Role Of Whole Genome Sequencing Research Articles

Understanding the potential role of whole genome sequencing (WGS) in managing patients with gonorrhoea: A systematic review of WGS use on human pathogens in individual patient care

The utility of whole genome sequencing (WGS) to inform sexually transmitted infection (STI) patient management is unclear. Timely WGS data might support clinical management of STIs by characterising epidemiological links and antimicrobial resistance profiles. We conducted a systematic review of clinical application of WGS to any human pathogen that may be transposable to gonorrhoea. We searched six databases for articles published between 01/01/2010-06/02/2023 that reported on real/near real-time human pathogen WGS to inform clinical intervention. All article types from all settings were included. Findings were analysed using narrative synthesis. We identified 12,179 articles, of which eight reported applications to inform tuberculosis (n=7) and gonorrhoea (n=1) clinical patient management. WGS data were successfully used as an adjunct to clinical and epidemiological data to enhance contact-tracing (n=2), inform antimicrobial therapy (n=5) and identify cross-contamination (n=1). WGS identified gonorrhoea transmission chains that were not established via partner notification. Future applications could include insights into pathogen exposure detected within sexual networks for targeted patient management. While there was some evidence of WGS use to provide individualised tuberculosis and gonorrhoea treatment, the eight identified studies contained few participants. Future research should focus on testing WGS intervention effectiveness and examining ethical considerations of STI WGS use.

Role of Whole Genome Sequencing in Assessing Resident and Transient Listeria monocytogenes in a Produce Packinghouse

Whole genome sequencing (WGS) is a powerful tool that may be used to assist in identifying Listeria contamination sources and movement within environments, and to assess persistence. This study investigated sites in a produce packinghouse where Listeria had been historically isolated; and aimed to characterize dispersal patterns and identify cases of transient and resident Listeria. Environmental swab samples (n = 402) were collected from 67 sites at two time-points on three separate visits. Each sample was tested for Listeria, and Listeria isolates were characterized by partial sigB sequencing to determine species and allelic type (AT). Representative isolates from the three most common L. monocytogenes ATs (n = 79) were further characterized by WGS. Of the 144 Listeria species positive samples (35.8%), L. monocytogenes was the most prevalent species. L. monocytogenes was often coisolated with another species of Listeria. WGS identified cases of sporadic and continued reintroduction of L. monocytogenes from the cold storages into the packinghouse and demonstrated cases of L. monocytogenes persistence over 2 years in cold storages, drains, and on a forklift. Nine distinct clusters were found in this study. Two clusters showed evidence of persistence. Isolates in these two clusters (N = 11, with one historical isolate) were obtained predominantly and over multiple samplings from cold storages, with sporadic movement to sites in the packing area, suggesting residence in cold storages with opportunistic dispersal within the packinghouse. The other seven clusters demonstrated evidence of transient Listeria, as isolation was sporadic over time and space during the packing season. Our data provide important insights into likely L. monocytogenes harborage points and transfer in a packinghouse, which is key to root cause analysis. While results support Listeria spp. as a suitable indicator organism for environmental monitoring surveys, findings were unable to establish a specific species as an index organism for L. monocytogenes. Findings also suggest long-term persistence with substantial SNP diversification, which may assist in identifying potential contamination sources and implementing control measures.

Whole genome sequencing in the 100,000 Genomes project identifies a RYR2 variant associating with dilated cardiomyopathy and sudden unexpected death in the young

