dominant in all of the treatment groups; however, Bacteroidetes was more common in the groups treated with antibiotics compared to the control group. Significant differences were observed among the different antibiotic-treated groups in beta but not alpha diversity, implying that the difference is the relative abundance of some bacterial community members. Bacteria from the Lachnospiraceae family (including Agathobacter, Anaerostipes, Lachnoclostridium 11308, Lachnospiraceae UCG-004, Lachnospiraceae NK3A20 group 11318, Lachnospiraceae NK4A136 group 11319, Roseburia, and Tyzzerella) showed an inverse relationship with the carriage rate of the ECKP strain, whereas members of Enterobacteriaceae and the ECKP strain have shown a correlational relationship. Our results suggest that the composition of the microbial community plays a primary role in the MDR-colonization rate, whereas the antibiotic susceptibility of individual MDR strains affects this process to a lesser extent. Distinct bacterial families have associated into microbial clusters, collecting taxonomically close species to produce survival benefits in the gut. These associations do not develop at random, as they may be attributed to the presence of specific metabolomic networks. A new concept should be introduced in designing future endeavors for MDR decolonization, supplemented by knowledge of the composition of the host bacterial community and the identification of bacterial clusters capable of suppressing or enhancing the invader species.
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22
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Lepuschitz S, Hauser K, Schriebl A, Schlagenhaufen C, Stöger A, Chakeri A, Vötsch K, Pekard-Amenitsch S, Springer B, Allerberger F, Ruppitsch W. Fecal Klebsiella pneumoniae Carriage Is Intermittent and of High Clonal Diversity. Front Microbiol 2020; 11:581081. [PMID: 33324367 PMCID: PMC7721676 DOI: 10.3389/fmicb.2020.581081] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 10/29/2020] [Indexed: 12/27/2022] Open
Abstract
The Klebsiella pneumoniae complex comprises several closely related entities, which are ubiquitous in the natural environment, including in plants, animals, and humans. K. pneumoniae is the major species within this complex. K. pneumoniae strains are opportunistic pathogens and a common cause of healthcare-associated infections. K. pneumoniae can colonize the human gastrointestinal tract, which may become a reservoir for infection. The aim of this study was to investigate the fecal K. pneumoniae carriage in six healthy individuals during a 1 year period. Stool samples were obtained once a week. Using direct and pre-enriched cultures streaked on ampicillin-supplemented agar plates, up to eight individual colonies per positive sample were selected for further characterization. Whole genome sequencing (WGS) was performed for strain characterization. Sequence type (ST), core genome complex type (CT), K and O serotypes, virulence traits, antibiotic resistance profiles, and plasmids were extracted from WGS data. In total, 80 K. pneumoniae isolates were obtained from 48 positive cultures of 278 stool samples from five of the six test subjects. The samples of the five colonized volunteers yielded at most two, three, four (two persons), and five different strains, respectively. These 80 K. pneumoniae isolates belonged to 60 STs, including nine new STs; they were of 70 CTs, yielded 48 K serotypes, 11 O serotypes, and 39 wzc and 51 wzi alleles. Four of the five subjects harbored serotypes K20 and K47, as well as STs ST37, ST101, ST1265, and ST20, which had previously been linked to high-risk K. pneumoniae clones. In total, 25 genes conferring antibiotic resistance and 42 virulence genes were detected among all 80 isolates. Plasmids of 15 different types were found among 65 of the isolates. Fecal carriage of individual strains was of short duration: 70 strains were found on a single sampling day only, and 5 strains were isolated in samples collected over two consecutive weeks. Two of the five colonized individuals—working colleagues having meals together—shared identical K. pneumoniae types four times during the study period. Our findings point toward the potential role of food as a reservoir for K. pneumoniae in humans.
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Affiliation(s)
- Sarah Lepuschitz
- Austrian Agency for Health and Food Safety, Institute of Medical Microbiology and Hygiene, Graz, Austria
| | - Kathrin Hauser
- Austrian Agency for Health and Food Safety, Institute of Medical Microbiology and Hygiene, Graz, Austria
| | - Agnes Schriebl
- Austrian Agency for Health and Food Safety, Institute of Medical Microbiology and Hygiene, Graz, Austria
| | - Claudia Schlagenhaufen
- Austrian Agency for Health and Food Safety, Institute of Medical Microbiology and Hygiene, Graz, Austria
| | - Anna Stöger
- Austrian Agency for Health and Food Safety, Institute of Medical Microbiology and Hygiene, Graz, Austria
| | - Ali Chakeri
- Austrian Agency for Health and Food Safety, Institute of Medical Microbiology and Hygiene, Graz, Austria
| | - Kornelia Vötsch
- Austrian Agency for Health and Food Safety, Institute of Medical Microbiology and Hygiene, Graz, Austria
| | - Shiva Pekard-Amenitsch
- Austrian Agency for Health and Food Safety, Institute of Medical Microbiology and Hygiene, Graz, Austria
| | - Burkhard Springer
- Austrian Agency for Health and Food Safety, Institute of Medical Microbiology and Hygiene, Graz, Austria
| | - Franz Allerberger
- Austrian Agency for Health and Food Safety, Institute of Medical Microbiology and Hygiene, Graz, Austria
| | - Werner Ruppitsch
- Austrian Agency for Health and Food Safety, Institute of Medical Microbiology and Hygiene, Graz, Austria
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