OBJECTIVES:Describe characteristics of gastroenteritis, bacteremia, and meningitis caused by nontyphoidal Salmonella among US infants.METHODS:We analyze national surveillance data during 1968-2015 and active, sentinel surveillance data during 1996-2015 for culture-confirmed Salmonella infections by syndrome, year, serotype, age, and race.RESULTS:During 1968-2015, 190 627 culture-confirmed Salmonella infections among infants were reported, including 165 236 (86.7%) cases of gastroenteritis, 6767 (3.5%) bacteremia, 371 (0.2%) meningitis, and 18 253 (9.7%) with other or unknown specimen sources. Incidence increased during the late 1970s-1980s, declined during the 1990s-early 2000s, and has gradually increased since the mid-2000s. Infants' median age was 4 months for gastroenteritis and bacteremia and 2 months for meningitis. The most frequently reported serotypes were Typhimurium (35 468; 22%) for gastroenteritis and Heidelberg for bacteremia (1954; 29%) and meningitis (65; 18%). During 1996-2015 in sentinel site surveillance, median annual incidence of gastroenteritis was 120, bacteremia 6.2, and meningitis 0.25 per 100 000 infants. Boys had a higher incidence of each syndrome than girls in both surveillance systems, but most differences were not statistically significant. Overall, hospitalization and fatality rates were 26% and 0.1% for gastroenteritis, 70% and 1.6% for bacteremia, and 96% and 4% for meningitis. During 2004-2015, invasive salmonellosis incidence was higher for Black (incident rate ratio, 2.7; 95% confidence interval, 2.6-2.8) and Asian (incident rate ratio, 1.8; 95% confidence interval, 1.7-1.8) than white infants.CONCLUSIONS:Salmonellosis causes substantial infant morbidity and mortality; serotype heidelberg caused the most invasive infections. Infants with meningitis were younger than those with bacteremia or gastroenteritis. Research into risk factors for infection and invasive illness could inform prevention efforts.

Salmonella is a major cause of foodborne illness in the United States, and antimicrobial-resistant strains pose a serious threat to public health. We used Bayesian hierarchical models of culture-confirmed infections during 2004–2016 from 2 Centers for Disease Control and Prevention surveillance systems to estimate changes in the national incidence of resistant nontyphoidal Salmonella infections. Extrapolating to the United States population and accounting for unreported infections, we estimated a 40% increase in the annual incidence of infections with clinically important resistance (resistance to ampicillin or ceftriaxone or nonsusceptibility to ciprofloxacin) during 2015–2016 (≈222,000 infections) compared with 2004–2008 (≈159,000 infections). Changes in the incidence of resistance varied by serotype. Serotypes I 4,[5],12:i:- and Enteritidis were responsible for two thirds of the increased incidence of clinically important resistance during 2015–2016. Ciprofloxacin-nonsusceptible infections accounted for more than half of the increase. These estimates can help in setting targets and priorities for prevention.

Abstract Although researchers have described numerous risk factors for salmonellosis and for infection with specific common serotypes, the drivers of Salmonella serotype diversity among human populations remain poorly understood. In this retrospective observational study, we partition records of serotyped non-typhoidal Salmonella isolates from human clinical specimens reported to CDC national surveillance by demographic, geographic and seasonal characteristics and adapt sample-based rarefaction methods from the field of community ecology to study how Salmonella serotype diversity varied within and among these populations in the USA during 1996–2016. We observed substantially higher serotype richness in children <2 years old than in older children and adults and steadily increasing richness with age among older adults. Whereas seasonal and regional variation in serotype diversity was highest among infants and young children, variation by specimen source was highest in adults. Our findings suggest that the risk for infection from uncommon serotypes is associated with host and environmental factors, particularly among infants, young children and older adults. These populations may have a higher proportion of illness acquired through environmental transmission pathways than published source attribution models estimate.

