scholarly journals Whole genome sequencing reveals high clonal diversity of Escherichia coli isolated from patients in a tertiary care hospital in Moshi, Tanzania

2018 ◽  
Vol 7 (1) ◽  
Author(s):  
Tolbert Sonda ◽  
Happiness Kumburu ◽  
Marco van Zwetselaar ◽  
Michael Alifrangis ◽  
Blandina T. Mmbaga ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Tertiary Care Hospital ◽  
Tertiary Care ◽  
Clonal Diversity ◽  
Whole Genome ◽  
Care Hospital

scholarly journals 531. Practical and Evidence-Based Considerations for Implementation of Bacterial Whole-Genome Sequencing Within Longitudinal Infection Control Practice

2019 ◽  
Vol 6 (Supplement_2) ◽  
pp. S255-S255
Author(s):  
Donald S Chen ◽  
Moira Quinn ◽  
Rita M Sussner ◽  
Guiqing Wang ◽  
John T Fallon ◽  
...  
Keyword(s):  
Infection Control ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Tertiary Care ◽  
False Negative ◽  
Lessons Learned ◽  
Evidence Based ◽  
Guidance Document ◽  
Whole Genome ◽  
Care Hospital

Abstract Background Whole-genome sequencing (WGS) of bacteria is becoming a routine tool within microbiology, yet its utility to help guide infection control (IC) practice longitudinally is underexplored. As with any technology adopted in the hospital, the integration of WGS into IC practice must be carefully managed and considered. We qualitatively report an evidence-based implementation workflow that considers WGS to help proactively guide IC professionals during investigation of infectious outbreaks. Methods We built upon lessons learned in an ongoing surveillance effort at a tertiary care hospital—utilizing retrospective WGS data within the Philips IntelliSpace Epidemiology system—to understand facilitators and barriers to the use of bacterial WGS longitudinally to inform IC workflow. Our team established a 9-month workgroup to study the practical aspects of implementing WGS in routine IC practice. From expert opinion collected via the workgroup, in addition to evidence from the literature, a workflow guidance document and checklist were codified. New ideas included incorporating education to promote the establishment of an IC triage process. Results Facilitators to implementation included ability to display genomic relatedness alongside relevant patient data to enable clinical actionability, ability to pivot time and resources rapidly when infections are a pseudo outbreak (false positive) or missed outbreak (false negative), opportunities for nuanced staff education, and willingness to be a first-of-kind adopter. Barriers were communication of genomic concepts to IC professionals and relevant institutional stakeholders, maintaining sharable notes of active investigations to promote data-sharing practices, and timing and review of relevant interventions into the facility workflow. Strategies to address these issues are considered. Conclusion This study provides a novel framework for adaptation of existing IC workflow strategies to leverage the utility of bacterial WGS, and it presents a schema to effectively engage relevant stakeholders, based on an analysis of the unique challenges inherent within IC practice. It also offers an innovative model for the development and implementation of IC workflows to account for, and adapt to, site-specific conditions. Disclosures All authors: No reported disclosures.

scholarly journals Hospital Epidemiology of Methicillin-ResistantStaphylococcus aureusin a Tertiary Care Hospital in Moshi, Tanzania, as Determined by Whole Genome Sequencing

2018 ◽  
Vol 2018 ◽  
pp. 1-12 ◽  
Author(s):  
Happiness H. Kumburu ◽  
Tolbert Sonda ◽  
Pimlapas Leekitcharoenphon ◽  
Marco van Zwetselaar ◽  
Oksana Lukjancenko ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Sequence Data ◽  
Tertiary Care ◽  
Illumina Miseq ◽  
Whole Genome ◽  
Care Hospital ◽  
Gene Detection ◽  
Online Tools ◽  
Sequence Types

