Louise K. Francois Watkins

While non‐pestis yersiniosis experienced the largest increase in reported incidence of any bacterial enteric infection in the United States during 2016–2023, yersiniosis source attribution remains poorly understood. To address this gap, we described all yersiniosis outbreaks reported to CDC during 1971–2024. Trends in annual single‐etiology foodborne outbreak frequency, including before‐versus‐after comparisons around major changes in yersiniosis surveillance and diagnostics, were estimated using Bayesian spline regression. Of 56 outbreaks reported, 38 were single‐etiology. Outbreaks were linked to foodborne (34), person‐to‐person (10), indeterminate (8), and waterborne (4) transmission, respectively. Pork (46%) and dairy (18%) products were the most frequently identified food vehicles. Reported contributing factors included pre‐harvest contamination, cross‐contamination, and inadequate time and temperature control. Outbreaks occurred across diverse exposure and preparation settings, including camps, homes, restaurants, and schools. While estimated annual outbreak frequency appeared to be higher following major surveillance and diagnostic changes, 95% credible intervals included 0 for all estimates, limiting confidence in the magnitude of these changes. Evolving diagnostic and surveillance practices may have facilitated outbreak detection, contributing to a broader understanding of yersiniosis transmission pathways, food vehicles, and exposure settings. The identification of pork and dairy as common food vehicles underscored well‐established yersiniosis exposure pathways, while the diversity of exposure settings highlighted the need for prevention efforts across multiple points in the food supply chain. Strengthening prevention efforts across food, particularly the pork and dairy supply chains, is critical to reducing the yersiniosis burden in the United States.

Salmonella infections are a major cause of human illness in the United States. Salmonella enterica serotype Infantis has re-emerged as a leading serotype with the emergence of a multidrug-resistant S. Infantis strain, designated as REPJFX01 by the Centers for Disease Control and Prevention (CDC). REPJFX01, which typically contains a megaplasmid of emerging Salmonella Infantis (pESI) harbouring multiple resistance genes and a chromosomal gyrA87 mutation conferring decreased susceptibility to ciprofloxacin, has caused human infections linked to chicken consumption. The study aimed to describe the epidemiology and antimicrobial resistance of human S. Infantis infections, including the emergence of REPJFX01, in the United States. The study used data from five CDC surveillance systems, with combined years from 1979 through 2022. Negative binomial and logistic regression models were used in the multivariable analyses of surveillance data. In 10 active surveillance sites, the mean annual incidence of human S. Infantis infections was twice as high during 2013-2022 vs. 2003-2012 (adjusted rate ratio = 1.96, 95% CI 1.75-2.20). REPJFX01 infections accounted for nearly one-third of S. Infantis infections during 2018-2022 (vs. 2013-2017, adjusted odds ratio = 2.09, 95% CI 1.56-2.79). Salmonella Infantis infections were more likely among persons who were ≥45 years old, female, from racial and ethnic minority groups, and had Salmonella isolated from urine, than infections with other common serotypes. The increase in S. Infantis infections during 2013-2022 was likely driven by an increase in REPJFX01 infections. Public health strategies to reduce Salmonella contamination of chicken could help prevent human infections.

Nontyphoidal Salmonella causes an estimated 1.35 million U.S. infections annually. Antimicrobial-resistant strains are a serious public health threat. We examined the association between resistance and the clinical outcomes of hospitalization, length-of-stay ≥3 days, and death. We linked epidemiologic data from the Foodborne Diseases Active Surveillance Network with antimicrobial resistance data from the National Antimicrobial Resistance Monitoring System (NARMS) for nontyphoidal Salmonella infections from 2004–2018. We defined any resistance as resistance to ≥1 antimicrobial and clinical resistance as resistance to ampicillin, azithromycin, ceftriaxone, ciprofloxacin, or trimethoprim-sulfamethoxazole (for the subset of isolates tested for all five agents). We compared outcomes before and after adjusting for age, state, race/ethnicity, international travel, outbreak association, and isolate serotype and source. Twenty percent of isolates (1,105/5,549) had any resistance and 16% (469/2,969) had clinical resistance. Persons whose isolates had any resistance were more likely to be hospitalized (31% vs. 28%, P=0.01) or have length-of-stay ≥3 days (20% vs. 16%, P=0.01). Deaths were rare, but more common among those with any than no resistance (1.0% vs. 0.4%, P=0.01). Outcomes for patients whose isolates had clinical resistance did not differ significantly from those with no resistance. After adjustment, any resistance (adjusted odds ratio 1.23, 95% confidence interval 1.04–1.46) remained significantly associated with hospitalization. We observed a significant association between nontyphoidal Salmonella infections caused by resistant pathogens and likelihood of hospitalization. Clinical resistance was not associated with poorer outcomes, suggesting that factors other than treatment failure (e.g., strain virulence, strain source, host factors) may be important.