Abstract Funding Acknowledgements Type of funding sources: None. Background Previous studies have shown genetic testing in sudden unexpected death in the young (SUDY) cases identify a pathogenic variant in 13-27% of cases. This diagnostic yield increased up to 39% when genetic testing was combined with family evaluation. The 100,000 Genomes Project was launched to investigate the role of whole genome sequencing (WGS) as a diagnostic tool for cancers and rare diseases in a national health care system. Young sudden death victims with no finding on postmortem testing were enrolled to the SUDY cohort. Purpose We aimed to analyse WGS data in the SUDY cohort of 100,000 Genomes Project with panel analysis and trio studies in order to examine the yield of WGS in this population. Methods Sudden death victims, aged 40 or younger, without pre-existing condition that would explain the event and with no diagnosis established on postmortem examination were enrolled between 2017 and 2019 at different Genomic Medicine Centres (GMCs) across the UK. Parents were recruited in all paediatric cases. DNA sequencing was performed by Illumina. The platform's automated pipeline was used for variant calling. Panel based and hypothesis free approaches were used for data analysis. Variant analysis was performed with focus on variants with combined annotation-dependent depletion (CADD) score >15 and American College of Medical Genetics and Genomics (ACMG) classification of pathogenic (P), likely pathogenic (LP), or variant of unknown significance (VUS). Results A total of 15 participants, including 6 trios, were included in the study. Participants had a median age of 18 [IQR 1-29.5] and two thirds were male. Following assessment of all protein coding and intronic variants identified, only the missense variant RYR2:c.10046C>T (p.Ser3349Leu) was thought to be suitable for investigation for upgrade to likely pathogenic, giving a diagnostic yield of 6.67% for WGS in SUDY cases. This variant was detected in a 24-year-old sudden death victim. Family evaluation led to the diagnosis of dilated cardiomyopathy (DCM) in four family members and segregation testing confirmed affected family members harboured the variant. Further investigation in 100,000 Genomes Project, laboratory data, and our inherited cardiac conditions database as well as previous publications, identified additional cases of this variant in association with DCM and sudden cardiac death (see table and figure). Conclusion WGS with targeted gene analysis can be an effective diagnostic tool for SUDY. The study’s findings show the importance of large population databases and collaboration in the research community, allowing reclassification of a RYR2 VUS as a LP variant, the strongest genetic data so far to associate a missense variant with familial DCM and the risk for SCD. This research was made possible through access to the data and findings generated by the 100,000 Genomes Project.

New Horizons in the Diagnosis of Tuberculosis of the Spine: The Role of Whole Genome Sequencing.

Prospective study. To evaluate the utility of whole genome sequencing (WGS) in drug resistance testing, lineage of the organisms, and organism- related factors responsible for bacilli settling in the spine. The workstream for the diagnosis of tuberculosis (TB) involves isolation and culture of the organism and drug resistance testing using phenotypic methods. Xpert MTB/RIF Ultra is a genetic-based method that detects for Mycobacterium tuberculosis DNA in the rpoB gene. Meanwhile, WGS is a newer genetic-based method that assesses the whole genome of the bacterium. Very few studies have reported the use of WGS for extrapulmonary TB. Herein, we used WGS to diagnose spinal TB. Tissues from 61 patients undergoing surgery for spinal TB underwent histologic examination, Xpert MTB/RIF Ultra, and culture and sensitivity testing. DNA from the cultured bacteria was sent for WGS. The test bacterial genome was compared to a reference strain of pulmonary TB. Acid-fast bacilli were observed in 9/58 specimens. Meanwhile, histology confirmed TB in all the patients. Bacilli were cultured in 28 patients (48.3%), and the average time to culture was 18.7 days. Xpert MTB/RIF Ultra was positive in 47 patients (85%). WGS was performed in 23 specimens. Overall, 45% of the strains belonged to lineage 2 (East Asian). There was one case of multidrug- resistant TB and two cases of non-tuberculous mycobacteria on WGS. We could not confirm any genomic difference between pulmonary and spinal TB strains. Xpert MTB/RIF Ultra of tissues or pus is the investigation of choice when diagnosing spinal TB. Meanwhile, WGS can diagnose multidrug-resistant TB and non-tuberculous mycobacteria more accurately. No mutations were identified in spinal and pulmonary TB bacteria.

