A recent study of CP K. pneumoniae in Israel suggested screening and isolation of carriers could help end current outbreaks and prevent future ones [3]. The present study aimed to find out the occurrence of Multidrug-resistant (MDR) K. Pneumoniae and their capsular resistance genes which were undocumented previously in cow farms of district Peshawar, Pakistan. WGS demonstrated that some isolates identified as K. pneumoniae by MALDI-TOF actually belonged to closely related groups that have recently been described as separate species [24], K. quasipneumoniae and K. variicola (Figure 2). All other patients transferred from another hospital were included in the HA/D3+ screening group. 3 TK Edwards Director, Clinical Research Computing Unit (CRCU) (Standing Faculty Sr. Screening for colonization on admission could limit risk of infection in the colonized patient and others. HHS Vulnerability Disclosure, Help In contrast, only 12% of infections showed evidence of resulting from intra-hospital transmission in this setting. Bethesda, MD 20894, Web Policies Klebsiella pneumoniae GI Carriage Detected at Baseline and Followup Screening of Alfred Hospital Patients. MA Please enable it to take advantage of the complete set of features! Lee Martin K Efforts were made to collect swabs as soon as possible following admission; however, delays due to obtaining consent and avoiding patient care disruption meant that it was often not possible to obtain screening swabs on the day of admission. A major reservoir in the patient population could not be unveiled. All statistical analyses were conducted using R (v3.3.1) (details in Supplementary Methods). Hypervirulent K. pneumoniae, which are K. pneumoniae with several acquired virulence determinants such as the siderophore aerobactin and others, are more prominent in countries in South and South-East Asia compared to European countries. Klebsiella pneumoniae is an opportunistic pathogen and leading cause of hospital-associated infections. AP Ethical approvals for these studies were granted by the Alfred Hospital Ethics Committee (project numbers 550/12 and 526/13). HA carriage among ICU patients was estimated to be much higher at 19%, with 12% of patients converting from culture-negative at baseline to culture-positive on follow-up. Additionally, as only 1 isolate was stored from each K. pneumoniae positive infection or carriage specimen, it is possible that the proportion of matching infection/carriage pairs underestimates the contribution of carriage to infection and misses some instances of transmission. sharing sensitive information, make sure youre on a federal Intensive care unit (ICU) patients are particularly at risk. Pommier T, Canbck B, Lundberg P, Hagstrm A, Tunlid A. RAMI: a tool for identification and characterization of phylogenetic clusters in microbial communities, Short read sequence typing (SRST): multi-locus sequence types from short reads, Genome-scale rates of evolutionary change in bacteria, Persistent carriage of gram negative bacteria on hands, Extended spectrum beta lactamase producing, Minor outbreak of extended-spectrum -lactamase-producing. Pea D Impact of carbapenem resistance on the outcome of patients hospital-acquired bacteraemia caused by, Infection control in the multidrug-resistant era: tending the human microbiome. Munoz-Price and transmitted securely. Pneumonia was the most frequent form of K. pneumoniae infection in ICU patients (60%), followed by wound infections (15%), nondisseminated urinary tract infection (UTI) (10%), and bacteremia with sepsis (8%). Melhus Krishna National Library of Medicine Full details are given in Supplementary Methods. Klebsiella pneumoniae GI Carriage Detected at Baseline and Followup Screening of Alfred Hospital Patients. Fifteen patients had both GI carriage and infection isolates available for genome comparison; 12 of these pairs matched at the lineage level (including 6 patients whose carriage isolate was collected >2 days prior to the infection). Whole-Genome Sequencing of Klebsiella pneumoniae Isolates to Track Circles indicate K. pneumoniae infection isolates (red, belonging to the lineage; black, other lineage); triangles indicate rectal screening swabs (red, K. pneumoniae belonging to the lineage; black, K. pneumoniae of another lineage; unfilled, negative for K. pneumoniae). Semantic Scholar extracted view of "Highlighting extended-spectrum beta-lactamase-producing Klebsiella pneumoniae outbreak by routine genomic typing" by F. Gravey et al. MeSH Moradigaravand D, Martin V, Peacock SJ, Parkhill J. mBio. Oxford University Press is a department of the University of Oxford. This work was supported by the National Health and Medical Research Council of Australia (Project 1043822 and Fellowship 1061409 to K. E. H.) and the Australian Government Research Training Program (Scholarship to C. L. G.). Conlan National Library of Medicine Bennett Reports on the isolation of K. pneumoniae from other sources are increasing, many of which express multidrug-resistant (MDR) phenotypes. Routine screening