Objective. To determine molecular epidemiology of methicillin-resistantS. aureusin Tanzania using whole genome sequencing.Methods. DNA from 33Staphylococcusspecies was recovered from subcultured archivedStaphylococcusisolates. Whole genome sequencing was performed on Illumina Miseq using paired-end2×250 bp protocol. Raw sequence data were analyzed using online tools.Results. Full susceptibility to vancomycin and chloramphenicol was observed. Thirteen isolates (43.3%) resisted cefoxitin and other antimicrobials tested. Multilocus sequence typing revealed 13 different sequence types among the 30S. aureusisolates, with ST-8 (n= seven, 23%) being the most common. Gene detection inS.aureusstains were as follows:mecA, 10 (33.3%);pvl, 5 (16.7%);tst, 2 (6.7%). The SNP difference among the six Tanzanian ST-8 MRSA isolates ranged from 24 to 196 SNPs and from 16 to 446 SNPs when using the USA300_FPR3757 or the USA500_2395 as a reference, respectively. The mutation rate was1.38×10-11SNPs/site/year or1.4×10-6SNPs/site/year as estimated by USA300_FPR3757 or the USA500_2395, respectively.Conclusion.S. aureusisolates causing infections in hospitalized patients in Moshi are highly diverse and epidemiologically unrelated. Temporal phylogenetic analysis provided better resolution on transmission and introduction of MRSA and it may be important to include this in future routines.

scholarly journals The Stealthy Superbug: the Role of Asymptomatic Enteric Carriage in Maintaining a Long-Term Hospital Outbreak of ST228 Methicillin-Resistant Staphylococcus aureus

mBio ◽  
2016 ◽  
Vol 7 (1) ◽  
Author(s):  
Laurence Senn ◽  
Olivier Clerc ◽  
Giorgio Zanetti ◽  
Patrick Basset ◽  
Guy Prod’hom ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Tertiary Care ◽  
Enteric Pathogens ◽  
Hospital Environment ◽  
Whole Genome ◽  
Care Hospital ◽  
Methicillin Resistant

ABSTRACT Whole-genome sequencing (WGS) of 228 isolates was used to elucidate the origin and dynamics of a long-term outbreak of methicillin-resistant Staphylococcus aureus (MRSA) sequence type 228 (ST228) SCC mec I that involved 1,600 patients in a tertiary care hospital between 2008 and 2012. Combining of the sequence data with detailed metadata on patient admission and movement confirmed that the outbreak was due to the transmission of a single clonal variant of ST228, rather than repeated introductions of this clone into the hospital. We note that this clone is significantly more frequently recovered from groin and rectal swabs than other clones ( P < 0.0001) and is also significantly more transmissible between roommates ( P < 0.01). Unrecognized MRSA carriers, together with movements of patients within the hospital, also seem to have played a major role. These atypical colonization and transmission dynamics can help explain how the outbreak was maintained over the long term. This “stealthy” asymptomatic colonization of the gut, combined with heightened transmissibility (potentially reflecting a role for environmental reservoirs), means the dynamics of this outbreak share some properties with enteric pathogens such as vancomycin-resistant enterococci or Clostridium difficile . IMPORTANCE Using whole-genome sequencing, we showed that a large and prolonged outbreak of methicillin-resistant Staphylococcus aureus was due to the clonal spread of a specific strain with genetic elements adapted to the hospital environment. Unrecognized MRSA carriers, the movement of patients within the hospital, and the low detection with clinical specimens were also factors that played a role in this occurrence. The atypical colonization of the gut means the dynamics of this outbreak may share some properties with enteric pathogens.

scholarly journals Unexpected details regarding nosocomial transmission revealed by whole-genome sequencing of severe acute respiratory coronavirus virus 2 (SARS-CoV-2)

2021 ◽  
pp. 1-5
Author(s):  
Sofia Myhrman ◽  
Josefin Olausson ◽  
Johan Ringlander ◽  
Linéa Gustavsson ◽  
Hedvig E. Jakobsson ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Tertiary Care ◽  
Epidemiological Data ◽  
Infection Prevention And Control ◽  
Whole Genome ◽  
Care Hospital ◽  
Outbreak Period ◽  
Outbreak Investigations ◽  
Respiratory Coronavirus

