scholarly journals Genomic Epidemiology of Carbapenemase Producing Klebsiella pneumoniae Strains at a Northern Portuguese Hospital Enables the Detection of a Misidentified Klebsiella variicola KPC-3 Producing Strain

2020 ◽  
Vol 8 (12) ◽  
pp. 1986
Author(s):  
João Perdigão ◽  
Cátia Caneiras ◽  
Rita Elias ◽  
Ana Modesto ◽  
Anton Spadar ◽  
...  
Keyword(s):  
Klebsiella Pneumoniae ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Bioinformatic Analysis ◽  
Multidrug Resistant ◽  
Control Measures ◽  
Whole Genome ◽  
Genomic Epidemiology ◽  
Infection Control Measures ◽  
Carbapenemase Gene

The evolutionary epidemiology, resistome, virulome and mobilome of thirty-one multidrug resistant Klebsiella pneumoniae clinical isolates from the northern Vila Real region of Portugal were characterized using whole-genome sequencing and bioinformatic analysis. The genomic population structure was dominated by two main sequence types (STs): ST147 (n = 17; 54.8%) and ST15 (n = 6; 19.4%) comprising four distinct genomic clusters. Two main carbapenemase coding genes were detected (blaKPC-3 and blaOXA-48) along with additional extended-spectrum β-lactamase coding loci (blaCTX-M-15, blaSHV-12, blaSHV-27, and blaSHV-187). Moreover, whole genome sequencing enabled the identification of one Klebsiella variicola KPC-3 producer isolate previously misidentified as K. pneumoniae, which in addition to the blaKPC-3 carbapenemase gene, bore the chromosomal broad spectrum β-lactamase blaLEN-2 coding gene, oqxAB and fosA resistance loci. The blaKPC-3 genes were located in a Tn4401b transposon (K. variicolan = 1; K. pneumoniaen = 2) and Tn4401d isoform (K. pneumoniaen = 28). Overall, our work describes the first report of a blaKPC-3 producing K. variicola, as well as the detection of this species during infection control measures in surveillance cultures from infected patients. It also highlights the importance of additional control measures to overcome the clonal dissemination of carbapenemase producing clones.

scholarly journals Prospective Surveillance and Rapid Whole-Genome Sequencing Detects Two Unsuspected Outbreaks of Carbapenemase-Producing Klebsiella pneumoniae in a UK Teaching Hospital

2017 ◽  
Vol 4 (suppl_1) ◽  
pp. S43-S44
Author(s):  
Estee Torok ◽  
Hayley Brodrick ◽  
Fahad Khokhar ◽  
Beth Blane ◽  
Petra Polgarova ◽  
...  
Keyword(s):  
Risk Factors ◽  
High Risk ◽  
Klebsiella Pneumoniae ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Teaching Hospital ◽  
Multidrug Resistant ◽  
Health Concern ◽  
Whole Genome ◽  
Prospective Surveillance

Abstract Background The increasing incidence of carbapenemase-producing Enterobacteriaceae (CPE) is a global health concern, as treatment options are extremely limited. The prevalence of CPE in UK hospitals is unknown, as national screening guidelines only recommend screening in patients considered to be at high-risk of CPE. Patients in intensive care units (ICU) are at high-risk of healthcare-associated infections caused by multidrug-resistant organisms (MDRO). Methods We conducted a six-month prospective surveillance study to determine the prevalence of MDRO in a UK teaching hospital ICU. Between June and December 2016, all adult patients admitted to ICU were screened for MDRO on admission, on discharge, and weekly during their ICU stay. Surveillance samples included stool or rectal swabs, urine, sputum or tracheal aspirates, and wound swabs (if wounds were present). Isolates were characterized phenotypically before undergoing whole-genome sequencing (WGS), epidemiological, and phylogenetic analyses. Results During the first week of the study we identified stool carriage of a multidrug-resistant Klebsiella pneumoniae strain in two patients neither of whom had recognized risk factors for CPE. Both isolates were resistant to all antibiotics tested, apart from colistin, and were PCR-positive for the blaNDM-1 gene. Enhanced surveillance by the infection control team identified four additional patients in several wards who had stool carriage (n = 3) or bloodstream infection (n = 1) with a blaNDM-1K. pneumoniae isolate. Epidemiological links were identified between these six patients. Five months later, a second outbreak of multidrug-resistant K. pneumoniae was detected, involving stool carriage by four patients on two different wards. Environmental screening identified environmental contamination with multidrug-resistant K. pneumoniae on one ward. DNA sequence analysis confirmed that a novel blaNDM-1K. pneumoniaelineage (ST78) was responsible for both outbreaks in the hospital. Conclusion We identified two unsuspected blaNDM-1K. pneumoniae outbreaks in patients with no recognized risk factors for CPE. This highlights the importance of prospective surveillance for MDRO in high-risk settings, such as ICUs, and supports the use of rapid WGS to support outbreak investigations in real-time. Disclosures All authors: No reported disclosures.

