Research Publications (Food Safety)

Background Microbial cell-free DNA (mcfDNA) sequencing of plasma can identify the presence of a pathogen in a host. In this study, we evaluated the duration of pathogen detection by mcfDNA sequencing vs conventional blood culture in patients with bacteremia. Methods Blood samples from patients with culture-confirmed bloodstream infection were collected within 24 hours of the index positive blood culture and 48 to 72 hours thereafter.

Background Diverse environmental exposures and risk factors have been implicated in the transmission of Salmonella Typhi, but the dominant transmission pathways through the environment to susceptible humans remain unknown. Here, we use spatial, bacterial genomic, and hydrological data to refine our view of typhoid transmission in an endemic setting.

Background The National Outbreak Reporting System (NORS) captures data on foodborne, waterborne, and enteric illness outbreaks in the United States. This study describes enteric illness outbreaks reported during 11 years of surveillance. Methods We extracted finalized reports from NORS for outbreaks occurring during 2009–2019.

Background Staphylococcus aureus bacteremia (SAB) is in 10% to 20% of cases complicated by infective endocarditis. Clinical prediction scores may select patients with SAB at highest risk for endocarditis, improving the diagnostic process of endocarditis.

Background Pneumonic plague (PP), caused by Yersinia pestis, is the most feared clinical form of plague due to its rapid lethality and potential to cause outbreaks. PP outbreaks are now rare due to antimicrobial therapy. Methods A PP outbreak in Madagascar involving transmission of a Y.

Background In 2018, the Centers for Disease Control and Prevention and the Vermont Department of Health investigated an outbreak of multidrug-resistant Shigella sonnei infections in a retirement community that offered a continuum of care from independent living through skilled nursing care. The investigation identified 24 culture-confirmed cases.

Background Persons who use drugs (PWUD) face substantial risk of Staphylococcus aureus infections. Limited data exist describing clinical and substance use characteristics of PWUD with invasive S. aureus infections or comparing treatment and mortality outcomes in PWUD vs non-PWUD. These are needed to inform optimal care for this marginalized population. Methods We identified adults hospitalized from 2013 to 2018 at 2 medical centers in San Francisco with S.

Background Listeriosis is caused by the foodborne pathogen Listeria monocytogenes. It can present as a maternal–neonatal infection. We implemented a nationwide prospective cohort and analyzed the features of neonatal listeriosis. Methods We studied all neonates born alive from mothers with microbiologically proven maternal–neonatal listeriosis enrolled from November 2009 to December 2017.

Background Bacterial diseases are the leading cause of mortality globally, and due to haphazard use of antibiotics, antimicrobial resistance has become an emerging threat. Methods This cross-sectional observational study utilized a minimally invasive tissue sampling procedure to determine the cause of death among an adult population.

Background Brucellosis is a severe occupational or foodborne zoonosis throughout much of the world. Although eradicated from domestic cattle in the United States, brucellosis remains a disease risk to people through acquisition and consumption of animal products from endemic countries. Methods Cases of human brucellosis reported through the California public health disease surveillance network were reviewed for 1993 to 2017.

Background Antibiotic stewardship programs (ASPs) have demonstrated success at reducing costs, yet there is limited quality evidence of their effectiveness in reducing infections of high-profile drug-resistant organisms. Methods This retrospective, cohort study included all Kaiser Permanente Southern California (KPSC) members aged ≥18 years hospitalized in 9 KPSC hospitals from 1 January 2008 to 31 December 2016.

Background Klebsiella pneumoniae is a critically important pathogen in the Philippines. Isolates are commonly resistant to at least 2 classes of antibiotics, yet mechanisms and spread of its resistance are not well studied. Methods A retrospective sequencing survey was performed on carbapenem-, extended spectrum beta-lactam-, and cephalosporin-resistant Klebsiella pneumoniae isolated at 20 antimicrobial resistance (AMR) surveillance sentinel sites from 2015 through 2017.

Background Klebsiella species, including the notable pathogen K. pneumoniae, are increasingly associated with antimicrobial resistance (AMR). Genome-based surveillance can inform interventions aimed at controlling AMR. However, its widespread implementation requires tools to streamline bioinformatic analyses and public health reporting.