Abstract Objective: Effective infection prevention and control (IPC) measures are key for protecting patients from nosocomial infections and require knowledge of transmission mechanisms in different settings. We performed a detailed outbreak analysis of the transmission and outcome of coronavirus disease 2019 (COVID-19) in a geriatric ward by combining whole-genome sequencing (WGS) with epidemiological data. Design: Retrospective cohort study. Setting: Tertiary-care hospital. Participants: Patients and healthcare workers (HCWs) from the ward with a nasopharyngeal sample (NPS) positive for severe acute respiratory coronavirus virus 2 (SARS-CoV-2) RNA during the outbreak period. Methods: Patient data regarding clinical characteristics, exposure and outcome were collected retrospectively from medical records. Stored NPSs from 32 patients and 15 HCWs were selected for WGS and phylogenetic analysis. Results: The median patient age was 84 years and 17 (53%) of 32 were male. Also, 14 patients (44%) died within 30 days of sampling. Viral loads were significantly higher among the deceased. WGS was successful in 28 (88%) of 32 patient samples and 14 (93%) of 15 HCW samples. Moreover, 3 separate viral clades were identified: 1 clade and 2 subclades among both patient and HCW samples. Integrated epidemiological and genetic analyses revealed 6 probable transmission events between patients and supported hospital-acquired COVID-19 among 25 of 32 patients. Conclusions: WGS provided an insight into the outbreak dynamics and true extent of nosocomial COVID-19. The extensive transmission between patients and HCWs indicated that current IPC measures were insufficient. We recommend increased use of WGS in outbreak investigations to identify otherwise unknown transmission links and to evaluate IPC measures.

scholarly journals Experimental evolution of gallium resistance in Escherichia coli

2019 ◽  
Vol 2019 (1) ◽  
pp. 169-180
Author(s):  
Joseph L Graves ◽  
Akamu J Ewunkem ◽  
Jason Ward ◽  
Constance Staley ◽  
Misty D Thomas ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Experimental Evolution ◽  
Molecular Mechanisms ◽  
Gallium Nitrate ◽  
Whole Genome ◽  
Mechanisms Of Resistance ◽  
Genomic Changes ◽  
K 12

Abstract Background and Objectives Metallic antimicrobial materials are of growing interest due to their potential to control pathogenic and multidrug-resistant bacteria. Yet we do not know if utilizing these materials can lead to genetic adaptations that produce even more dangerous bacterial varieties. Methodology Here we utilize experimental evolution to produce strains of Escherichia coli K-12 MG1655 resistant to, the iron analog, gallium nitrate (Ga(NO3)3). Whole genome sequencing was utilized to determine genomic changes associated with gallium resistance. Computational modeling was utilized to propose potential molecular mechanisms of resistance. Results By day 10 of evolution, increased gallium resistance was evident in populations cultured in medium containing a sublethal concentration of gallium. Furthermore, these populations showed increased resistance to ionic silver and iron (III), but not iron (II) and no increase in traditional antibiotic resistance compared with controls and the ancestral strain. In contrast, the control populations showed increased resistance to rifampicin relative to the gallium-resistant and ancestral population. Genomic analysis identified hard selective sweeps of mutations in several genes in the gallium (III)-resistant lines including: fecA (iron citrate outer membrane transporter), insl1 (IS30 tranposase) one intergenic mutations arsC →/→ yhiS; (arsenate reductase/pseudogene) and in one pseudogene yedN ←; (iapH/yopM family). Two additional significant intergenic polymorphisms were found at frequencies &gt; 0.500 in fepD ←/→ entS (iron-enterobactin transporter subunit/enterobactin exporter, iron-regulated) and yfgF ←/→ yfgG (cyclic-di-GMP phosphodiesterase, anaerobic/uncharacterized protein). The control populations displayed mutations in the rpoB gene, a gene associated with rifampicin resistance. Conclusions This study corroborates recent results observed in experiments utilizing pathogenic Pseudomonas strains that also showed that Gram-negative bacteria can rapidly evolve resistance to an atom that mimics an essential micronutrient and shows the pleiotropic consequences associated with this adaptation. Lay summary We utilize experimental evolution to produce strains of Escherichia coli K-12 MG1655 resistant to, the iron analog, gallium nitrate (Ga(NO3)3). Whole genome sequencing was utilized to determine genomic changes associated with gallium resistance. Computational modeling was utilized to propose potential molecular mechanisms of resistance.

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