for nasal carriage of methicillin-resistant S. aureus or gut carriage of vancomycin-resistant Enterococcus or ESBL/CP Enterobacteriaceae has been introduced in various hospital settings [2528]. MN This work was supported by the National Health and Medical Research Council of Australia (Project 1043822 and Fellowship 1061409 to K. E. H.) and the Australian Government Research Training Program (Scholarship to C. L. G.). Consisting of data provided by the authors to benefit the reader, the posted materials are not copyedited and are the sole responsibility of the authors, so questions or comments should be addressed to the corresponding author. Most (n = 38) were in the ICU when the K. pneumoniaepositive diagnostic specimen was taken, and 10 were in another ward shortly after transfer from ICU. Patients first swabbed on day 3 or later of their hospital admission are included in the HA/Day 3+ screening group. E Three phylogroups were identified based on nucleotide differences. . For the first 9 months verbal consent was required to participate. Careers. Our data demonstrate that K. pneumoniae is a fairly common component of the human GI microbiome (5.9%) and of clinical significance in the ICU setting, as: (i) K. pneumoniae carriage on admission to ICU was significantly associated with subsequent K. pneumoniae infection (OR = 6.9, P = .0003), consistent with the results reported from the 1970s Denver study (OR = 4.0, P = .0009 [11]) and the 2016 Michigan study (OR = 4.1, P = .00002 [12]); and (ii) the WGS data confirmed a direct link between colonizing and infecting strains in 13 patients (80% of those with paired isolates available for testing), also consistent with the Michigan study [12]. Klebsiella pneumoniae : Prevalence, Reservoirs, Antimicrobial Malays J Med Sci. To assess whether K. pneumoniae GI carriage on admission to ICU was a risk factor for subsequent K. pneumoniae infection during hospital stay, we examined the subset of 491 individuals whose baseline screening swab was obtained at least 2 days prior to collection of any clinical specimen from which K. pneumoniae was isolated (Figure 1). These data confirm K. pneumoniae colonization is a significant risk factor for infection in ICU, and indicate ~50% of K. pneumoniae infections result from patients own microbiota. (C), Midpoint rooted species tree for K. pneumoniae sensu stricto isolates. The Klebsiella Acquisition Surveillance Project at Alfred Health (KASPAH) was conducted from April 1, 2013, to March 31, 2014. Klebsiella pneumoniae is considered an opportunistic pathogen, constituting an ongoing health concern for immunocompromised patients, the elderly, and neonates. Klebsiella pneumoniae is an opportunistic pathogen and leading cause of hospital-associated infections. Vats Population genomics of Klebsiella pneumoniae - Nature Half the infections (n = 24/48) were caused by a lineage unique to the patient. Ledeboer B Klebsiella pneumoniae, belonging to the Enterobacteriaceae family, is a natural inhabitant of the gastrointestinal tract microbiome of healthy human and animals. *These indicate 2 patients from whom swabs yielded isolates that were identified in the hospital laboratory as K. pneumoniae, but sequencing of subcultures identified substantial E. coli, indicating likely presence of both species. A maximum likelihood phylogenetic tree was inferred from an alignment of all single-nucleotide polymorphisms (SNPs) identified within core K. pneumoniae genes using FastTree v2.1.8 [13, 14]. Recently, . None of the 19 CA baseline carriage isolates were MDR (Table 1). A total of 143 high-quality whole genome sequences were obtained from 106 patients, including 56 clinical, 80 GI carriage, and 7 throat carriage isolates. Abbreviation: SNP, single-nucleotide polymorphism. NA Six infection episodes (n = 6/49, 12%) were attributable to these intra-hospital transmission chains (n = 4 ST681 [K. variicola], n = 1 ST323, n = 1 ST231; Figure 4). The prevalence of K. pneumoniae colonic colonization was 23.0% among patients admitted to intensive care units of one hospital in the United States, and was estimated as 6% in a similar case in Australia. Highlighting extended-spectrum beta-lactamase-producing Klebsiella Infections with K. pneumoniae can be transmitted through contaminated food or water and can be associated with community-acquired infections or between persons and animals involved in hospital-acquired infections. Klebsiella pneumoniae : an increasing threat to public health M Gut colonization on admission was significantly associated with subsequent infection (infection risk 16% vs 3%, odds ratio [OR] = 6.9, P < .001), and genome data indicated matching carriage and infection isolates in 80% of isolate pairs. Segre The antimicrobial resistance profiles and the virulence profiles of these strains vary with the former tagged as notorious [3, 5].Notwithstanding, several clones of these ncKp have also . Cimon Core genome phylogenetic analysis (Figure 2) revealed the presence of 61 lineages of K. pneumoniae sensu stricto (n = 111 