Can multidrug-resistant organisms become resistant to ultraviolet (UV) light following serial exposures? Characterization of post-UV genomic changes using whole-genome sequencing

2021 ◽  
pp. 1-7
Author(s):  
Hosoon Choi ◽  
Piyali Chatterjee ◽  
Munok Hwang ◽  
Eileen M. Stock ◽  
Janell S. Lukey ◽  
...  
Keyword(s):  
Klebsiella Pneumoniae ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Uv Light ◽  
Multidrug Resistant ◽  
Uv Disinfection ◽  
Whole Genome ◽  
Uv Resistance ◽  
Kill Rate ◽  
Uv Lamp

Abstract Objectives: No-touch disinfection systems like xenon- or mercury-based ultraviolet (UV) are now commonly being used for hospital room disinfection. However, serial exposure to UV light can potentially lead to the development of bacterial resistance. We sought to determine whether UV resistance develops due to serial exposure to UV light using 3 epidemiologically important multidrug-resistant microbial strains. Methods: Methicillin-resistant Staphylococcus aureus (MRSA), carbapenemase–producing Klebsiella pneumoniae (KPC) and metallo-β-lactamase–producing Klebsiella pneumoniae (MBL) were serially exposed to 25 growth-irradiation cycles of UV produced by a xenon-based UV (Xe-UV) lamp for 5 minutes or a mercury-based UV (Hg-UV) lamp for 10 minutes. After each UV exposure cycle, the surviving colony-forming units (CFUs) were measured and compared with the initial inoculum of each cycle for each strain, respectively. Results: In each cycle, ˜1–10 million of MRSA, KPC, and MBL were used to test the effect of UV irradiation. Postexposure colony counts remained low (3–100 colonies) throughout the 25 serial exposures to both xenon- and mercury-based UV. The log-kill rate after each exposure showed no changes following UV disinfection by Xe-UV. The MRSA log-kill rate increased after repeated exposure to Hg-UV unlike KPC and MBL K. pneumoniae, which did not change. Whole-genome sequencing (WGS) analyses performed on these 3 strains demonstrated no significant genetic changes after multiple UV irradiation cycles. Conclusions: Exposure of multidrug-resistant bacteria to UV produced from 2 different UV sources did not engender UV resistance after 25 serial exposures, as demonstrated by WGS analysis; thus, UV disinfection is unlikely to generate UV-resistant hospital flora.

scholarly journals mSphere of Influence: Whole-Genome Sequencing, a Vital Tool for the Interruption of Nosocomial Transmission

mSphere ◽  
2021 ◽  
Vol 6 (2) ◽  
Author(s):  
Ahmed Babiker
Keyword(s):  
Health Care ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Multidrug Resistant ◽  
Nosocomial Transmission ◽  
Whole Genome ◽  
Content Type ◽  
Genomic Epidemiology ◽  
Hospital Outbreak ◽  
Carbapenem Resistant

ABSTRACT Ahmed Babiker’s work focuses on the clinical and genomic epidemiology of multidrug-resistant health care-associated pathogens and other high-consequence pathogens. In this mSphere of Influence article, he reflects on how the paper “Tracking a Hospital Outbreak of Carbapenem-Resistant Klebsiella pneumoniae with Whole-Genome Sequencing” by Evan S. Snitkin et al. (Sci Transl Med 4:148ra116, 2012, https://doi.org/10.1126/scitranslmed.3004129) impacted his thinking on the use of whole-genome sequencing for nosocomial transmission investigation.

scholarly journals 1627. Outbreaks of Klebsiella pneumoniae in Special Care Nurseries (SCN) in Jamaica: Role of Whole-Genome Sequencing