Objective: The “ledsmanageR”, a data management platform built in R, aims to improve the timeliness and accuracy of national foodborne surveillance data submitted to the Laboratory-based Enteric Disease Surveillance (LEDS) system by automating the data processing, validating, and reporting workflow.Introduction: The National Surveillance Team in the Enteric Diseases Epidemiology Branch of the Centers for Disease Control and Prevention (CDC) collects electronic data from all state and regional public health laboratories on human infections caused by Campylobacter, Salmonella, Shiga toxin-producing E. coli, and Shigella in LEDS. These data inform annual estimates of the burden of illness, assessments of patterns in bacterial subtypes, and can be used to describe trends in incidence. Robust digital infrastructure is required to process, validate, and summarize data on approximately 60,000 infections annually while optimizing use of financial and personnel resources.Methods: We leveraged the robust and extensible programming facilities of the R programming language and the active community of R users to develop a data integration, processing, and reporting pipeline for LEDS via an internal software package we named “ledsmanageR”. We designed all data retrieval, cleaning, and provisioning algorithms using tools from RStudio software packages1–3 and tracked changes to source code and data using CDC’s internal Gitlab server. We automated data validation requests to reporting partners by generating customizable emails directly from the R console4. We streamlined the data reconciliation process using OpenRefine5, a point-and-click tool for cleaning big data. We automated generation of annual reports, a process that was previously manual, using parameterized RMarkdown documents. Staff epidemiologists performed design and implementation internally, requiring no external consulting.Results: Developing our free and open-source software platform for national foodborne surveillance data management has saved the Enteric Diseases Epidemiology Branch thousands of dollars because we no longer depend on proprietary software requiring annual licensing fees. This transition occurred without any disruption in surveillance operations. Partial automation of email-based data validation and annual report generation processes reduced employee time requirement from one full-time position to one part-time position. The modular nature of ledsmanageR permitted LEDS to collect an expanded set of data elements with no changes to the core data processing and reporting workflow.Conclusions: We developed and implemented a flexible tool that helps maintain the integrity of surveillance data and reduces the need for manual data cleaning, which can be laborious and error-prone. The user-friendly design features of ledsmanageR demonstrate that data management can be optimized using programming skills that are increasingly common among epidemiologists. Our work on improving the accuracy and efficiency of enteric disease surveillance has served as a proof of concept for plans to streamline data processing for other surveillance systems.

Newport is the third most common Salmonella enterica serotype identified among the estimated 1.2 million human salmonellosis infections occurring annually in the United States. Risk factors for infection and food items implicated in outbreaks vary by antimicrobial resistance pattern. We conducted a descriptive analysis of data from four enteric disease surveillance systems capturing information on incidence, demographics, seasonality, geographic distribution, outbreaks, and antimicrobial resistance of Newport infections over a 10-year period from 2004 through 2013. Incidence increased through 2010, then declined to rates similar to those in the early years of the study. Incidence was highest in the South and among children <5 years old. Among isolates submitted for antimicrobial susceptibility testing, 88% were susceptible to all antimicrobials tested (pansusceptible) and 8% were resistant to at least seven agents, including ceftriaxone. Rates of pansusceptible isolates were also highest in the South and among young children, particularly in 2010. Pansusceptible strains of Newport have been associated with produce items and environmental sources, such as creek water and sediment. However, the role of environmental transmission of Newport in human illness is unclear. Efforts to reduce produce contamination through targeted legislation, as well as collaborative efforts to identify sources of contamination in agricultural regions, are underway.