isolates) and 24 lineages of 2 closely related species: 20 K. variicola lineages (n = 28 isolates) and 4 K. quasipneumoniae lineages (n = 4 isolates). Klebsiella pneumoniae is known to asymptomatically colonize the skin, mouth, respiratory and GI tracts, although few studies address this specifically. Lau The Klebsiella pneumoniae complex is a member of the Klebsiella genus of the family Enterobacteriaceae. It is a common opportunistic hospital-associated pathogen, accounting for about one third of all Gram-negative infections overall. T Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom; 5 We estimated the rate of CA K. pneumoniae GI carriage, among patients recruited and swabbed in the ICU within 2 days of their first recorded admission to the Hospital (CA/D0-2 group), to be 5.9% (95% confidence interval [CI], 3% 8%, Table 1, Supplementary Table 2). Phylogenetic lineages to which more than one ICU isolate belongs are highlighted and labeled with their corresponding multi-locus sequence type (ST) and the total number of SNPs identified between isolates in the lineage; darker shading indicates multiple patients contributed isolates in that cluster, as per inset legend. Y For 5/7 patients the resistance profiles for the follow-up isolate remained the same as the baseline isolate, and for 2/7 patients the follow-up isolate was more resistant (see Supplementary Tables 1 and 3). Of the 4 donors in the transmission chains, 3 had pneumonia and 1 had a wound infection. It has been reported that gastrointestinal colonization (GI) is likely to be a common and significant reservoir for the transmission and infections of K. pneumoniae in both adults and neonates. Klebsiella pneumoniae is part of the healthy human microbiome, providing a potential reservoir for infection. When bacteria called Klebsiella pneumoniae spread from the intestines and feces, they cause a range of infection types and tend to be antibiotic resistant. A Intra-patient genetic distances were nearly all (97%) less than 25 SNPs per 5 Mbp, and most (82%) were less than 10 SNPs, whereas inter-patient genetic distances ranged from 0 to >5000 SNPs (Figure 3). This represents 33% of eligible patients during the consent-based recruitment period and 75% in the universal surveillance period (18% of all ICU admissions in the study period). A All clinical isolates recovered from ICU patients and identified as K. pneumoniae infections by the hospital diagnostic laboratory as part of routine care were included in the study. Klebsiella pneumoniae is an important opportunistic pathogen associated with severe invasive disease in humans. Sixteen Klebsiella lineages were detected in more than 1 patient (dark shading, Figure 2). Ultimately, we find that host-to-host spread of K. pneumoniae occurs principally from its intestinal reservoir, and that commensal-colonization-factor-producing Bacteroidetes are sufficient to . These studies have demonstrated transmission of ESBL or CP K. pneumoniae between patients and show that gastrointestinal (GI) tract colonization with ESBL or CP K. pneumoniae can be a risk factor for infection [3, 4]. HHS Vulnerability Disclosure, Help Full details are given in Supplementary Methods. There is likely a significant false negative rate. However, the frequency of gut colonization and its contribution to infections are not well characterized. Larson . Weber JA . Timelines for all lineages detected in multiple patients that show any inter-patient pairwise genetic distance between isolates of 25 SNPs per 5 Mbp. Carriage was detected at the same frequency in males and females (11.0% vs 10.4%; P = .9), and the median age of carriers was moderately higher than that of carriage-negative participants (67 vs 58 years, Supplementary Figure 2; P = .06, Wilcoxon rank-sum test). Conway The https:// ensures that you are connecting to the . . Severin Hypervirulent Klebsiella pneumoniae; healthy people; human gut; reservoir Introduction Klebsiella pneumoniae is a member of the family Enterobacteriaceae that is best known for its capa-city to cause infections, including healthcare- associated infections and community-acquired infections (CAIs). TT government site. The aim of this study was to explore and characterize K. pneumoniae from healthy broilers and turkeys. ES The HA GI carriage rate, among patients who were first swabbed in the ICU on or after the third day of admission to the Alfred hospital or following referral from another hospital (HA/D3+ group, Supplementary Figure 3), was significantly higher at 19% (95% CI, 13.6% 25.7%, odds ratio [OR] = 3.75, P = .00001). Klebsiella pneumoniae is an important uropathogen that increasingly harbors broad-spectrum antibiotic resistance determinants. Using 25 and 10 SNPs per 5 Mbp as cut-offs to indicate likely and very likely strain sharing between patients, we identified 5 groups of ICU patients that likely shared Klebsiella strains. Ko For the first 9 months verbal consent was required to participate. This suggests that although measures to reduce cross-contamination between patients are