scholarly journals Microarrays for Public Health: Genomic Epidemiology of Tuberculosis

2002 ◽  
Vol 3 (4) ◽  
pp. 362-365 ◽  
Author(s):  
Jamila Shafi ◽  
Peter W. Andrew ◽  
Michael R. Barer
Keyword(s):  
Genomic Analysis ◽  
Pcr Analysis ◽  
Outbreak Strain ◽  
Outbreak Management ◽  
Genomic Epidemiology ◽  
School Based ◽  
Rapid Pcr ◽  
Initial Comparison ◽  
Microarray Studies ◽  
Public Health Genomic

In response to a large local school-based outbreak of tuberculosis, we have been evaluating the utility of microarray bacterial genomic analysis in outbreak management. After initial comparison of the isolate from the index case withMycobacterium tuberculosisH37Rv, it was possible to design robust PCRs directed towards strain-specific deletions. Rapid PCR analysis of isolates proved valuable in determining whether or not other isolates were compatible with the outbreak strain and further microarray studies revealed genetic markers that could be used to discriminate between locally circulating strains.We suggest that this approach forms the basis for developing rapid local genotyping schemes applicable toM. tuberculosisand that application to other pathogens warrants consideration.

scholarly journals Epidemiological and Genomic analysis of a Sydney Hospital COVID-19 Outbreak

2021 ◽  
Author(s):  
Elaine Tennant ◽  
Melanie Figtree ◽  
Jo Tallon ◽  
Rowena A Bull ◽  
Malinna Yeang ◽  
...  
Keyword(s):  
Local Community ◽  
Cohort Analysis ◽  
Care Facility ◽  
Genomic Analysis ◽  
Epidemiological Data ◽  
Aged Care ◽  
Aged Care Facility ◽  
Outbreak Management ◽  
Hospital Outbreak ◽  
Hospitalised Patients

AbstractAustralia’s early COVID-19 experience involved clusters in northern Sydney, including hospital and aged-care facility (ACF) outbreaks. We explore transmission dynamics, drivers and outcomes of a metropolitan hospital COVID-19 outbreak that occurred in the context of established local community transmission. A retrospective cohort analysis is presented, with integration of viral genome sequencing, clinical and epidemiological data. We demonstrate using genomic epidemiology that the hospital outbreak (n=23) was linked to a concurrent outbreak at a local aged care facility, but was phylogenetically distinct from other community clusters. Thirty day survival was 50% for hospitalised patients (an elderly cohort with significant comorbidities) and 100% for staff. Staff who acquired infection were unable to attend work for a median of 26.5 days (range 14-191); an additional 140 staff were furloughed for quarantine. Transmission from index cases showed a wide dispersion (mean 3.5 persons infected for every patient case and 0.6 persons infected for every staff case). One patient, who received regular nebulised medication prior to their diagnosis being known, acted as an apparent superspreader. No secondary transmissions occurred from isolated cases or contacts who were quarantined prior to becoming infectious. This analysis elaborates the wide-ranging impacts on patients and staff of nosocomial COVID-19 transmission and highlights the utility of genomic analysis as an adjunct to traditional epidemiological investigations. Delayed case recognition resulted in nosocomial transmission but once recognised, prompt action by the outbreak management team and isolation with contact and droplet (without airborne) precautions were sufficient to prevent transmission within this cohort. Our findings support current PPE recommendations in Australia but demonstrate the risk of administering nebulised medications when COVID-19 is circulating locally.

scholarly journals State-wide Genomic Epidemiology Investigations of COVID-19 Infections in Healthcare Workers: Insights for Future Pandemic Preparedness

2021 ◽  
Author(s):  
Anne E Watt ◽  
Norelle L Sherry ◽  
Patiyan Andersson ◽  
Courtney R Lane ◽  
Sandra Johnson ◽  
...  
Keyword(s):  
Healthcare Workers ◽  
Genomic Analysis ◽  
Epidemiological Data ◽  
Pandemic Preparedness ◽  
Transmission Networks ◽  
Healthcare Facilities ◽  
Multiple Introductions ◽  
Genomic Epidemiology ◽  
Sequencing Coverage ◽  
Healthcare Settings