2019 ◽  
Vol 6 (Supplement_2) ◽  
pp. S593-S593
Author(s):  
Maliha Aziz ◽  
Alison M Nicholson ◽  
Maya Nadimpalli ◽  
Sanjeev Sariya ◽  
Lance Price ◽  
...  
Keyword(s):  
Klebsiella Pneumoniae ◽  
Infection Control ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Control Strategies ◽  
Special Care ◽  
Control Measures ◽  
Nosocomial Transmission ◽  
Whole Genome ◽  
Single Source

Abstract Background Klebsiella pneumoniae is a frequent cause of neonatal sepsis and carries a high mortality rate in lower and middle-income countries (LMICs). From March-November 2015, two Jamaican hospitals experienced K. pneumoniae outbreaks in their Special Care Nurseries (SCNs). New admissions to both SCNs were temporarily halted while additional infection control strategies were implemented. 31 babies were infected, of which 15 died. International collaboration was requested to help investigate if the sepsis cases were nosocomial transmission, repeated introductions from the community, or both using whole-genome sequencing Methods We sequenced DNA from 19 outbreak isolates (n = 13 from Hospital A, n = 6 from Hospital B) on an Illumina HiSeq2500 instrument and assembled short-reads using SPAdes. We used ResFinder v3.1.0 to screen resistance genes and assigned MLSTs using in-house scripts. To compare the outbreak isolates, we selected a reference genome from among the assembled isolates, aligned raw reads using the Burrows–Wheeler Aligner (BWA), identified SNPs using GATK UnifiedGenotyper, and removed the recombined regions using Gubbins v2.3.4. We further contextualized the 19 outbreak isolates against a global collection of more than 300 K. pneumoniae genomes. Results All 13 isolates from Hospital A appeared to be from a single source. All were ST45 and encoded blaCTX-M-15, which confers extended-spectrum β-lactam (ESBL) resistance. Five of 6 isolates from Hospital B appeared to be from a separate, single source. These 5 isolates were ST268 and susceptible to most antibiotics. 1 isolate from Hospital B was ST628, encoded blaCTX-M-15, and grouped separately from other Hospital B outbreak isolates. Hospital A and B outbreak isolates formed independent, unique clades within a global K. pneumoniae collection. Conclusion Our findings indicate nosocomial transmission was responsible for both neonatal K. pneumoniae outbreaks, rather than repeat introductions from the community. The main sequence types we detected (ST45 and ST268) are not known pandemic clones and may circulate regionally. Multifaceted infection control measures were implemented for effectively halting outbreaks. Disclosures All authors: No reported disclosures.

Retrospective analysis of whole genome sequencing compared to prospective typing data in further informing the epidemiological investigation of an outbreak of Shigella sonnei in the UK

2013 ◽  
Vol 141 (12) ◽  
pp. 2568-2575 ◽  
Author(s):  
J. McDONNELL ◽  
T. DALLMAN ◽  
S. ATKIN ◽  
D. A. TURBITT ◽  
T. R. CONNOR ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Shigella Sonnei ◽  
Control Measures ◽  
Whole Genome ◽  
Single Strain ◽  
Local Schools ◽  
Infection Control Measures ◽  
Typing Methods ◽  
The Uk

SUMMARYThe aim of this study was to retrospectively assess the value of whole genome sequencing (WGS) compared to conventional typing methods in the investigation and control of an outbreak of Shigella sonnei in the Orthodox Jewish (OJ) community in the UK. The genome sequence analysis showed that the strains implicated in the outbreak formed three phylogenetically distinct clusters. One cluster represented cases associated with recent exposure to a single strain, whereas the other two clusters represented related but distinct strains of S. sonnei circulating in the OJ community across the UK. The WGS data challenged the conclusions drawn during the initial outbreak investigation and allowed cases of dysentery to be implicated or ruled out of the outbreak that were previously misclassified. This study showed that the resolution achieved using WGS would have clearly defined the outbreak, thus facilitating the promotion of infection control measures within local schools and the dissemination of a stronger public health message to the community.