necessary, they are not sufficient to eliminate K. pneumoniae infections in hospitalized patients, and measures to minimize the risk of infection with the patients own microbiome deserves significant attention [2123]. et al. The overall GI carriage rate at follow-up was 15.3% (n = 26/170), similar to the HA GI carriage rate of 19% (OR = 1.3; 95% CI, 0.712.38). . Each horizontal dashed line indicates the time line for a patient, labelled to the left (crosses indicate date of death where applicable). eCollection 2018. Additionally, as only 1 isolate was stored from each K. pneumoniae positive infection or carriage specimen, it is possible that the proportion of matching infection/carriage pairs underestimates the contribution of carriage to infection and misses some instances of transmission. Background: Klebsiella pneumoniae is an opportunistic pathogen and leading cause of hospital-associated infections. Increasing reports are describing detections along the food chain, suggesting the possibility exists that this could be a hitherto unexplored reservoir for this opportunistic bacterial pathogen. Ranks), Autopsy Pathologist and CLIA Medical Director Leadership Opportunity University of Vermont Health Network, MEDICAL MICROBIOLOGY AND CLINICAL LABORATORY MEDICINE PHYSICIAN, Copyright 2023 Infectious Diseases Society of America. WC It furthers the University's objective of excellence in research, scholarship, and education by publishing worldwide, This PDF is available to Subscribers Only. Gut colonization on admission was significantly associated with subsequent infection (infection risk 16% vs 3%, odds ratio [OR] = 6.9, P < .001), and genome data indicated matching carriage and infection isolates in 80% of isolate pairs. FOIA RN These included 2 episodes of pneumonia, 2 wound infections, and 2 UTIs, one of which disseminated to cause bacteremia with sepsis (Table 2, Supplementary Table 3). One third of the participants in the ICU screening study (n = 170) contributed 1 or more follow-up screening swabs (Table 1). This likely reflects acquisition of bacteria in the hospital (transmission of strains was directly observed in 5% of cases) and/or selection for growth of pre-existing K. pneumoniae in the GI microbiome during hospitalization (MDR rate was 18% in HA baseline carriage and 15% at follow-up, but MDR was not detected in CA baseline carriage). Intensive care unit (ICU) patients are particularly at risk. Klebsiella pneumoniae carriage frequencies were estimated at 6% (95% confidence interval [CI], 3%8%) among ICU patients admitted direct from the community, and 19% (95% CI, 14%51%) among those with recent healthcare contact. *These indicate 2 patients from whom swabs yielded isolates that were identified in the hospital laboratory as K. pneumoniae, but sequencing of subcultures identified substantial E. coli, indicating likely presence of both species. Genomic surveillance for hypervirulence and multi-drug resistance in invasive Klebsiella pneumoniae from South and Southeast Asia. A total of seven patients contributed both baseline and follow-up GI carriage isolates (Table 1). Information on age, sex, dates of hospital and ICU admission/s, surgery in the last 30 days, and antibiotic treatment in the last 7 days were extracted from hospital records at the time each swab was taken. Hence our study probably underestimates the rate of colonization in the community and the contribution of colonisation to subsequent infection. Klebsiella pneumoniae is known to asymptomatically colonize the skin, mouth, respiratory and GI tracts, although few studies address this specifically. Conflicts that the editors consider relevant to the content of the manuscript have been disclosed. Klebsiella pneumoniae bacterial outbreak at Seattle hospital: 9 deaths Pujol Clinical features, diagnosis, and treatment of Klebsiella pneumoniae The HA GI carriage rate, among patients who were first swabbed in the ICU on or after the third day of admission to the Alfred hospital or following referral from another hospital (HA/D3+ group, Supplementary Figure 3), was significantly higher at 19% (95% CI, 13.6% 25.7%, odds ratio [OR] = 3.75, P = .00001). All clinical isolates recovered from ICU patients and identified as K. pneumoniae infections by the hospital diagnostic laboratory as part of routine care were included in the study. Ethical approvals for these studies were granted by the Alfred Hospital Ethics Committee (project numbers 550/12 and 526/13). AM Flowchart outlining number of patients included in each part of carriage rates analyses. GI carriage of MDR strains was detected at similar rates among HA baseline isolates (18%, including 4 ESBL and 2 CP isolates, all in patients who had received antibiotics in the last 7 days) and follow-up screening isolates (16% of patients, including 4 with ESBL and 1 with CP isolates). Intensive care unit outbreak of extended-spectrum beta-lactamase-producing, Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America, http://creativecommons.org/licenses/by/4.0/, cix270_suppl_supplementary_information.pdf. R