Molecular characterization of circulating Salmonella Typhi strains in an urban informal settlement in Kenya.

A high burden of Salmonella enterica subspecies enterica serovar Typhi (S. Typhi) bacteremia has been reported from urban informal settlements in sub-Saharan Africa, yet little is known about the introduction of these strains to the region. Understanding regional differences in the predominant strains of S.

Whole-Genome Sequencing Reveals Multiple Subpopulations of Dominant and Persistent Lineage I Isolates of in Two Meat Processing Facilities during 2011-2015.

is a foodborne pathogen with a highly clonal population structure comprising multiple phylogenetic sub-groups that can persist within food processing environments and contaminate food. The epidemiology of is well-described in some developed countries; however, little is known about the prevalence and population structure of this pathogen in food and food processing environments located in less developed regions. The aim of this study was to determine the genetic characteristics and clonal relatedness of that were isolated from two Jamaican meat processing facilities.

SARS-CoV-2 Breakthrough Infections among US Embassy Staff Members, Uganda, May-June 2021.

The SARS-CoV-2 Delta variant emerged shortly after COVID-19 vaccines became available in 2021. We describe SARS-CoV-2 breakthrough infections in a highly vaccinated, well-monitored US Embassy community in Kampala, Uganda. Defining breakthrough infection rates in highly vaccinated populations can help determine public health messaging, guidance, and policy globally.

Reading intervention targeting phonemic awareness and symbol imagery in children with sickle cell disease.

Children with sickle cell disease (SCD) frequently have diminished academic attainment and are particularly vulnerable to reading dysfunction. We explored the effectiveness of a multisensory reading intervention offered during the summer to children with SCD at our institution. Subjects with reading deficits were identified through parent report, clinical findings, or school meetings.

Developmental screening of three-year-old children with sickle cell disease compared to controls.

We previously found that neurodevelopmental deficits commonly occurred in three-year-olds with sickle cell disease (SCD), but clinical significance was uncertain because a comparison group was lacking. Our objective in the current study was to prospectively compare neurodevelopment in three-year-old children with SCD to an age-appropriate control group. The Brigance Preschool Screen II is a neurodevelopmental screening examination which can be administered in 15-20 min.

Salmonella Bloodstream Infections in Hospitalized Children with Acute Febrile Illness-Uganda, 2016-2019.

Invasive Salmonella infection is a common cause of acute febrile illness (AFI) among children in sub-Saharan Africa; however, diagnosing Salmonella bacteremia is challenging in settings without blood culture. The Uganda AFI surveillance system includes blood culture-based surveillance for etiologies of bloodstream infection (BSIs) in hospitalized febrile children in Uganda. We analyzed demographic, clinical, blood culture, and antimicrobial resistance data from hospitalized children at six sentinel AFI sites from July 2016 to January 2019.

Outpatient Anesthesia Facilitates Stereotactic Body Radiation Therapy for Early Stage Lung Cancer Patients With Advanced Cognitive Impairments.

Purpose: To report on the use of outpatient anesthesia (OPA) facilitating delivery of stereotactic body radiation therapy (SBRT) in patients with severe cognitive impairments (CI) diagnosed with inoperable early stage lung cancer.

Methods And Materials: We surveyed our institutional review board-approved prospective lung SBRT data registry to document the feasibility of using anesthesia in CI patients and to determine their SBRT outcomes.

Results: From 2004 to 2018, 8 from a total 2084 patients were identified for this analysis.

Sequencing and Characterization of Five Extensively Drug-Resistant Salmonella enterica Serotype Typhi Isolates Implicated in Human Infections from Punjab, Pakistan.

A large outbreak of extensively drug-resistant (XDR) serotype Typhi infections is ongoing in Pakistan, predominantly in Sindh Province. Here, we report the sequencing and characterization of five XDR Typhi isolates from the Punjab province of Pakistan that are closely related to the outbreak strain and carry the same IncY plasmid.

CLONAL SPREAD OF 1B/O:8 IN MULTIPLE ZOO SPECIES.