Metagenomics and Whole Genome Sequencing in Clinical Microbiology: A Narrative Review

The role of Whole Genome Sequencing (WGS) in clinical microbiology is increasing and is not restricted to molecular epidemiology alone. With the advent of third-generation sequencing technologies, its applications in infectious disease diagnostics have further expanded to include the direct identification of microorganisms from primary clinical samples, prediction of antimicrobial resistance (including antiviral resistance) by detecting resistance genes, and detection of virulence genes. Untargeted metagenomic sequencing of clinical samples can provide a promising platform for the comprehensive diagnosis of infections. This article outlines the applications and scope of WGS and metagenomic sequencing in routine clinical microbiology, along with the challenges and practical issues in their implementation.

Multidrug-resistant tuberculosis in Finland: treatment outcome and the role of whole-genome sequencing.

Treatment of multidrug-resistant tuberculosis (MDR-TB) is a global challenge requiring long treatment with costly drugs. We assessed treatment combinations, outcome and the utility of whole-genome sequencing (WGS) in MDR-TB cases. Clinical, demographic and microbiological data were obtained of all patients with MDR-TB who started treatment in Finland in 2007-2016. Definitions of MDR, pre-extensively drug-resistant (pre-XDR) and XDR tuberculosis were those applicable at the study period. Treatment outcome was defined according to World Health Organization (WHO) guidelines. Mycobacterium tuberculosis isolates were analysed by WGS in addition to routinely performed phenotypic drug susceptibility testing and genotyping. Among the 47 cases, 35 (74%) had a successful treatment outcome. Risk factors for non-successful outcome were Finnish origin and XDR. Almost 90% of our cases had an adverse event for at least one drug. Phenotypic and WGS drug resistance results were fully concordant for isoniazid, fluoroquinolones and amikacin, and >90% concordant for rifampicin, pyrazinamide, kanamycin and capreomycin. >60% of phenotypically ethambutol-susceptible isolates were genotypically resistant. The results of the rifampicin and isoniazid nucleic acid amplification tests (NAATs) performed for the isolates were identical to the WGS results except for three isolates having uncommon resistance mutations not included in the NAATs. WGS did not reveal unexpected clustering. More training is needed for physicians treating MDR-TB, and especially XDR-TB, to improve treatment outcome. Phenotypic drug susceptibility testing was shown to be unreliable for ethambutol. WGS could aid in the selection of optimal treatment regimen in the future.

Promising Role of Whole Genome Sequencing in Blood Cancers

Promising Role of Whole Genome Sequencing in Blood Cancers

Prosthetic hip joint infection by Bacillus Calmette-Guerin therapy following intravesical instillation for bladder cancer identified using whole-genome sequencing: a case report

BackgroundJoint replacement is an effective intervention and prosthetic joint infection (PJI) is one of the most serious complications of such surgery. Diagnosis of PJI is often complex and requires multiple modalities of investigation. We describe a rare cause of PJI which highlights these challenges and the role of whole-genome sequencing to achieve a rapid microbiological diagnosis to facilitate prompt and appropriate management.Case presentationA 79-year-old man developed chronic hip pain associated with a soft-tissue mass, fluid collection and sinus adjacent to his eight-year-old hip prosthesis. His symptoms started after intravesical Bacillus Calmette-Guerin (BCG) therapy for bladder cancer. Synovasure™ and 16S polymerase chain reaction (PCR) tests were negative, but culture of the periarticular mass and genome sequencing diagnosed BCG infection. He underwent a two-stage joint revision and a prolonged duration of antibiotic therapy which was curative.ConclusionsBCG PJI after therapeutic exposure can have serious consequences, and awareness of this potential complication, identified from patient history, is essential. In addition, requesting appropriate testing is required, together with recognition that traditional diagnostics may be negative in non-pyogenic PJI. Advanced molecular techniques have a role to enhance the timely management of these infections.

Genomic Investigation of Virulence Potential in Shiga Toxin Escherichia coli (STEC) Strains From a Semi-Hard Raw Milk Cheese.