Niche environments, including plants, animals, and humans appear to be colonized by different phylogroups, among which KpI (K. pneumoniae) is commonly associated with human infection. Tunlid Klebsiella pneumoniae; Raman spectroscopy; antimicrobial resistance; foodborne pathogen; infection; pathogenicity; prevalence; virulence. Gardam Klebsiella [klebseeelluh] is a type of gram-negative bacteria that can cause different types of healthcare-associated infections, including pneumonia, bloodstream infections, wound or surgical site infections, and meningitis. Zhang F, Meng Y, Xu L, Tian Y, Lu H, Xie J, Ma R, Li M, Li B. Vet Res. C Five likely transmission chains were identified, responsible for 12% of K. pneumoniae infections in ICU. . Sixteen Klebsiella lineages were detected in more than 1 patient (dark shading, Figure 2). N For full access to this pdf, sign in to an existing account, or purchase an annual subscription. LS One third of the participants in the ICU screening study (n = 170) contributed 1 or more follow-up screening swabs (Table 1). Patient groups: ICU CA/Day 02, rectal screening swab obtained on day 0, 1, or 2 of admission to Alfred Hospital and not referred from another hospital (except from trauma unit); ICU HA/Day 3+, rectal screening swab obtained on day 3 or later of admission to Alfred Hospital or referred from another hospital. . All authors have submitted the ICMJE Form for Disclosure of Potential Conflicts of Interest. Using bacteriological culture, a 2010 study detected nasopharyngeal carriage in 15% of Indonesian adults and 7% of children [8], whereas a 2014 study detected nasopharyngeal carriage in 2.7% of Vietnamese adults and throat carriage in 14% [9]. R These studies have demonstrated transmission of ESBL or CP K. pneumoniae between patients and show that gastrointestinal (GI) tract colonization with ESBL or CP K. pneumoniae can be a risk factor for infection [3, 4]. AB 2020 Jan 16;12(1):11. doi: 10.1186/s13073-019-0706-y. Lineages were defined based on this tree using RAMI [15] and multilocus sequence types were assigned using SRST2 [16]. Klebsiella pneumoniae is a leading cause of hospital-associated (HA) infections. R Please check for further notifications by email. Most of the infections associated with transmission were MDR (3/4 donors and 3/6 recipients), yielding a strong association between MDR infections and transmission in the ICU (OR = 13.6, P = .002). N A recent study of CP K. pneumoniae in Israel suggested screening and isolation of carriers could help end current outbreaks and prevent future ones [3]. Huang As a library, NLM provides access to scientific literature. Klebsiella variicola: an emerging pathogen in humans - PMC These may reflect coinfection followed by selection for different subpopulations in the laboratory used for the different tests. All other patients transferred from another hospital were included in the HA/D3+ screening group. Five likely transmission chains were identified, responsible for 12% of K. pneumoniae infections in ICU. Acknowledgments. Hagstrm This represents 33% of eligible patients during the consent-based recruitment period and 75% in the universal surveillance period (18% of all ICU admissions in the study period). Klebsiella pneumoniae is part of the healthy human microbiome, providing a poten-tial reservoir for infection. We used rectal swab culture to determine K. pneumoniae GI colonization status; however, although this approach is standard for pathogen carriage screening [2527], its sensitivity to detect K. pneumoniae is not well characterized and likely depends on the K. pneumoniae strain, GI microbiome composition, and recent antimicrobial exposures. SB LC We found strong evidence that a large proportion of ICU K. pneumoniae infections are attributable to patients own GI microbiota: (i) of all 49 K. pneumoniae infections diagnosed in ICU patients during the study period, 49% were associated with K. pneumoniae lineages unique to the patient; and (ii) of the 27 K. pneumoniae infections diagnosed in ICU patients from whom screening swabs were obtained, 48% occurred in patients who tested positive for prior GI colonization with K. pneumoniae. Abbreviations: GI, gastrointestinal; ICU, intensive care unit; MDR, multidrug-resistant. . Faron Violin plots showing distribution of pairwise genetic distances intra- and inter-patient; black bars indicate the median value. The overall GI carriage rate at follow-up was 15.3% (n = 26/170), similar to the HA GI carriage rate of 19% (OR = 1.3; 95% CI, 0.712.38). The Author 2017. Eickhoff 2020 Sep 2;11(5):1287-1299. doi: 10.1080/19490976.2020.1748257. (A), Unrooted tree of all isolates, revealing three distinct species that are typically identified as K. pneumoniae in diagnostic laboratories. L Pneumonia was the most frequent form of K. pneumoniae infection in ICU patients (60%), followed by wound infections (15%), nondisseminated urinary tract infection (UTI) (10%), and bacteremia with sepsis (8%).
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