Salmonella enterica serotype Dublin is a cattle-adapted bacterium that typically causes bloodstream infections in humans. To summarize demographic, clinical, and antimicrobial drug resistance characteristics of human infections with this organism in the United States, we analyzed data for 1968-2013 from 5 US surveillance systems. During this period, the incidence rate for infection with Salmonella Dublin increased more than that for infection with other Salmonella. Data from 1 system (FoodNet) showed that a higher percentage of persons with Salmonella Dublin infection were hospitalized and died during 2005-2013 (78% hospitalized, 4.2% died) than during 1996-2004 (68% hospitalized, 2.7% died). Susceptibility data showed that a higher percentage of isolates were resistant to > 7 classes of antimicrobial drugs during 2005-2013 (50.8%) than during 1996-2004 (2.4%)

Salmonella infections are a major cause of illness in the United States. The antimicrobial agents used to treat severe infections include ceftriaxone, ciprofloxacin, and ampicillin. Antimicrobial drug resistance has been associated with adverse clinical outcomes. To estimate the incidence of resistant culture-confirmed nontyphoidal Salmonella infections, we used Bayesian hierarchical models of 2004-2012 data from the Centers for Disease Control and Prevention National Antimicrobial Resistance Monitoring System and Laboratory-based Enteric Disease Surveillance. We based 3 mutually exclusive resistance categories on susceptibility testing: ceftriaxone and ampicillin resistant, ciprofloxacin nonsusceptible but ceftriaxone susceptible, and ampicillin resistant but ceftriaxone and ciprofloxacin susceptible. We estimated the overall incidence of resistant infections as 1.07/100,000 person-years for ampicillin-only resistance, 0.51/100,000 person-years for ceftriaxone and ampicillin resistance, and 0.35/100,000 person-years for ciprofloxacin nonsusceptibility, or ≈6,200 resistant culture-confirmed infections annually. These national estimates help define the magnitude of the resistance problem so that control measures can be appropriately targeted.

Background. Little is known about how human immunodeficiency virus (HIV) infection affects influenza transmission within homes in sub-Saharan Africa. Methods. We used respiratory illness surveillance and HIV testing data gathered in Kibera, an urban slum in Nairobi, Kenya, to examine the impact of HIV status on (1) introducing influenza to the home and (2) transmitting influenza to household contacts. Results. While HIV status did not affect the likelihood of being an influenza index case, household contacts of HIV-infected influenza index cases had twice the risk of developing secondary influenza-like illness than contacts of HIV-negative index cases. Conclusions. HIV-infected influenza index cases may facilitate transmission of influenza within the home.

To the Editor: Health authorities from Cambodia and European Union member states recently described a pronounced increase in Salmonella enterica serotype Paratyphi A infections in Cambodia resulting from an ongoing outbreak (1,2). To further characterize this outbreak, we analyzed 2013–2014 data on Paratyphi A infections associated with travel to Southeast Asia that were reported to the Centers for Disease Control and Prevention (CDC) National Typhoid and Paratyphoid Fever Surveillance (NTPFS) system and the CDC National Antimicrobial Monitoring System (NARMS). NTPFS began tracking Salmonella Paratyphi A infections in 2008. During 2008–2012, ten cases were reported in patients who had traveled to Southeast Asia within 30 days before illness onset; only 1, who also reported travel to Sri Lanka, Nepal, and Nigeria, reported travel to Cambodia. During January 1, 2013–August 22, 2014, however, NTPFS received 19 reports of laboratory-confirmed Paratyphi A infection in travelers returning from Southeast Asia; 13 traveled to Cambodia, and 8 of them reported travel only to Cambodia (Table). Of the 7 patients who traveled only to Cambodia and reported reason for travel, all cited “visiting friends and relatives.” Six (75%) of the 8 patients who traveled only to Cambodia were hospitalized (median duration 7 days, range 2–10 days), and all recovered. Cases occurring in 2014, especially later in the year, might not yet have been reported, so the 2014 data most likely are an underestimate. Although many cases reported to health authorities in Cambodia and the European Union clustered in the Phnom Penh region (1,2), we lack information about destinations within Cambodia for US patients. Table Characteristics of patients with Salmonella enterica serotype Paratyphi A infection returning to the United States from Southeast Asia, NTPFS, 2013–2014* Paratyphi A isolates from southern Asia (e.g., India, Pakistan, Bangladesh) often are resistant to the quinolone nalidixic acid or are multidrug resistant (i.e., resistant to ampicillin, chloramphenicol, and trimethoprim/sulfamethoxazole) (3), but little is known about antimicrobial drug resistance among Paratyphi A strains from Southeast Asia. However, most outbreak-associated isolates from Cambodia reported by others have been pansusceptible (1,2). CDC NARMS characterized the antimicrobial susceptibility of isolates from all patients who reported travel only to Cambodia; 7 (87.5%) were pansusceptible, and 1 (12.5%) was resistant to nalidixic acid and had reduced susceptibility to the fluoroquinolone ciprofloxacin. CDC NARMS also tested isolates from all patients who reported travel to Cambodia and other countries in Southeast Asia and from 2 patients who reported travel to other countries in Southeast Asia only; all were pansusceptible. The Paratyphi A outbreak in Cambodia appears to be large and ongoing. To our knowledge, information about possible sources and risk factors that could help inform prevention activities is not yet available. This outbreak highlights the urgent need for a paratyphoid fever vaccine; although typhoid fever vaccines exist, persons living in and visiting regions of active Paratyphi A transmission have no alternative to relying exclusively on close attention to food and water safety to mitigate risk (4). Furthermore, although most isolates from this outbreak appear to have been pansusceptible, antimicrobial drug resistance has emerged quickly among Paratyphi A strains in southern Asia (5–7). More comprehensive surveillance of antimicrobial resistance among Paratyphi A strains is warranted in Southeast Asia to determine the extent of geographic expansion of resistant strains from southern Asia and to inform treatment options for management of patients. We recommend a systematic outbreak investigation to determine source and routes of transmission.

