Research Publications (Food Safety)

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 Reports suggest that some persons previously infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lack detectable immunoglobulin G (IgG) antibodies. We aimed to determine the proportion IgG seronegative and predictors for seronegativity among persons previously infected with SARS-CoV-2.

To the Editor—We read with interest the article by Moradi et al on the use of an automated electronic health record–best practice alert (BPA) to decrease antimicrobial utilization in patients with low procalcitonin levels and a virus detected in an upper respiratory polymerase chain reaction panel [1, 2].

Background The etiology and optimal clinical management of acute febrile illness (AFI) is poorly understood. Methods Blood samples taken from study participants with acute fever (≥37.5°C) or a history of fever and recruited into the previous Typhoid Fever Surveillance in Africa (TSAP) study were evaluated using a polymerase chain reaction (PCR)-based TaqMan-Array Card designed to detect a panel of bacterial, viral, and parasitic pathogens.

Background As children with isolated vomiting are rarely able to provide a specimen suitable for routine pathogen testing, we have limited knowledge about their infecting pathogens. Methods Between December 2014 and August 2018, children <18 years old with presumed acute gastroenteritis who presented to 2 emergency departments (EDs) in Alberta, Canada, were recruited.

Background QuantiFERON enzyme-linked immunosorbent assay (ELISA; Qiagen) with Borrelia burgdorferi peptide antigens was previously shown to reliably detect interferon-γ (IFN-γ) in blood samples from adult patients with early Lyme disease and the response disappeared rapidly after treatment. We evaluated the response before and after appropriate antibiotic therapy in adolescent and adult subjects with more diverse stages of the illness.

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.

Open-source DNA sequence databases have long been touted as beneficial to public health, including the facilitation of earlier detection and response to infectious disease outbreaks. Of critical importance to harnessing these benefits is the metadata that describe general and other domain-specific attributes (eg, collection location, isolate type) of a sample. Unlike the sequence data, metadata are often incomplete and lack adherence to an international standard.

Background Norovirus is a leading cause of epidemic acute gastroenteritis (AGE), with most outbreaks occurring during winter. The majority of outbreaks are caused by GII.4 noroviruses; however, data to support whether this is true for sporadic medically attended AGE are limited. Therefore, we sought to compare the clinical characteristics and seasonality of GII.4 vs non-GII.4 viruses.

Background Children living with human immunodeficiency virus (HIV) (CLHIV) receiving antiretroviral therapy (ART) in resource-limited settings are susceptible to high rates of acquired HIV drug resistance (HIVDR), but few studies include children initiating age-appropriate World Health Organization (WHO)-recommended first-line regimens. We report data from a cohort of ART-naive South African children who initiated first-line ART.

Background Leukocyte telomere length (TL) shortens with age and is associated with coronary artery disease (CAD) events in the general population. Persons living with human immunodeficiency virus (HIV; PLWH) may have accelerated atherosclerosis and shorter TL than the general population. It is unknown whether TL is associated with CAD in PLWH. Methods We measured TL by quantitative polymerase chain reaction (PCR) in white Swiss HIV Cohort Study participants.

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.

Background Candidatus (Ca.) Neoehrlichia (N.) mikurensis is an emerging tick-borne pathogen of humans that is closely related to Ehrlichia and Anaplasma species. This strict intracellular bacterium escapes detection by routine microbiologic diagnostic methods such as blood culture, leading to considerable under-diagnosis of the infectious disease it causes, neoehrlichiosis.

Background In generalized drug-resistant tuberculosis (DR-TB) human immunodeficiency virus (HIV) epidemics, identifying subpopulations at high risk for treatment failure and loss to care is critically important to improve treatment outcomes and prevent amplification of drug resistance. We hypothesized that an electronic dose-monitoring (EDM) device could empirically identify adherence-challenged patients and that a mixed-methods approach would characterize treatment challenges.

Background The efficacy of currently available anthelminthics against Trichuris trichiura infections is significatively lower than for other soil-transmitted helminths. The combination of ivermectin (IVM) and albendazole (ALB) has shown significant improvements in efficacy. Methods Safety and efficacy randomized controlled clinical trial comparing 3 experimental regimens against ALB monotherapy for the treatment of T. trichiura infections in northern Honduras.

Background Antibiotic overprescribing in long-term care settings is driven by prescriber preferences and is associated with preventable harms for residents. We aimed to determine whether peer comparison audit and feedback reporting for physicians reduces antibiotic overprescribing among residents.

Background Bancroftian filariasis remains endemic in Fiji despite >10 years of mass drug administration (MDA) using diethylcarbamazine and albendazole (DA). The addition of ivermectin to this combination (IDA) has improved efficacy of microfilarial clearance at 12 months in individually randomized trials in nocturnal transmission settings, but impact in a setting of diurnally subperiodic filarial transmission has not been evaluated.

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 Acute gastroenteritis (AGE) causes a substantial burden in the United States, but its etiology frequently remains undetermined. Active surveillance within an integrated healthcare delivery system was used to estimate the prevalence and incidence of medically attended norovirus, rotavirus, sapovirus, and astrovirus. Methods Active surveillance was conducted among all enrolled members of Kaiser Permanente Northwest during July 2014–June 2016.

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.