(YE) bioserotype 1B/O:8 (YE 1B/O:8) was identified in routine culture of a variety of zoo species housed at Omaha's Henry Doorly Zoo and Aquarium (OHDZA) from April to July 2011. Animal cases representing 12 species had YE detected from 34 cases during routine fecal monitoring and/or during postmortem examination: Coquerel's sifakas (, two cases), black & white (BW) ruffed lemurs (, six cases), red ruffed lemurs (, seven cases), white handed gibbon one case), black lemurs ( three cases), mongoose lemurs (, two cases), African hunting dogs (, five cases), agile gibbons (, three cases), siamangs (, two cases), colobus monkey (, one case), argus pheasant (, one case), and orangutan (, one case). Most species were not symptomatic; however, three symptomatic cases in Coquerel's sifakas (two) and a white handed gibbon (one) showed clinical signs of diarrhea and lethargy that resulted in death for the Coquerel's sifakas.

PulseNet: Entering the Age of Next-Generation Sequencing.

Since 1996, PulseNet has served as the national laboratory-based surveillance system for the rapid detection of outbreaks caused by foodborne bacterial pathogens in the United States. For the past two decades, pulsed-field gel electrophoresis was the gold standard subtyping method for the pathogens tracked by PulseNet. A new gold standard is now being implemented with the introduction of cost-effective whole genome sequencing (WGS) for analysis of all the organisms tracked by PulseNet.

A Cross-Cutting Approach to Surveillance and Laboratory Capacity as a Platform to Improve Health Security in Uganda.

Global health security depends on effective surveillance for infectious diseases. In Uganda, resources are inadequate to support collection and reporting of data necessary for an effective and responsive surveillance system. We used a cross-cutting approach to improve surveillance and laboratory capacity in Uganda by leveraging an existing pediatric inpatient malaria sentinel surveillance system to collect data on expanded causes of illness, facilitate development of real-time surveillance, and provide data on antimicrobial resistance.

Ebola Virus Disease Diagnostics, Sierra Leone: Analysis of Real-time Reverse Transcription-Polymerase Chain Reaction Values for Clinical Blood and Oral Swab Specimens.

During the Ebola virus outbreak of 2013-2016, the Viral Special Pathogens Branch field laboratory in Sierra Leone tested approximately 26 000 specimens between August 2014 and October 2015. Analysis of the B2M endogenous control Ct values showed its utility in monitoring specimen quality, comparing results with different specimen types, and interpretation of results. For live patients, blood is the most sensitive specimen type and oral swabs have little diagnostic utility.

Ebola Virus Diagnostics: The US Centers for Disease Control and Prevention Laboratory in Sierra Leone, August 2014 to March 2015.

In August 2014, the Viral Special Pathogens Branch of the US Centers for Disease Control and Prevention established a field laboratory in Sierra Leone in response to the ongoing Ebola virus outbreak. Through March 2015, this laboratory tested >12 000 specimens from throughout Sierra Leone. We describe the organization and procedures of the laboratory located in Bo, Sierra Leone.

Canonical Single Nucleotide Polymorphisms (SNPs) for High-Resolution Subtyping of Shiga-Toxin Producing Escherichia coli (STEC) O157:H7.

The objective of this study was to develop a canonical, parsimoniously-informative SNP panel for subtyping Shiga-toxin producing Escherichia coli (STEC) O157:H7 that would be consistent with epidemiological, PFGE, and MLVA clustering of human specimens. Our group had previously identified 906 putative discriminatory SNPs, which were pared down to 391 SNPs based on their prevalence in a test set. The 391 SNPs were screened using a high-throughput form of TaqMan PCR against a set of clinical isolates that represent the most diverse collection of O157:H7 isolates from outbreaks and sporadic cases examined to date.

PFGE for Shiga toxin-producing Escherichia coli O157:H7 (STEC O157) and non-O157 STEC.

This chapter describes the procedure of generating pulsed-field gel electrophoresis (PFGE) profiles (DNA fingerprints) of Shiga toxin-producing Escherichia coli O157:H7 (STEC O157) and non-O157 STEC strains within 48 h, based on the standardized laboratory protocol developed by the Centers for Disease Control and Prevention, USA. The protocol describes the preparation of agarose plugs containing STEC O157 and non-O157 STEC cells, the digestion of bacterial DNA in the plugs using restriction endonuclease enzymes, and the electrophoresis conditions to generate the characteristic PFGE profiles of STEC O157 and non-O157 STEC isolates.

Establishing an enteric bacteria reference laboratory in Sierra Leone.