Background COVID-19 has resulted in many infections in healthcare workers (HCWs) globally. We performed state-wide SARS-CoV-2 genomic epidemiological investigations to identify HCW transmission dynamics and provide recommendations to optimise healthcare system preparedness for future outbreaks. Methods Genome sequencing was attempted on all COVID-19 cases in Victoria, Australia. We combined genomic and epidemiologic data to investigate the source of HCW infections across multiple healthcare facilities (HCFs) in the state. Phylogenetic analysis and fine-scale hierarchical clustering were performed for the entire Victorian dataset including community and healthcare cases. Facilities provided standardised epidemiological data and putative transmission links. Findings Between March and October 2020, approximately 1,240 HCW COVID-19 infection cases were identified; 765 are included here. Genomic sequencing was successful for 612 (80%) cases. Thirty-six investigations were undertaken across 12 HCFs. Genomic analysis revealed that multiple introductions of COVID-19 into facilities (31/36) were more common than single introductions (5/36). Major contributors to HCW acquisitions included mobility of staff and patients between wards and facilities, and characteristics and behaviours of individual patients including super-spreading events. Key limitations at the HCF level were identified. Interpretation Genomic epidemiological analyses enhanced understanding of HCW infections, revealing unsuspected clusters and transmission networks. Combined analysis of all HCWs and patients in a HCF should be conducted, supported by high rates of sequencing coverage for all cases in the population. Established systems for integrated genomic epidemiological investigations in healthcare settings will improve HCW safety in future pandemics.

scholarly journals Measles outbreak linked to a minority group in Austria, 2008

2009 ◽  
Vol 138 (3) ◽  
pp. 415-425 ◽  
Author(s):  
D. SCHMID ◽  
H. HOLZMANN ◽  
K. SCHWARZ ◽  
S. KASPER ◽  
H-W. KUO ◽  
...  
Keyword(s):  
Vaccination Coverage ◽  
Measles Virus ◽  
Minority Group ◽  
Age Groups ◽  
Case Definition ◽  
Outbreak Strain ◽  
School Based ◽  
Measles Outbreak ◽  
Source Case ◽  
2010 Target

SUMMARYWe report on a measles outbreak originating in an anthroposophic community in Austria, 2008. A total of 394 (94·9%) cases fulfilled the outbreak case definition including 168 cases affiliated to the anthroposophic community. The source case was a school pupil from Switzerland. The Austrian outbreak strain was genotype D5, indistinguishable from the Swiss outbreak strain. A school-based retrospective cohort study in the anthroposophic school demonstrated a vaccine effectiveness of 97·3% in pupils who had received a single dose of measles-containing vaccine and 100% in those who had received two doses. The vaccination coverage of the cases in the anthroposophic community was 0·6%. Of the 226 outbreak cases not belonging to the anthroposophic community, the 10–24 years age group was the most affected. Our findings underline the epidemiological significance of suboptimal vaccination coverage in anthroposophic communities and in older age groups of the general population in facilitating measles virus circulation. The findings of this outbreak investigation suggest that the WHO European Region is unlikely to achieve its 2010 target for measles and rubella elimination.

scholarly journals Genomic epidemiologic assessment implicates prolonged silent carriage, virulence factors and transmission between staff and patients in a NICU outbreak of MRSA.

2021 ◽  
Author(s):  
sharline madera ◽  
Nicole McNeil ◽  
Paula Hayakawa Serpa ◽  
Jack Kamm ◽  
Christy Pak ◽  
...  
Keyword(s):  
Virulence Factors ◽  
Neonatal Intensive Care ◽  
Infection Prevention ◽  
Control Strategies ◽  
Genomic Analysis ◽  
Severe Infection ◽  
Healthcare Personnel ◽  
Outbreak Strain ◽  
Early Implementation ◽  
Prevention Interventions

Introduction: Methicillin-resistant Staphylococcus aureus (MRSA) is an important pathogen in neonatal intensive care units (NICU) that carries significant morbidity and mortality. Improving our understanding of MRSA transmission dynamics, especially among high risk patients, is an infection prevention priority. Methods: We investigated a cluster of clinical MRSA cases in the NICU using a combination of epidemiologic review and whole genome sequencing (WGS) of isolates from clinical and surveillance cultures obtained from patients and healthcare personnel (HCP). Results: Phylogenetic analysis identified two genetically distinct phylogenetic clades and revealed multiple silent transmission events between HCP and infants. The predominant outbreak strain harbored multiple virulence factors. Epidemiologic investigation and genomic analysis identified a HCP colonized with the dominant MRSA outbreak strain who cared for the majority of NICU patients who were infected or colonized with the same strain, including one NICU patient with severe infection seven months before the described outbreak. These results guided implementation of infection prevention interventions that prevented further transmission events. Conclusion: Silent transmission of MRSA between HCP and NICU patients likely contributed to a NICU outbreak involving a virulent MRSA strain. WGS enabled data-driven decision making to inform implementation of infection control policies that mitigated the outbreak. Prospective WGS coupled with epidemiologic analysis can be used to detect transmission events and prompt early implementation of control strategies.