Shiga-toxin-producing Escherichia coli (STEC) represents a significant cause of foodborne disease. In the last years, an increasing number of STEC infections associated with the consumption of raw and pasteurized milk cheese have been reported, contributing to raise the public awareness. The aim of this study is to evaluate the main genomic features of STEC strains isolated from a semi-hard raw milk cheese, focusing on their pathogenic potential. The analysis of 75 cheese samples collected during the period between April 2019 and January 2020 led to the isolation of seven strains from four stx-positive enrichment. The genome investigation evidenced the persistence of two serotypes, O174:H2 and O116:H48. All strains carried at least one stx gene and were negative for eae gene. The virulence gene pattern was homogeneous among the serogroup/ST and included adherence factors (lpfA, iha, ompT, papC, saa, sab, hra, and hes), enterohemolysin (ehxA), serum resistance (iss, tra), cytotoxin-encoding genes like epeA and espP, and the Locus of Adhesion and Autoaggregation Pathogenicity Islands (LAA PAIs) typically found in Locus of Enterocyte Effacement (LEE)-negative STEC. Genome plasticity indicators, namely, prophagic sequences carrying stx genes and plasmid replicons, were detected, leading to the possibility to share virulence determinants with other strains. Overall, our work adds new knowledge on STEC monitoring in raw milk dairy products, underlining the fundamental role of whole genome sequencing (WGS) for typing these unknown isolates. Since, up to now, some details about STEC pathogenesis mechanism is lacking, the continuous monitoring in order to protect human health and increase knowledge about STEC genetic features becomes essential.

Role of Whole-Genome Sequencing in Characterizing the Mechanism of Action of para-Aminosalicylic Acid and Its Resistance.

para-Aminosalicylic acid (PAS) remains one of the drugs of last resort for the treatment of tuberculosis, but its mechanism of action is still not completely understood. The main aim of this project was to identify new potential mechanisms of action and resistance to PAS by performing whole-genome sequencing on PAS-resistant laboratory mutants. A new variant in the folC gene was identified, as well as some other mutations that require further study.

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

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 sequencingMethodsWe 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.ResultsAll 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.ConclusionOur 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.

1256. New Acquisitions of ET-12 Burkholderia cenocepacia in Adults With Cystic Fibrosis: Role of Whole Genome Sequencing in Outbreak Investigation

BackgroundTransmission of Burkholderia cenocepacia ET-12 strain (ET-12Bc) can cause epidemics in the cystic fibrosis (CF) population. The Toronto Adult CF center currently follows 500 patients; 20% have infection with B. cepacia complex (BCC), including 48 patients infected with ET-12Bc. The center adheres to the 2013 infection prevention and control guidelines and patients are also segregated by clinics. Despite this, there have been 11 new acquisitions of ET-12Bc since 2008. The objective of this study was to describe the investigation of an ET-12Bc outbreak in CF patients, using whole-genome sequencing (WGS).MethodsInvestigations included multilocus sequence typing (MLST) and WGS of 34 isolates (11 new ET-12Bc acquisitions, 18 isolates of known ET-12Bc patients (including all patients with hospital admissions that overlapped with new acquisitions), four isolates from CF patients in the USA and the J2315 reference strain). Each of the seven MLST alleles from ET12Bc strain J2315 was downloaded from PubMLST and used to “Blast” each of the 16 WGS databases. WGS was done using 150 bp paired-end runs on an Illumina HiSeq4000. Single nucleotide polymorphisms (SNPs) between the newly sequenced strains and J2315 were profiled.ResultsTen patients had a hospital admission within the 2 months preceding their first ET-12Bc positive sputum culture, except for one in whom ET-12Bc was detected 12 months following hospital admission. In all isolates, the seven alleles (atpD, gltB, gyrB, recA, lepA, phaC and trpB) matched 100% to sequence type 28 and clonal complex 31, and were identical to J2315. WGS SNP analysis confirmed that transmission occurred from known cases on the unit in 10/11 (90.9%) patients. To date, 8/11 patients with new acquisitions have died (median survival of 95 days).ConclusionOur investigations found epidemiological evidence suggestive of ET-12Bc transmission on the CF unit, which was confirmed by MLST and WGS SNP analysis. Compared with MLST, WGS SNP analysis had better discriminatory power and was well correlated with the identified epidemiological links between patients. Recognition of ET-12Bc transmission with associated high mortality rates has led to a change in our hospital policy. ET-12Bc positive patients will no longer be cared for on the same unit as ET-12Bc negative patients with CF.Disclosures All authors: No reported disclosures.

