Publications by authors named "Vatsala Srinivasa"
Background: Respiratory virus transmission in healthcare settings is not well understood. To investigate the transmission dynamics of common healthcare-associated respiratory virus infections, we performed retrospective whole genome sequencing (WGS) surveillance at one pediatric and two adult teaching hospitals in Pittsburgh, PA.
Methods: From January 2, 2018, to January 4, 2020, nasal swab specimens positive for rhinovirus, influenza, human metapneumovirus (HMPV), or respiratory syncytial virus (RSV) from patients hospitalized for ≥3 days were sequenced on Illumina platform.
Article Synopsis
- Current outbreak detection methods in hospitals are inadequate on their own; a new program called the Enhanced Detection System for Healthcare-associated Transmission (EDS-HAT) uses real-time genomic surveillance to identify outbreaks.
- The study, conducted at UPMC Presbyterian Hospital from November 2021 to October 2023, involved weekly whole genome sequencing of bacterial isolates, leading to the identification of 172 outbreaks and successful intervention strategies that prevented further transmission in over 95% of cases.
- Results revealed significant benefits: 62 infections were avoided, translating to over $1 million in gross savings and a net savings of nearly $700,000, showing that integrating genomic surveillance can greatly enhance infection control and patient safety.
Prolonged bacterial carriage and hospital transmission detected by whole genome sequencing surveillance.
Antimicrob Steward Healthc Epidemiol
January 2024
Article Synopsis
- NDM (New Delhi metallo-β-lactamase) is a significant threat due to its role in carbapenem resistance, leading to high mortality and few treatment options.
- An outbreak at an acute care hospital was detected using traditional infection prevention methods and supplemented with weekly whole genome sequencing (WGS), which revealed complex plasmid transfer dynamics between various bacterial species.
- The investigation identified 15 patients with NDM-5-producing Enterobacterales, illustrating the effectiveness of combining traditional and genomic approaches in tracking and controlling outbreaks involving plasmid transfer and bacterial spread.
Incidence and transmission associated with respiratory viruses in an acute care facility: An observational study.
Infect Control Hosp Epidemiol
June 2024
We estimated the extent of respiratory virus transmission over three pre-COVID-19 seasons. Of 16,273 assays, 22.9% (3,726) detected ≥1 respiratory virus.
View Article and Find Full Text PDFArticle Synopsis
- Many bacterial species are resistant to antibiotics, making infections hard to treat and prompting interest in bacteriophage therapy as an alternative.
- Researchers investigated the ability of prophages (virus-like elements in bacteria) in these species to kill similar and different bacterial strains, identifying four distinct phages with varying effectiveness.
- The study indicates that prophages in bacteria could be a valuable resource for developing new phage therapy options, particularly since one type of bacteria was found to be more susceptible to these phages than another.
The utility of whole-genome sequencing to inform epidemiologic investigations of SARS-CoV-2 clusters in acute-care hospitals.
Infect Control Hosp Epidemiol
February 2024
Article Synopsis
- The study evaluated how selective whole-genome sequencing (WGS) can help in investigating COVID-19 outbreaks in healthcare settings.
- Researchers conducted a mixed-methods study across 8 facilities, analyzing 17 COVID-19 clusters and providing real-time WGS results to Infection Prevention and Control (IPC) teams.
- The findings showed that WGS identified previously unknown transmission pathways in many cases, significantly altering how IPC teams understood and responded to the outbreaks.
Background: New Delhi metallo-β-lactamase (NDM) represents an emergent mechanism of carbapenem resistance associated with high mortality and limited antimicrobial treatment options. Because the resistance gene is often carried on plasmids, traditional infection prevention and control (IP&C) surveillance methods like speciation, antimicrobial resistance testing, and reactive whole genome sequencing (WGS) may not detect plasmid transfer in multispecies outbreaks.