scholarly journals Genomic epidemiology of COVID-19 in care homes in the east of England

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
William L Hamilton ◽  
Gerry Tonkin-Hill ◽  
Emily R Smith ◽  
Dinesh Aggarwal ◽  
Charlotte J Houldcroft ◽  
...  
Keyword(s):  
Infection Control ◽  
Older People ◽  
Severe Disease ◽  
Care Home ◽  
Genomic Analysis ◽  
Viral Transmission ◽  
Care Homes ◽  
Temporal Data ◽  
Genomic Epidemiology ◽  
Care Home Resident

COVID-19 poses a major challenge to care homes, as SARS-CoV-2 is readily transmitted and causes disproportionately severe disease in older people. Here, 1167 residents from 337 care homes were identified from a dataset of 6600 COVID-19 cases from the East of England. Older age and being a care home resident were associated with increased mortality. SARS-CoV-2 genomes were available for 700 residents from 292 care homes. By integrating genomic and temporal data, 409 viral clusters within the 292 homes were identified, indicating two different patterns – outbreaks among care home residents and independent introductions with limited onward transmission. Approximately 70% of residents in the genomic analysis were admitted to hospital during the study, providing extensive opportunities for transmission between care homes and hospitals. Limiting viral transmission within care homes should be a key target for infection control to reduce COVID-19 mortality in this population.

scholarly journals Genomic epidemiology and global diversity of the emerging bacterial pathogen Elizabethkingia anophelis

2016 ◽  
Author(s):  
Sebastien Breurec ◽  
Alexis Criscuolo ◽  
Laure Diancourt ◽  
Olaya Rendueles-Garcia ◽  
Mathias Vandenbogaert ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Population Biology ◽  
Capsular Polysaccharide ◽  
Bacterial Pathogen ◽  
Genomic Analysis ◽  
Gene Families ◽  
Neonatal Meningitis ◽  
Genomic Epidemiology ◽  
Niche Adaptation ◽  
Antimicrobial Resistance Genes

Elizabethkingia anophelis is an emerging pathogen. Genomic analysis of strains from clinical, environmental or mosquito sources is needed to understand the epidemiological emergence of E. anophelis and to uncover genetic elements implicated in antimicrobial resistance, pathogenesis, or niche adaptation. Here, the genomic sequences of two nosocomial isolates that caused neonatal meningitis in Bangui, Central African Republic, were determined and compared with Elizabethkingia isolates from other world regions and sources. Average nucleotide identity firmly confirmed that E. anophelis, E. meningoseptica and E. miricola represent distinct genomic species and led to re-identification of several strains. Phylogenetic analysis of E. anophelis strains revealed several sublineages and demonstrated a single evolutionary origin of African clinical isolates, which carry unique antimicrobial resistance genes acquired by horizontal transfer. The Elizabethkingia genus and the species E. anophelis had pan-genomes comprising respectively 7,801 and 6,880 gene families, underlining their genomic heterogeneity. African isolates were capsulated and carried a distinctive capsular polysaccharide synthesis cluster. A core-genome multilocus sequence typing scheme applicable to all Elizabethkingia isolates was developed, made publicly available (http://bigsdb.web.pasteur.fr/elizabethkingia), and shown to provide useful insights into E. anophelis epidemiology. Furthermore, a clustered regularly interspaced short palindromic repeats (CRISPR) locus was uncovered in E. meningoseptica, E. miricola and in a few E. anophelis strains. CRISPR spacer variation was observed between the African isolates, illustrating the value of CRISPR for strain subtyping. This work demonstrates the dynamic evolution of E. anophelis genomes and provides innovative tools for Elizabethkingia identification, population biology and epidemiology.

scholarly journals Identification of a novel receptor for an invertebrate oxytocin/vasopressin superfamily peptide: molecular and functional evolution of the oxytocin/vasopressin superfamily