Background: Salmonella enterica includes the major serovars associated with human salmonellosis.In this study, 1,764 clinical Salmonella enterica isolates from diarrhea outpatients were collected from fifteen cities in Guangdong Province, China, between 2007 and 2012.Methods: The isolates were characterized by serovar determination, antimicrobial susceptibility tests, and PFGE fingerprint typing. Results:The serovar distribution results demonstrated that Salmonella Typhimurium (29.65%) and Salmonella 4,5,12:i:-(13.83%) are the most common serovars causing infant salmonellosis, whereas Salmonella Enteritidis (14.57%) mainly causes human salmonellosis in adults.The serovar shift from Salmonella Enteritidis to Salmonella Typhimurium occurred in 2008.Antimicrobial susceptibility data showed a high burden of multidrug resistance (MDR) (56.58%), and a 20%-30% increase in the number of isolates resistant to ciprofloxacin (8.05%) and cephalosporins (4.99%) from 2007-2012.Only 9.97% of isolates were fully susceptible to all agents tested.A high burden of MDR was observed in Salmonella Typhimurium and Salmonella 4,5,12:i:-for all age groups, and a reduced susceptibility to third-generation cephalosporins and quinolones occurred particularly in infants.The dominant PFGE patterns were JPXX01.GD0004, JEGX01.GD0006, JEGX01.GD0007, JNGX01.GD0006, JNGX01.GD0007.ACSSuT was the predominant MDR profile in the Salmonella Typhimurium & S. 4,5,12:i:-clonal complexes.The predominant PFGE patterns of the Salmonella Typhimurium & S. 4,5,12:i:-clonal complexes and Salmonella Stanley were most prevalent in infants.However, no obvious relationship was observed between these PFGE profiles and geographic location.Conclusions: These data reveal the serovar distribution of isolates recovered from diarrhea patients, the characteristics of resistant strains and fingerprint typing in Guangdong from 2007 to 2012.These results highlight a serovar shift and a worrying percentage of MDR strains with increasing resistance to quinolones and third-generation cephalosporins.Thus, continued surveillance of Salmonella and their MDR profiles using combined molecular tools and efforts to control the rapid increase in antimicrobial resistance among Salmonella in Guangdong are needed.