Bronchoscope-associated clusters of multidrug-resistant Pseudomonas aeruginosa and carbapenem-resistant Klebsiella pneumoniae

2018 ◽  
Vol 40 (1) ◽  
pp. 40-46 ◽  
Author(s):  
Alison L. Galdys ◽  
Jane W. Marsh ◽  
Edgar Delgado ◽  
A. William Pasculle ◽  
Marissa Pacey ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Klebsiella Pneumoniae ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genetic Relatedness ◽  
Multidrug Resistant ◽  
Molecular Testing ◽  
Whole Genome ◽  
Carbapenem Resistant ◽  
Clinical Culture

AbstractObjectiveRecovery of multidrug-resistant (MDR) Pseudomonas aeruginosa and Klebsiella pneumoniae from a cluster of patients in the medical intensive care unit (MICU) prompted an epidemiologic investigation for a common exposure.MethodsClinical and microbiologic data from MICU patients were retrospectively reviewed, MICU bronchoscopes underwent culturing and borescopy, and bronchoscope reprocessing procedures were reviewed. Bronchoscope and clinical MDR isolates epidemiologically linked to the cluster underwent molecular typing using pulsed-field gel electrophoresis (PFGE) followed by whole-genome sequencing.ResultsOf the 33 case patients, 23 (70%) were exposed to a common bronchoscope (B1). Both MDR P. aeruginosa and K. pneumonia were recovered from the bronchoscope’s lumen, and borescopy revealed a luminal defect. Molecular testing demonstrated genetic relatedness among case patient and B1 isolates, providing strong evidence for horizontal bacterial transmission. MDR organism (MDRO) recovery in 19 patients was ultimately linked to B1 exposure, and 10 of 19 patients were classified as belonging to an MDRO pseudo-outbreak.ConclusionsSurveillance of bronchoscope-derived clinical culture data was important for early detection of this outbreak, and whole-genome sequencing was important for the confirmation of findings. Visualization of bronchoscope lumens to confirm integrity should be a critical component of device reprocessing.

scholarly journals An Outbreak of Streptococcus pyogenes in a Mental Health Facility: Advantage of Well-Timed Whole-Genome Sequencing Over emm Typing

2018 ◽  
Vol 39 (07) ◽  
pp. 852-860 ◽  
Author(s):  
Sarah M. Bergin ◽  
Balamurugan Periaswamy ◽  
Timothy Barkham ◽  
Hong Choon Chua ◽  
Yee Ming Mok ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Streptococcus Pyogenes ◽  
Tertiary Care ◽  
Time Frame ◽  
Control Measures ◽  
Management Decision ◽  
Whole Genome ◽  
Infection Control Measures ◽  
Genome Phylogeny

OBJECTIVEWe report the utility of whole-genome sequencing (WGS) conducted in a clinically relevant time frame (ie, sufficient for guiding management decision), in managing a Streptococcus pyogenes outbreak, and present a comparison of its performance with emm typing.SETTINGA 2,000-bed tertiary-care psychiatric hospital.METHODSActive surveillance was conducted to identify new cases of S. pyogenes. WGS guided targeted epidemiological investigations, and infection control measures were implemented. Single-nucleotide polymorphism (SNP)–based genome phylogeny, emm typing, and multilocus sequence typing (MLST) were performed. We compared the ability of WGS and emm typing to correctly identify person-to-person transmission and to guide the management of the outbreak.RESULTSThe study included 204 patients and 152 staff. We identified 35 patients and 2 staff members with S. pyogenes. WGS revealed polyclonal S. pyogenes infections with 3 genetically distinct phylogenetic clusters (C1–C3). Cluster C1 isolates were all emm type 4, sequence type 915 and had pairwise SNP differences of 0–5, which suggested recent person-to-person transmissions. Epidemiological investigation revealed that cluster C1 was mediated by dermal colonization and transmission of S. pyogenes in a male residential ward. Clusters C2 and C3 were genomically diverse, with pairwise SNP differences of 21–45 and 26–58, and emm 11 and mostly emm120, respectively. Clusters C2 and C3, which may have been considered person-to-person transmissions by emm typing, were shown by WGS to be unlikely by integrating pairwise SNP differences with epidemiology.CONCLUSIONSWGS had higher resolution than emm typing in identifying clusters with recent and ongoing person-to-person transmissions, which allowed implementation of targeted intervention to control the outbreak.Infect Control Hosp Epidemiol 2018;852–860

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