2004 ◽  
Vol 382 (1) ◽  
pp. 231-237 ◽  
Author(s):  
Tsuyoshi KAWADA ◽  
Atsuhiro KANDA ◽  
Hiroyuki MINAKATA ◽  
Osamu MATSUSHIMA ◽  
Honoo SATAKE
Keyword(s):  
Sequence Similarity ◽  
Genomic Analysis ◽  
Egg Laying ◽  
Pcr Analysis ◽  
High Sequence Similarity ◽  
Calcium Dependent ◽  
Functional Correlation ◽  
Dependent Signal ◽  
Egg Laying Behaviour

Annetocin is structurally related to an OT (oxytocin)/VP (vasopressin) family peptide, which has been isolated from the earthworm Eisenia foetida and has been shown to induce OT-like egg-laying behaviour. We now report the identification of an endogenous AnR (annetocin receptor). The deduced AnR precursor displays high sequence similarity with OT/VP receptors. Genomic analysis of the AnR gene revealed that the intron-inserted position is conserved between the AnR gene and the mammalian OT/VP receptor genes. These results indicate that AnR and mammalian OT/VP receptors share a common ancestor gene. Administration of annetocin to the AnR expressed in Xenopus oocytes induced a calcium-dependent signal transduction. Reverse transcriptase–PCR analysis and in situ hybridization showed that the AnR gene is expressed specifically in the nephridia located in the clitellum region, although the nephridia are distributed throughout the worm body. This result suggests that annetocin induces egg-laying behaviour through its action on the nephridia. This is the first description concerning the functional correlation between an invertebrate OT/VP-related peptide and egg-laying behaviour.

scholarly journals Molecular Epidemiology of Community-Onset (CO), Community-Onset Healthcare-Associated (CO-HA) and Hospital-Onset (HO) Methicillin-Resistant Staphylococcus aureus (MRSA)

2020 ◽  
Vol 41 (S1) ◽  
pp. s70-s71
Author(s):  
Stephanie Thiede ◽  
Darjai Payne ◽  
Alla Aroutcheva ◽  
Michael Schoeny ◽  
Robert Weinstein ◽  
...  
Keyword(s):  
Drug Use ◽  
Illicit Drug ◽  
Genomic Analysis ◽  
Illicit Drug Use ◽  
Cook County ◽  
Public Healthcare ◽  
Genomic Epidemiology ◽  
History Of ◽  
Healthcare Associated ◽  
Community Onset

Background: Previous work suggests an intermingling of community and hospital transmission networks driving the MRSA epidemic, but how those with CO-HA infections fit into the network remains unclear. We integrated epidemiologic data and whole-genome sequencing (WGS) from existing MRSA clinical isolates to determine whether there were distinguishable features of CO-HA MRSA infections that could guide interventions. Methods: We examined 955 existing clinical MRSA isolates from 2011 to 2013 from patients at Cook County Health, the major public healthcare network in Chicago, Illinois. We performed electronic and manual chart review to ascertain community (eg, illicit drug use, incarceration history) and healthcare exposures and comorbidities. WGS was performed on all sequences, and sequences were typed with multilocus sequence typing (MLST). We assessed the distribution of epidemiological factors and sequence type (ST) across onset type. Results: Infections were more frequent in males (70%); 61% of individuals with infection were African American and 21% were Hispanic. Overall, wound infections were the most common (81%) followed by blood (7%) and respiratory (6%). 82% of infections were ST8 (most USA300), 8% were ST5 (USA100) and 10% were other STs (Fig. 1a). Using standard epidemiologic definitions, we identified 523 CO, 295 CO-HA, and 137 HO infections. USA300 infections were common across CO, CO-HA, and HO categories, whereas USA100 was more frequently observed among CO-HA and HO. Current illicit drug use and history of incarceration—factors typically associated with CO-MRSA—were observed among both CO-HA and HO infections. 38% of CO-HA and 36% of HO had a history of MRSA infection or nasal colonization in the prior 6 months. As expected, 73% of CO-HA had a history of recent hospitalization, but this was also true for 44% of HO cases; points for intervention for both groups, especially CO-HA patients, include outpatient, inpatient, and ER care. Diabetes was common across categories, and HIV was more commonly observed among CO-HA cases (Fig. 1b). Conclusions: We characterized the genomic and epidemiologic features of CO-HA MRSA infections relative to CO and HO. By MLST and epidemiological analysis, CO-HA infections share similarities to both CO and HO. Although USA300 infections were the most common strain type, our findings highlight the need for WGS to discern relationships between individuals to understand the intermixing of healthcare and community networks for CO-HA infections. Higher resolution genomic analysis may help guide whether interventions need to be at hospital discharge or in the community to have the most impact on decreasing CO-HA MRSA infections.Funding: Funding: from CDC Broad Agency Announcement: Genomic Epidemiology of Community-Onset Invasive USA300 MRSA Infections; Contract ID: 75D30118C02923Disclosures: None

scholarly journals Genomic epidemiology of COVID-19 in care homes in the East of England