In 2012, Sierra Leone experienced its worst cholera outbreak in over 15 years affecting 12 of the country's 13 districts. With limited diagnostic capability, particularly in bacterial culture, the cholera outbreak was initially confirmed by microbiological testing of clinical specimens outside of Sierra Leone. During 2012 - 2013, in direct response to the lack of diagnostic microbiology facilities, and to assist in investigating and monitoring the cholera outbreak, diagnostic and reference services were established in Sierra Leone at the Central Public Health Reference Laboratory focusing specifically on isolating and identifying Vibrio cholerae and other enteric bacterial pathogens.

Household water treatment uptake during a public health response to a large typhoid fever outbreak in Harare, Zimbabwe.

Locally manufactured sodium hypochlorite (chlorine) solution has been sold in Zimbabwe since 2010. During October 1, 2011-April 30, 2012, 4,181 suspected and 52 confirmed cases of typhoid fever were identified in Harare. In response to this outbreak, chlorine tablets were distributed.

Shifts in geographic distribution and antimicrobial resistance during a prolonged typhoid fever outbreak--Bundibugyo and Kasese Districts, Uganda, 2009-2011.

Background: Salmonella enterica serovar Typhi is transmitted by fecally contaminated food and water and causes approximately 22 million typhoid fever infections worldwide each year. Most cases occur in developing countries, where approximately 4% of patients develop intestinal perforation (IP). In Kasese District, Uganda, a typhoid fever outbreak notable for a high IP rate began in 2008.

Evolutionary dynamics of Vibrio cholerae O1 following a single-source introduction to Haiti.

Unlabelled: Prior to the epidemic that emerged in Haiti in October of 2010, cholera had not been documented in this country. After its introduction, a strain of Vibrio cholerae O1 spread rapidly throughout Haiti, where it caused over 600,000 cases of disease and >7,500 deaths in the first two years of the epidemic. We applied whole-genome sequencing to a temporal series of V.

Toxigenic Vibrio cholerae O1 in water and seafood, Haiti.

During the 2010 cholera outbreak in Haiti, water and seafood samples were collected to detect Vibrio cholerae. The outbreak strain of toxigenic V. cholerae O1 serotype Ogawa was isolated from freshwater and seafood samples.

Characterization of toxigenic Vibrio cholerae from Haiti, 2010-2011.

In October 2010, the US Centers for Disease Control and Prevention received reports of cases of severe watery diarrhea in Haiti. The cause was confirmed to be toxigenic Vibrio cholerae, serogroup O1, serotype Ogawa, biotype El Tor. We characterized 122 isolates from Haiti and compared them with isolates from other countries.

Neurocognitive screening with the Brigance preschool screen-II in 3-year-old children with sickle cell disease.

Background: Neurocognitive deficits have been described in school age children with sickle cell disease (SCD), even in the absence of stroke or silent infarcts. However, the age of onset and factors contributing to this problem have not been well studied. We hypothesized that in children with SCD the failure rate with Brigance screening would be higher than in the normal population.

United States rotavirus strain surveillance from 2005 to 2008: genotype prevalence before and after vaccine introduction.

Background: A live, attenuated rotavirus vaccine, RotaTeq®, was approved in 2006 for immunization of infants in the United States. To monitor the distribution of rotavirus genotypes before and after vaccine introduction, the Centers for Disease Control and Prevention conducted strain surveillance with the National Rotavirus Strain Surveillance System.

Methods: Over 3 rotavirus seasons, 2005-2006, 2006-2007, and 2007-2008, National Rotavirus Strain Surveillance System laboratories collected rotavirus-positive stool specimens and submitted them to the Centers for Disease Control and Prevention.

G and P types of circulating rotavirus strains in the United States during 1996-2005: nine years of prevaccine data.

Background: Rotavirus vaccine was recommended for routine use among US infants in 2006. To provide prevaccine data, we conducted strain surveillance for 9 consecutive seasons during 1996-2005.

Methods: Using reverse-transcriptase polymerase chain reaction genotyping and nucleotide sequencing, we determined P/G genotypes of >3100 rotavirus strains collected in up to 12 cities each year from different US regions.

Enhancement of detection and quantification of rotavirus in stool using a modified real-time RT-PCR assay.

A sensitive and specific real-time RT-PCR assay to detect rotavirus in stool samples was optimized and validated using a wide range of rotavirus genotypes. The target of the original TaqMan(R) assay is an 87 bp fragment of the highly conserved non-structural protein 3 (NSP3) gene. Here we modified the original assay by introducing degeneracy into the forward primer to account for sequence variation between rotavirus genotypes, added four nucleotides at the 3' end of the reverse primer to reduce its stability, and modified the probe label.