Background: The Global Typhoid Genomics Consortium was established to bring together the typhoid research community to aggregate and analyse Salmonella enterica serovar Typhi (Typhi) genomic data to inform public health action. This analysis, which marks 22 years since the publication of the first Typhi genome, represents the largest Typhi genome sequence collection to date (n=13,000).Methods: This is a meta-analysis of global genotype and antimicrobial resistance (AMR) determinants extracted from previously sequenced genome data and analysed using consistent methods implemented in open analysis platforms GenoTyphi and Pathogenwatch.Results: Compared with previous global snapshots, the data highlight that genotype 4.3.1 (H58) has not spread beyond Asia and Eastern/Southern Africa; in other regions, distinct genotypes dominate and have independently evolved AMR. Data gaps remain in many parts of the world, and we show the potential of travel-associated sequences to provide informal ‘sentinel’ surveillance for such locations. The data indicate that ciprofloxacin non-susceptibility (>1 resistance determinant) is widespread across geographies and genotypes, with high-level ciprofloxacin resistance (≥3 determinants) reaching 20% prevalence in South Asia. Extensively drug-resistant (XDR) typhoid has become dominant in Pakistan (70% in 2020) but has not yet become established elsewhere. Ceftriaxone resistance has emerged in eight non-XDR genotypes, including a ciprofloxacin-resistant lineage (4.3.1.2.1) in India. Azithromycin resistance mutations were detected at low prevalence in South Asia, including in two common ciprofloxacin-resistant genotypes.Conclusions: The consortium’s aim is to encourage continued data sharing and collaboration to monitor the emergence and global spread of AMR Typhi, and to inform decision-making around the introduction of typhoid conjugate vaccines (TCVs) and other prevention and control strategies.Funding: No specific funding was awarded for this meta-analysis. Coordinators were supported by fellowships from the European Union (ZAD received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 845681), the Wellcome Trust (SB, Wellcome Trust Senior Fellowship), and the National Health and Medical Research Council (DJI is supported by an NHMRC Investigator Grant [GNT1195210]).

Public health genomic surveillance systems typically measure genome relatedness and infer molecular epidemiological relationships using chromosomal loci alone – an approximation of vertical evolution, or homology-by-descent. The accessory genome, composed of plasmids and other mobile genetic elements, reflects horizontal gene transfer and serves as an important mechanism of bacterial evolution, enabling rapid adaptation. Measuring homology in the accessory genome – homology-by-admixture – could offer important molecular epidemiological information for public health application. We applied Jaccard Index and a novel genome length distance metric to compute pangenome relatedness for the globally-important pathogen Salmonella enterica serotype Typhi (Typhi), and graphically express both homology-by-descent and homology-by-admixture in a reticulate network. Jaccard Index Network Analysis revealed structure in the Typhi pangenome that can be harnessed to enhance discriminatory power for surveillance, track antimicrobial resistance, and refine our understanding of homology for outbreak management and prevention. This offers a more intricate, multidimensional framework for understanding pathogen evolution. Significance Statement: Bacterial relatedness is often measured and visualized using chromosomal comparison and phylogenetic trees. While valuable, this approach captures only the vertical evolutionary dimension and excludes genetic material acquired or lost through horizontal gene transfer. We present an approach for measuring and visualizing bacterial relatedness using all core and accessory genetic material and discuss the interpretation of resulting reticulate networks of bacterial genomes. In application to Salmonella Typhi, Jaccard Index Network Analysis revealed structure in populations of this pathogen that may be harnessed for public health applications. This approach captures both vertical and horizontal evolutionary dimensions, offering an intricate genetic framework for exploring pathogen evolution.

Campylobacter is the most common cause of bacterial diarrhea in the United States; resistance to macrolides and fluoroquinolones limits treatment options. We examined the epidemiology of US Campylobacter infections and changes in resistance over time. The Foodborne Diseases Active Surveillance Network receives information on laboratory-confirmed Campylobacter cases from 10 US sites, and the National Antimicrobial Resistance Monitoring System receives a subset of isolates from these cases for antimicrobial susceptibility testing. We estimated trends in incidence of Campylobacter infection, adjusting for sex, age, and surveillance changes attributable to culture-independent diagnostic tests. We compared percentages of isolates resistant to erythromycin or ciprofloxacin during 2005–2016 with 2017–2018 and used multivariable logistic regression to examine the association of international travel with resistance. Adjusted Campylobacter incidence remained stable or decreased for all groups analyzed since 2012. Among 2449 linked records in 2017–2018, the median patient age was 40.2 years (interquartile range, 21.6–57.8 years), 54.8% of patients were male, 17.2% were hospitalized, and 0.2% died. The percentage of resistant infections increased from 24.5% in 2005–2016 to 29.7% in 2017–2018 for ciprofloxacin (P < .001) and from 2.6% to 3.3% for erythromycin (P = .04). Persons with recent international travel had higher odds than nontravelers of having isolates resistant to ciprofloxacin (adjusted odds ratio [aOR] varied from 1.7 to 10.6 by race/ethnicity) and erythromycin (aOR = 1.7; 95% confidence interval, 1.3–2.1). Campylobacter incidence has remained stable or decreased, whereas resistance to antimicrobials recommended for treatment has increased. Recent international travel increased the risk of resistance.

Colistin is a last-resort antibiotic used to treat infections caused by multidrug-resistant Gram-negative bacteria. People with a history of travel to the Dominican Republic have become sick with pathogenic bacteria carrying the mobile colistin resistance gene, mcr-1, during and after traveling. This investigation aimed to identify mcr genes in Enterobacteriaceae isolated from food animal sources in the Dominican Republic. Three hundred and eleven samples were tested, from which 1354 bacterial isolates were obtained. Real-time PCR tests showed that 70.7% (220 out of 311) of the samples and 3.2% (44 out of 1354) of the isolates tested positive for the mcr gene. All RT-PCR presumptive mcr-positive isolates (n = 44) and a subset (n = 133) of RT-PCR presumptive mcr-negative isolates were subjected to whole-genome sequencing. WGS analysis showed that 39 isolates carried the mcr gene, with 37 confirmed as positive through RT-PCR and two as negative. Further, all of the mcr-positive genomes were identified as Escherichia coli and all contained a IncX4 plasmid replicon. Resistant determinants for other antibiotics important for human health were found in almost all isolates carrying mcr genes.