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

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.

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Centralised or Localised Pathogen Whole Genome Sequencing: Lessons Learnt From Implementation in a Clinical Diagnostic Laboratory

Frontiers in Cellular and Infection Microbiology ◽

10.3389/fcimb.2021.636290 ◽

2021 ◽

Vol 11 ◽

Author(s):

Alicia G. Beukers ◽

Frances Jenkins ◽

Sebastiaan J. van Hal

Keyword(s):

Public Health ◽

Infection Control ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Control Strategies ◽

Real Life ◽

Whole Genome ◽

Clinical Diagnostic Laboratory ◽

Diagnostic Laboratory ◽

Clinical Diagnostic

Whole genome sequencing (WGS) has had widespread use in the management of microbial outbreaks in a public health setting. Current models encompass sending isolates to a central laboratory for WGS who then produce a report for various levels of government. This model, although beneficial, has multiple shortcomings especially for localised infection control interventions and patient care. One reason for the slow rollout of WGS in clinical diagnostic laboratories has been the requirement for professionally trained personal in both wet lab techniques and in the analysis and interpretation of data, otherwise known as bioinformatics. A further bottleneck has been establishment of regulations in order to certify clinical and technical validity and demonstrate WGS as a verified diagnostic test. Nevertheless, this technology is far superior providing information that would normally require several diagnostic tests to achieve. An obvious barrier to informed outbreak tracking is turnaround time and requires isolates to be sequenced in real-time to rapidly identify chains of transmission. One way this can be achieved is through onsite hospital sequencing with a cumulative analysis approach employed. Onsite, as opposed to centralised sequencing, has added benefits including the increased agility to combine with local infection control staff to iterate through the data, finding links that aide in understanding transmission chains and inform infection control strategies. Our laboratory has recently instituted a pathogen WGS service within a diagnostic laboratory, separate to a public health laboratory. We describe our experience, address the challenges faced and demonstrate the advantages of de-centralised sequencing through real-life scenarios.

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Investigation of a suspected nosocomial transmission of blaKPC3-mediated carbapenem-resistant Klebsiella pneumoniae by whole genome sequencing

Diagnostic Microbiology and Infectious Disease ◽

10.1016/j.diagmicrobio.2015.12.019 ◽

2016 ◽

Vol 84 (4) ◽

pp. 337-342 ◽

Cited By ~ 9

Author(s):

Shangxin Yang ◽

Peera Hemarajata ◽

Janet Hindler ◽

Kevin Ward ◽

Helty Adisetiyo ◽

...

Keyword(s):

Klebsiella Pneumoniae ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Nosocomial Transmission ◽

Whole Genome ◽

Carbapenem Resistant

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Using Whole Genome Sequencing to Investigate a Mock-Outbreak of Carbapenem-Resistant Klebsiella pneumoniae in Real-Time

Acta Médica Portuguesa ◽

10.20344/amp.15174 ◽

2021 ◽

Vol 34 (13) ◽

Author(s):

Alexandra Sofia Simões ◽

Tiago Touret ◽

Nuno Alexandre Faria ◽

Susana Peres Ladeiro ◽

João Costa ◽

...

Keyword(s):

Klebsiella Pneumoniae ◽

Infection Control ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Environmental Samples ◽