798. The Role of Whole-Genome Sequencing in Characterizing the Mechanism of Action of Anti-Tuberculosis Compounds: Demonstrated With Para-Amino Salicylic Acid and Its Analogue

BackgroundPara-aminosalicylic acid (PAS) was one of the first antibiotics to be used against tuberculosis (TB) and it is still one of the last remaining drugs available to treat extensively drug-resistant (XDR) disease. Despite being on the market for decades, the mechanism of action of PAS is not completely understood yet. Sixteen new compounds against Mycobacterium tuberculosis were created in the laboratory as salicylate analogues (based on their chemical structures) and their antimycobacterial activity had never been tested before. The main aim of this project was to test the activity of these new analogues and to understand their mechanism of action (including PAS).MethodsThe compounds were tested using three different methods (spot culture, resazurin, and MGIT system). Additionally, resistant mutants were created against PAS and the most promising analogue; whole-genome sequencing (WGS) was performed to understand their mechanism of action.ResultsOne compound in particular, AD25a, showed the lowest critical concentration (0.04 µg/mL) among the salicylate analogues. The WGS analysis identified a total of 28 single nucleotide polymorphisms (SNPs) in the AD25a-resistant mutants and 40 SNPs in the PAS-resistant mutants (when compared with the reference strain H37Rv). The SNPs identified in the AD25a and PAS-resistant mutants did not overlap. The genes rrs, rrl and folC were mostly involved in the PAS-resistant mutants.ConclusionThe complete difference in the mutation profiles suggests that AD25a has a mechanism of action different to that of PAS, despite AD25a being synthesized as a salicylate analogue. WGS analysis of PAS-resistant mutants has also provided some interesting results. In particular, all our PAS mutants showed mutations in the rrs and rrl genes (16S and 23S RNA genes, respectively). These mutations should affect the ribosomes and the overall synthesis of proteins. This highlights a new potential mechanism of resistance for PAS that has never been observed before.Disclosures All authors: No reported disclosures.

The role of whole genome sequencing in monitoring antimicrobial resistance: A biosafety and public health priority in the Arabian Peninsula.

The recent declaration by the United Nations to establish an interagency coordination group (IACG) on antimicrobial resistance (AMR) emphasises the global nature of the AMR threat. Rapid dissemination and spread of AMR is exacerbated by the movements of humans, animals, foods and materials. International monitoring and surveillance of AMR indicates to policy makers, regulators and auditors the magnitude of the problem and also informs appropriate and mindful interventions that will impact public health policy and mitigate AMR. Identifying the drivers of AMR requires a 'one-health' approach to capture cross-sectoral utilization, phenotypic and genetic data. Capacity building in diagnostic and reference laboratories is required for traditional phenotypic testing as well as newer technologies (e.g. whole genome sequencing, WGS), in order to enhance the detection, characterisation, tracking and surveillance of AMR. The Gulf Health Council (GHC) for the cooperation council states have developed national AMR plans and will standardise pathogen identification and susceptibility testing to gain useful, reliable and comparable data. Additional plans are to establish, for the region, a state-of-the-art 'one-health' WGS service to identify and examine emerging AMR issues as well as the associated healthcare and financial burden(s). Currently, there is a paucity of WGS based research for tackling AMR challenges in the GHC countries. In this article, we have considered the current surveillance landscape and the potential role of whole genome sequencing (WGS) for monitoring antimicrobial resistance in the Arabian Peninsula. We highlighted the importance of using WGS for monitoring AMR in these countries as there remains a dearth of microbial genomic data and studies from the GHC countries. Development of WGS-based AMR surveillance is required to identify the burden and prevalence of AMR in the GHC countries.

