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The global epidemic of multidrug-resistant Salmonella Typhimurium DT104 provides an important example, both in terms of the agent and its resistance, of a widely disseminated zoonotic pathogen. Here, with an unprecedented national collection of isolates collected contemporaneously from humans and animals and including a sample of internationally derived isolates, we have used whole-genome sequencing to dissect the phylogenetic associations of the bacterium and its antimicrobial resistance genes through the course of an epidemic. Contrary to current tenets supporting a single homogeneous epidemic, we demonstrate that the bacterium and its resistance genes were largely maintained within animal and human populations separately and that there was limited transmission, in either direction. We also show considerable variation in the resistance profiles, in contrast to the largely stable bacterial core genome, which emphasizes the critical importance of integrated genotypic data sets in understanding the ecology of bacterial zoonoses and antimicrobial resistance.

Reptile-associated outbreaks of human Salmonella infections are increasing in Canada, coinciding with a rise in the popularity of reptiles as pets. We conducted a retrospective analysis of surveillance data for human Salmonella case-patients in Ontario during 2015-2022. We compared serotypes and reptile types for those reporting domestic reptile or amphibian exposure with veterinary Salmonella isolates reported during the same period. Case-patients commonly reported contact with reptile types from which Salmonella was most frequently isolated. Some serotypes from human case-patients were closely associated with contact with specific reptile types, including Salmonella Paratyphi B biovar Java (Salmonella Paratyphi B variant L (+) tartrate +) with snakes, Salmonella Agbeni with turtles, and Salmonella Cotham, Salmonella Chester, and Salmonella Tennessee with bearded dragons. Salmonella was most likely to be reported from reptiles fed a carnivorous diet. Education of reptile owners could help promote proper veterinary care and reduce transmission of zoonotic infections.

Salmonella Typhimurium is a major diarrheal pathogen and associated with invasive nontyphoid Salmonella (iNTS) disease in vulnerable populations. We present the first characterization of iNTS organisms in Southeast Asia and describe a different evolutionary trajectory from that of organisms causing iNTS in sub-Saharan Africa. In Vietnam, the globally distributed monophasic variant of Salmonella Typhimurium, the serovar I:4,[5],12:i:− ST34 clone, has reacquired a phase 2 flagellum and gained a multidrug-resistant plasmid to become associated with iNTS disease in HIV-infected patients. We document distinct communities of S . Typhimurium and I:4,[5],12:i:− in animals and humans in Vietnam, despite the greater mixing of these host populations here. These data highlight the importance of whole-genome sequencing surveillance in a One Health context in understanding the evolution and spread of resistant bacterial infections. Nontyphoidal Salmonella (NTS), particularly Salmonella enterica serovar Typhimurium, is among the leading etiologic agents of bacterial enterocolitis globally and a well-characterized cause of invasive disease (iNTS) in sub-Saharan Africa. In contrast, S . Typhimurium is poorly defined in Southeast Asia, a known hot spot for zoonotic disease with a recently described burden of iNTS disease. Here, we aimed to add insight into the epidemiology and potential impact of zoonotic transfer and antimicrobial resistance (AMR) in S . Typhimurium associated with iNTS and enterocolitis in Vietnam. We performed whole-genome sequencing and phylogenetic reconstruction on 85 human (enterocolitis, carriage, and iNTS) and 113 animal S . Typhimurium isolates isolated in Vietnam. We found limited evidence for the zoonotic transmission of S . Typhimurium. However, we describe a chain of events where a pandemic monophasic variant of S . Typhimurium (serovar I:4,[5],12:i:− sequence type 34 [ST34]) has been introduced into Vietnam, reacquired a phase 2 flagellum, and acquired an IncHI2 multidrug-resistant plasmid. Notably, these novel biphasic ST34 S . Typhimurium variants were significantly associated with iNTS in Vietnamese HIV-infected patients. Our study represents the first characterization of novel iNTS organisms isolated outside sub-Saharan Africa and outlines a new pathway for the emergence of alternative Salmonella variants into susceptible human populations. IMPORTANCE Salmonella Typhimurium is a major diarrheal pathogen and associated with invasive nontyphoid Salmonella (iNTS) disease in vulnerable populations. We present the first characterization of iNTS organisms in Southeast Asia and describe a different evolutionary trajectory from that of organisms causing iNTS in sub-Saharan Africa. In Vietnam, the globally distributed monophasic variant of Salmonella Typhimurium, the serovar I:4,[5],12:i:− ST34 clone, has reacquired a phase 2 flagellum and gained a multidrug-resistant plasmid to become associated with iNTS disease in HIV-infected patients. We document distinct communities of S . Typhimurium and I:4,[5],12:i:− in animals and humans in Vietnam, despite the greater mixing of these host populations here. These data highlight the importance of whole-genome sequencing surveillance in a One Health context in understanding the evolution and spread of resistant bacterial infections.