Background Klebsiella pneumoniae is a World Health Organization high-priority antibiotic-resistant pathogen. However, little is known about Klebsiella lineages circulating in Nigeria. Methods We performed whole-genome sequencing (WGS) of 141 Klebsiella isolated between 2016 and 2018 from clinical specimens at 3 antimicrobial-resistance (AMR) sentinel surveillance tertiary hospitals in southwestern Nigeria.

Background Acute gastroenteritis (AGE) burden, etiology, and severity in adults is not well characterized. We implemented a multisite AGE surveillance platform in 4 Veterans Affairs Medical Centers (Atlanta, Georgia; Bronx, New York; Houston, Texas; and Los Angeles, California), collectively serving >320 000 patients annually.

Background While there are ongoing regulatory convergence efforts, differences remain in primary end points recommended for community-acquired bacterial pneumonia (CABP) trials. The US Food and Drug Administration (FDA) recommends assessing CABP symptom resolution at an early time point (3–5 days after randomization). Other regulatory agencies recommend assessing overall clinical response at a later time point (5–10 days after therapy ends).

Background Maternal overweight and obesity are related to risks of pregnancy and delivery complications that, in turn, are associated with newborn infections. We examined the associations between early pregnancy body mass index (BMI; kg/m2) and risk of early-onset neonatal bacterial sepsis (EOS). Methods We conducted a nationwide population-based retrospective cohort study of 1 971 346 live singleton infants born in Sweden between 1997 and 2016.

Background We aimed to assess the proportion of multidrug-resistant tuberculosis (MDR-TB) cases with initial bedaquiline (BDQ) resistance, monitor the dynamics of BDQ susceptibility of Mycobacterium tuberculosis isolates during therapy, and correlate susceptibility with MDR-TB patient clinical outcomes in China. Methods A retrospective, cohort study of MDR-TB patients was conducted, with positive cultures collected from cases at 13 sites.

Background Chronic Q fever usually develops within 2 years after primary infection with Coxiella burnetii. We determined the interval between acute Q fever and diagnosis of chronic infection, assessed what factors contribute to a longer interval, and evaluated the long-term follow-up. Methods From 2007 to 2018, patients with chronic Q fever were included from 45 participating hospitals.

Background Salmonella Enteritidis and Salmonella Typhimurium are major causes of bloodstream infection and diarrheal disease in East Africa. Sources of human infection, including the role of the meat pathway, are poorly understood. Methods We collected cattle, goat, and poultry meat pathway samples from December 2015 through August 2017 in Tanzania and isolated Salmonella using standard methods.

To the Editor—We read with great interest the article by Ellingson et al [1]. They report a 79% decrease in the environmental bioburden that led to a reduction in hospital-acquired infection by self-disinfection of surfaces. Their study showed “the mean baseline level of 208.0 CFU/cm2 decreased to 74.6 CFU/cm2 following the first application.” Surprisingly, no standard deviation or confidence limits were given.

Background The Global Enteric Multicenter Study (GEMS) determined the etiologic agents of moderate-to-severe diarrhea (MSD) in children under 5 years old in Africa and Asia. Here, we describe the prevalence and antimicrobial susceptibility of nontyphoidal Salmonella (NTS) serovars in GEMS and examine the phylogenetics of Salmonella Typhimurium ST313 isolates.

Background Shigella is a leading cause of childhood diarrhea and target for vaccine development. Microbiologic and clinical case definitions are needed for pediatric field vaccine efficacy trials.

Background Diarrheal pathogens have been associated with linear growth deficits. The effect of diarrheal pathogens on growth is likely due to inflammation, which also adversely affects neurodevelopment. We hypothesized that diarrheagenic pathogens would be negatively associated with both growth and neurodevelopment.

Background Fluoroquinolone resistance in Mycobacterium tuberculosis (Mtb) is conferred by DNA gyrase mutations, but not all fluoroquinolone-resistant Mtb isolates have mutations detected. The optimal allele frequency threshold to identify resistance-conferring mutations by whole-genome sequencing is unknown.