Epidemiological and genomic determinants of tuberculosis outbreaks in First Nations communities in Canada

BackgroundIn Canada, tuberculosis disproportionately affects foreign-born and First Nations populations. Within First Nations’ peoples, a high proportion of cases occur in association with outbreaks. Tuberculosis transmission in the context of outbreaks is thought to result from the convergence of several factors including characteristics of the cases, contacts, the environment, and the pathogen.MethodsWe examined the epidemiological and genomic determinants of two well-characterized tuberculosis outbreaks attributed to two super-spreaders among First Nations in the province of Alberta. These outbreaks were associated with two distinct DNA fingerprints (restriction fragment-length polymorphisms or RFLPs 0.0142 and 0.0728). We compared outbreak isolates with endemic isolates not spatio-temporarily linked to outbreak cases. We extracted epidemiological variables pertaining to tuberculosis cases and contacts from individual public health records and the provincial tuberculosis registry. We conducted group analyses using parametric and non-parametric statistical tests. We carried out whole-genome sequencing and bioinformatic analysis using validated protocols.ResultsWe observed differences between outbreak and endemic groups in the mean number of total and child-aged contacts and the number of contacts with new positive and converted tuberculin skin tests in all group comparisons (p < 0.05). Differences were also detected in the proportion of cases with cavitation on a chest radiograph and the mean number of close contacts in selected group comparisons (p < 0.02). A phylogenetic network analysis of whole-genome sequencing data indicated that most outbreak and endemic strains were closely related to the source case for the 0.0142 fingerprint. For the 0.0728 fingerprint, the source case haplotype was circulating among endemic cases prior to the outbreak. Genetic and temporal distances were not correlated for either RFLP 0.0142 (r2 = − 0.05) or RFLP 0.0728 (r2 = 0.09) when all isolates were analyzed.ConclusionsWe found no evidence that endemic strains acquired mutations resulting in their emergence in outbreak form. We conclude that the propagation of these outbreaks was likely driven by the combination of characteristics of the source cases, contacts, and the environment. The role of whole-genome sequencing in understanding mycobacterial evolution and in assisting public health authorities in conducting contact investigations and managing outbreaks is important and expected to grow in the future.

Unmasking leading to a healthcare worker Mycobacterium tuberculosis transmission

Mycobacterium tuberculosis is a major health burden worldwide. The disease may present as an individual case, community outbreak, or more rarely as a nosocomial outbreak. Even in countries with a low prevalence such as the UK, tuberculosis (TB) presents a risk to healthcare workers (HCWs). To report an outbreak which manifested 12 months after a patient with pulmonary tuberculosis was admitted to Queen Elizabeth Hospital Birmingham. We present the epidemiological and outbreak investigations; the role of whole genome sequencing (WGS) in identifying the outbreak and control measures to prevent further outbreaks. Subsequent to a diagnosis of open TB in a patient, transmission was confirmed in one HCW who had active TB; HCWs with latent TB infection (LTBI) were also identified among seven HCW contacts of the index patient. Of note, all the LBTI patients had other risk factors for TB. Routine use of WGS identified the outbreak link between the index patient and the HCW with active TB disease, and informed our investigations. Exposure most likely occurred during an aerosol-generating procedure (AGP) which was done in accordance with national guidance at that time without using respiratory protection. Enhanced control measures were implemented following the outbreak.