Methods: Initial outbreak detection of NDM-producing Enterobacterales identified at an acute care hospital occurred via traditional IP&C methods and was supplemented by real-time WGS surveillance, which was performed weekly using the Illumina platform.
We describe two cases of XDR infection caused by a strain of public health concern recently associated with a nationwide outbreak of contaminated artificial tears. Both cases were detected through database review of genomes in the Enhanced Detection System for Hospital-Associated Transmission (EDS-HAT), a routine genome sequencing-based surveillance program. We generated a high-quality reference genome for the outbreak strain from one of the case isolates from our center and examined the mobile elements encoding and carbapenemases.
View Article and Find Full Text PDFBackground: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) control on college campuses is challenging given communal living and student social dynamics. Understanding SARS-CoV-2 transmission among college students is important for the development of optimal control strategies.
Methods: SARS-CoV-2 nasal swab samples were collected from University of Pittsburgh students for symptomatic testing and asymptomatic surveillance from August 2020 through April 2021 from 3 campuses.
We performed whole genome sequencing on SARS-CoV-2 from 59 vaccinated individuals from southwest Pennsylvania who tested positive between February and September, 2021. A comparison of mutations among vaccine breakthrough cases to a time-matched control group identified potential adaptive responses of SARS-CoV-2 to vaccination.
View Article and Find Full Text PDFObjective: We used SARS-CoV-2 whole-genome sequencing (WGS) and electronic health record (EHR) data to investigate the associations between viral genomes and clinical characteristics and severe outcomes among hospitalized COVID-19 patients.
Methods: We conducted a case-control study of severe COVID-19 infection among patients hospitalized at a large academic referral hospital between March 2020 and May 2021. SARS-CoV-2 WGS was performed, and demographic and clinical characteristics were obtained from the EHR.
Healthcare-associated infections (HAIs) cause mortality, morbidity, and waste of health care resources. HAIs are also an important driver of antimicrobial resistance, which is increasing around the world. Beginning in November 2016, we instituted an initiative to detect outbreaks of HAIs using prospective whole-genome sequencing-based surveillance of bacterial pathogens collected from hospitalized patients.
View Article and Find Full Text PDFSevere infections caused by methicillin-resistant Staphylococcus aureus (MRSA) are often complicated by persistent bacteremia (PB) despite active antibiotic therapy. Antibiotic resistance rarely contributes to MRSA-PB, suggesting an important role for antibiotic tolerance pathways. To identify bacterial factors associated with PB, we sequenced the whole genomes of 206 MRSA isolates derived from 20 patients with PB and looked for genetic signatures of adaptive within-host evolution.
View Article and Find Full Text PDFBackground: Most hospitals use traditional infection prevention (IP) methods for outbreak detection. We developed the Enhanced Detection System for Healthcare-Associated Transmission (EDS-HAT), which combines whole-genome sequencing (WGS) surveillance and machine learning (ML) of the electronic health record (EHR) to identify undetected outbreaks and the responsible transmission routes, respectively.
Methods: We performed WGS surveillance of healthcare-associated bacterial pathogens from November 2016 to November 2018.
Background: Traditional methods of outbreak investigations utilize reactive whole genome sequencing (WGS) to confirm or refute the outbreak. We have implemented WGS surveillance and a machine learning (ML) algorithm for the electronic health record (EHR) to retrospectively detect previously unidentified outbreaks and to determine the responsible transmission routes.
Methods: We performed WGS surveillance to identify and characterize clusters of genetically-related Pseudomonas aeruginosa infections during a 24-month period.
Hospital-associated Clostridium difficile infection and reservoirs within the hospital environment.
Am J Infect Control
July 2019
Background: Clostridium difficile infection (CDI) is a leading cause of hospital-associated infections. Antibiotic stewardship, environmental disinfection, and reduction of transmission via health care workers are the major modes of CDI prevention within hospitals.
Methods: The aim of this study was to evaluate the role of the environment in the spread of CDI within hospital rooms.