Clinical Isolates ◽

Whole Genome ◽

Healthcare Associated Infections ◽

Carbapenem Resistant ◽

Healthcare Associated

Introduction: Healthcare associated infections due to carbapenem-resistant Klebsiella pneumoniae (CRKP) are a major concern in Portuguese hospitals. Whole genome sequencing (WGS) can improve infection control, but this practice is not routinely used by hospital clinical laboratories in Portugal. We simulated the investigation of a CRKP outbreak based on WGS, with the aim of determining, in the minimum possible time, genetic relatedness between CRKP clinical and environmental isolates.Material and Methods: Ten CRKP clinical isolates routinely obtained in the hospital laboratory were used. Forty environmental samples - from sinks and sink drains of ward rooms - were collected. Environmental samples were plated on selective media and presumptive CRKP colonies were isolated. Total DNA was extracted from all putative CRKP isolates and sequenced. Clonal relatedness was determined by multi-locus sequence typing and core genome single nucleotide polymorphism analysis; the presence of carbapenemase genes was evaluated.Results: Clinical isolates were characterized in 48 hours: eight strains were confirmed as CRKP, of which six were of ST13 and carried blaKPC-3. Environmental samples results were obtained in six days: eight CRKP were isolated from which five were of ST13 and carried blaKPC-3. Clinical and environmental ST13 isolates were highly related: ten (of 11) isolates differed from each other in < 0.001% of 2 172 367 core nucleotides.Discussion: WGS can be used as a high-resolution effective tool to investigate healthcare associated infections and track routes of dissemination in real-time.Conclusion: In Portugal, routine use of WGS to improve infection control could thrive through collaborative initiatives between hospitals and research institutes.

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The impact of real-time whole genome sequencing in controlling healthcare-associated SARS-CoV-2 outbreaks

10.1101/2021.04.15.21253894 ◽

2021 ◽

Author(s):

Harriet Billam ◽

Rodric V Francis ◽

Mitch Clarke ◽

Carl Yates ◽

Theocharis Tsoleridis ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Point Of Care ◽

Patient Flow ◽

Epidemiological Data ◽

Control Measures ◽

Nosocomial Transmission ◽

Whole Genome ◽

University Hospitals ◽

The Impact

Background Nosocomial infections have posed a significant problem during the COVID-19 pandemic, affecting bed capacity and patient flow in hospitals. Effective infection control measures and identifying areas of highest risk is required to reduce the risk of spread to patients who are admitted with other illnesses. This is the first pandemic where whole genome sequencing (WGS) has been readily available. We demonstrate how WGS can be deployed to help identify and control outbreaks. Aims & Methods Swabs performed on patients to detect SARS-CoV-2 underwent RT-PCR on one of multiple different platforms available at Nottingham University Hospitals NHS Trust. Positive samples underwent WGS on the GridION platform using the ARTIC amplicon sequencing protocol at the University of Nottingham. Results Phylogenetic analysis from WGS and epidemiological data was used to identify an initial transmission that occurred in the admissions ward. It also showed high prevalence of asymptomatic staff infection with genetically identical viral sequences which may have contributed to the propagation of the outbreak. Actions were taken to help reduce the risk of nosocomial transmission by the introduction of rapid point of care testing in the admissions ward and introduction of portable HEPA14 filters. WGS was also used in two instances to exclude an outbreak by discerning that the phylotypes were not identical, saving time and resources. Conclusions In conjunction with accurate epidemiological data, timely WGS can identify high risk areas of nosocomial transmission, which would benefit from implementation of appropriate control measures. Conversely, WGS can disprove nosocomial transmission, validating existing control measures and maintaining clinical service, even where epidemiological data is suggestive of an outbreak.

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Burkholderia cenocepacia ET12 transmission in adults with cystic fibrosis

Thorax ◽

10.1136/thoraxjnl-2019-214098 ◽

2019 ◽

Vol 75 (1) ◽

pp. 88-90 ◽

Cited By ~ 4

Author(s):

Ana C Blanchard ◽

Lin Tang ◽

Manal Tadros ◽

Matthew Muller ◽

Theodore Spilker ◽

...

Keyword(s):

Cystic Fibrosis ◽

Infection Control ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Genomic Data ◽

Burkholderia Cenocepacia ◽

Nosocomial Transmission ◽

Whole Genome ◽

Epidemiological Investigation

This report describes transmission of a Burkholderia cenocepacia ET12 strain (ET12-Bc) at the Toronto Adult Cystic Fibrosis (CF) Centre occurring from 2008 to 2017. Epidemiological and genomic data from 11 patients with CF were evaluated. Isolates were analysed using whole genome sequencing (WGS). Epidemiological investigation and WGS analysis suggested nosocomial transmission, despite enhanced infection control precautions. This was associated with subsequent deaths in 10 patients. ET12-Bc positive patients are no longer cared for on the same unit as ET12-Bc negative patients.

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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

Microorganisms ◽

10.3390/microorganisms8121986 ◽

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.

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