Management and investigation of a Serratia marcescens outbreak in a neonatal unit in Switzerland – the role of hand hygiene and whole genome sequencing

BackgroundMany outbreaks due to Serratia marcescens among neonates have been described in the literature but little is known about the role of whole genome sequencing in outbreak analysis and management.MethodsBetween February and March 2013, 2 neonates and 2 infants previously hospitalised in the neonatal unit of a tertiary care centre in Switzerland, were found to be colonised with S. marcescens. An investigation was launched with extensive environmental sampling and neonatal screening in four consecutive point prevalence surveys between April and May 2013. All identified isolates were first investigated by fingerprinting and later by whole genome sequencing. Audits of best practices were performed and a hand hygiene promotion programme was implemented.ResultsTwenty neonates were colonised with S. marcescens. No invasive infection due to S. marcescens occurred. All 231 environmental samples were negative. Hand hygiene compliance improved from 51% in April 2013 to 79% in May 2013 and remained high thereafter. No S. marcescens was identified in point prevalence surveys in June and October 2013. All strains were identical in the fingerprinting analysis and closely related according to whole genome sequencing.ConclusionsImproving best practices and particularly hand hygiene proved effective in terminating the outbreak. Whole genome sequencing is a helpful tool for genotyping because it allows both sufficient discrimination of strains and comparison to other outbreaks through the use of an emerging international database.

Control of healthcare- and community-associated MRSA: recent progress and persisting challenges.

Healthcare adapted meticillin-resistant Staphylococcus aureus (MRSA) has spread to hospitals around the world over 50 years. More recently, other strains of MRSA have emerged with the ability to spread in the community and infect otherwise healthy individuals. Morbidity and mortality associated with MRSA remains high and its control in both the healthcare and community setting has proven challenging. Pubmed (Medline). The use of targeted screening and decolonization, hand hygiene and antimicrobial stewardship is supported by the most robust studies, though many studies have implemented bundles for effective healthcare-associated (HA)-MRSA control. Universal screening, universal decolonization and contact precautions for HA-MRSA control are supported by less evidence. Some interventions may not be cost-effective. Contact precautions may be associated with potential for patient harm. Evidence for effective control community acquired (CA)-MRSA is largely lacking. Programmes that focus on implementing bundles of interventions aimed at targeting HA-MRSA are more likely to be effective, with an emphasis on hand hygiene as a key component. Control of CA-MRSA is likely to be more difficult to achieve and relies on prevalence, risk factors and community healthcare interactions on a broader scale. Further research in the area of CA-MRSA in particular is required. Antimicrobial stewardship for both CA and HA-MRSA is promising, as is the role of whole genome sequencing in characterizing transmission. However, further work is required to assess their long-term roles in controlling MRSA. With many institutions applying widespread use of chlorhexidine washes, monitoring for chlorhexidine resistance is paramount to sustaining efforts at controlling MRSA.

Tracking and responding to an outbreak of tuberculosis using MIRU-VNTR genotyping and whole genome sequencing as epidemiological tools.

We describe an outbreak that contributed to a near doubling of the incidence of tuberculosis in Southampton, UK. We examine the importance of 24 locus mycobacterial interspersed repetitive unit variable number tandem repeat (MIRU-VNTR) genotyping in its identification and management and the role of whole genome sequencing (WGS) in tracing the spread of the strain. Outbreak cases were defined as those diagnosed between January and December 2011 with indistinguishable 24 locus-MIRU-VNTR genotypes or, cases linked epidemiologically. A cluster questionnaire was administered by TB nurses to identify contacts and social settings. Overall, 25 patients fulfilled the case definition. No cases with this MIRU-VNTR genotype had been detected in the UK previously. Connections were found between all cases through household contacts or social venues including a football club, Internet cafe and barber's shop. Public health actions included extended contact tracing, venue screening and TB awareness-raising. The outbreak resulted in a high rate of transmission and high incidence of clinical disease among contacts. This outbreak illustrates the value of combining active case-finding with prospective MIRU-VNTR genotyping to identify settings to undertake public health action. In addition WGS revealed that the VNTR-defined cluster was a single outbreak and that active TB transmission not reactivation was responsible for this outbreak in non-UK born individuals.

The Role of Whole Genome Sequencing in Defining Institutional Influenza Outbreaks

The Role of Whole Genome Sequencing in Defining Institutional Influenza Outbreaks