2020 ◽  
Author(s):  
William L. Hamilton ◽  
Gerry Tonkin-Hill ◽  
Emily Smith ◽  
Dinesh Aggarwal ◽  
Charlotte J. Houldcroft ◽  
...  
Keyword(s):  
Infection Control ◽  
Older People ◽  
Severe Disease ◽  
Care Home ◽  
Genomic Analysis ◽  
Viral Transmission ◽  
Care Homes ◽  
Temporal Data ◽  
Genomic Epidemiology ◽  
Care Home Resident

AbstractCOVID-19 poses a major challenge to care homes, as SARS-CoV-2 is readily transmitted and causes disproportionately severe disease in older people. Here, we report on 6,600 COVID-19 cases from the East of England, 1,167 of which were identified as residents from 337 care homes. Older age and being a care home resident were associated with increased mortality. SARS-CoV-2 genomes were available for 700 residents from 292 care homes. By integrating genomic and temporal data we defined 409 viral clusters within the 292 homes, indicating two different patterns - outbreaks among care home residents and independent introductions with limited onward transmission. Approximately 70% of residents in the genomic analysis were admitted to hospital during the study period, providing extensive opportunities for transmission between care homes and hospitals. Limiting viral transmission between care home residents should be a key target for infection control to reduce COVID-19 mortality in this population.

scholarly journals Genomic Epidemiology and Global Population Structure of Exfoliative Toxin A-Producing Staphylococcus aureus Strains Associated With Staphylococcal Scalded Skin Syndrome

2021 ◽  
Vol 12 ◽  
Author(s):  
Taj Azarian ◽  
Eleonora Cella ◽  
Sarah L. Baines ◽  
Margot J. Shumaker ◽  
Carol Samel ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Neonatal Intensive Care ◽  
Genomic Analysis ◽  
Global Distribution ◽  
Toxin A ◽  
Staphylococcal Scalded Skin Syndrome ◽  
Genomic Epidemiology ◽  
Exfoliative Toxin ◽  
Causative Agents ◽  
Global Population

Staphylococci producing exfoliative toxins are the causative agents of staphylococcal scalded skin syndrome (SSSS). Exfoliative toxin A (ETA) is encoded by eta, which is harbored on a temperate bacteriophage ΦETA. A recent increase in the incidence of SSSS in North America has been observed; yet it is largely unknown whether this is the result of host range expansion of ΦETA or migration and emergence of established lineages. Here, we detail an outbreak investigation of SSSS in a neonatal intensive care unit, for which we applied whole-genome sequencing (WGS) and phylogenetic analysis of Staphylococcus aureus isolates collected from cases and screening of healthcare workers. We identified the causative strain as a methicillin-susceptible S. aureus (MSSA) sequence type 582 (ST582) possessing ΦETA. To then elucidate the global distribution of ΦETA among staphylococci, we used a recently developed tool to query extant bacterial WGS data for biosamples containing eta, which yielded 436 genomes collected between 1994 and 2019 from 32 countries. Applying population genomic analysis, we resolved the global distribution of S. aureus with lysogenized ΦETA and assessed antibiotic resistance determinants as well as the diversity of ΦETA. The population is highly structured with eight dominant sequence clusters (SCs) that generally aligned with S. aureus ST clonal complexes. The most prevalent STs included ST109 (24.3%), ST15 (13.1%), ST121 (10.1%), and ST582 (7.1%). Among strains with available data, there was an even distribution of isolates from carriage and disease. Only the SC containing ST121 had significantly more isolates collected from disease (69%, n = 46) than carriage (31%, n = 21). Further, we identified 10.6% (46/436) of strains as methicillin-resistant S. aureus (MRSA) based on the presence of mecA and the SCCmec element. Assessment of ΦETA diversity based on nucleotide identity revealed 27 phylogroups, and prophage gene content further resolved 62 clusters. ΦETA was relatively stable within lineages, yet prophage variation is geographically structured. This suggests that the reported increase in incidence is associated with migration and expansion of existing lineages, not the movement of ΦETA to new genomic backgrounds. This revised global view reveals that ΦETA is diverse and is widely distributed on multiple genomic backgrounds whose distribution varies geographically.

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