Salmonella enterica serovar Weltevreden (S. Weltevreden) is an emerging cause of diarrheal and invasive disease in humans residing in tropical regions. Despite the regional and international emergence of this Salmonella serovar, relatively little is known about its genetic diversity, genomics or virulence potential in model systems. Here we used whole genome sequencing and bioinformatics analyses to define the phylogenetic structure of a diverse global selection of S. Weltevreden. Phylogenetic analysis of more than 100 isolates demonstrated that the population of S. Weltevreden can be segregated into two main phylogenetic clusters, one associated predominantly with continental Southeast Asia and the other more internationally dispersed. Subcluster analysis suggested the local evolution of S. Weltevreden within specific geographical regions. Four of the isolates were sequenced using long read sequencing to produce high quality reference genomes. Phenotypic analysis in Hep-2 cells and in a murine infection model indicated that S. Weltevreden were significantly attenuated in these models compared to the classical S. Typhimurium reference strain SL1344. Our work outlines novel insights into this important emerging pathogen and provides a baseline understanding for future research studies.

We analyzed whole-genome sequences of Salmonella enterica serovar Enteritidis isolates in South Korea that had the SEGX01.049 pulsed-field gel electrophoresis pattern. That lineage has emerged and circulated in South Korea since 2020, leading to 2 fatal infection cases. We investigated the genomic characteristics and identified potential sources of that lineage. Isolates from outbreaks during 2020-2023 clustered in the Global IIa clade, along with other Salmonella Enteritidis strains from chicken farms in South Korea and human isolates from the United Kingdom. Bayesian molecular clock analysis estimated the time to the most recent common ancestor of our isolates in the Global IIa clade was 2017.57. Moreover, phylogeographic analysis supported substantial statistical evidence (Bayes factor 111.415; posterior probability 0.97) for the introduction of this lineage into South Korea from the United Kingdom. Continued genomic surveillance will be needed to monitor the spread of foodborne pathogens such as Salmonella Enteritidis and improve prevention strategies.

Diverse salmonellae have the potential to cause disease and may be carried asymptomatically within the intestine of many vertebrate species. The relative contribution of human, animal, and environmental hosts to the transmission of Salmonella is unknown within and between households in low-income settings, especially where humans and animals may live in close contact and sanitary infrastructure is often inadequate. Between November 2018 and December 2019, we isolated Salmonella spp. from thirty households in urban and rural locations in Malawi, sampling at three time points from the stool of humans, animals, and their household environment. Using whole genome sequencing and fine-resolution bioinformatic and phylogenetic analyses we found evidence of sharing of Salmonella species and strains between humans, animals and the environment, both within and between households. The intricate web of interconnected salmonellae within this ecosystem underscores the importance of adopting a multi-faceted ‘One Health’ strategy when considering control of Salmonella in low-intensity agricultural systems. In this work, Wilson et al., examined sharing of Salmonella between humans, animals and the environment using household samples from Malawi. They revealed an interconnected web of Salmonella circulation, underscoring the importance of the One Health concept.

Salmonella enterica serovar Muenchen emerged in Israel in 2018 and became a major public health threat. We aimed to determine the role of poultry in rising human cases, transmission routes within the broiler industry, and genetic similarity to Salmonella Muenchen found globally. We used whole-genome sequencing to compare Salmonella Muenchen isolates from poultry, food, and humans collected in Israel (2020-2023; n = 109) and globally (n = 125). Salmonella Muenchen sequence type 82 isolates from Israel harbored pESI plasmid, exhibited high genetic similarity between human and poultry sources, and closely resembled international pESI-positive strains; we found quinolone-resistance determinants in 58.6% of isolates. Salmonella Muenchen prevalence in commercial broiler flocks was 61.5% (95% CI 51.5%-71.5%); strains could not be traced to breeder flocks, but on-farm persistence existed. The clonal spread of Salmonella Muenchen in poultry contributes to increased incidence in humans. Horizontal transmission in broilers requires control measures to protect public health.

Non-typhoidal Salmonella are important foodborne zoonotic pathogens closely linked to poultry and poultry products. Despite their public health importance, limited data are available on the epidemiology and antimicrobial resistance patterns of nontyphoidal Salmonella in poultry production systems in Ethiopia. This cross-sectional study aimed to estimate the prevalence, identify risk factors, and assess the antimicrobial resistance profiles of Salmonella enterica from poultry farms in Bahir Dar city, northwestern Ethiopia. Standard bacteriological methods, PCR-based detection, and serotyping were used to investigate the presence of Salmonella in chicken (n = 126), environmental (n = 198), and human (n = 45) samples collected from 22 poultry farms. Antimicrobial susceptibility profiles were determined using the Kirby–Bauer disk diffusion method. Data from questionnaires and Fisher’s exact tests were used to identify risk factors associated with the occurrence of Salmonella . Nontyphoidal Salmonella species were detected on 18.1% (4/22) of the farms. Salmonella enterica was recovered from 3.1% (6/198) of environmental boot samples, 3.2% (4/126) of cloacal swabs, and 4.4% (2/45) of human stool samples. Two Salmonella serotypes were identified from among 12 Salmonella isolates: S. Enteritidi s (41.6%, 5/12) and S. Typhimurium (16.6%, 2/12). All Salmonella isolates demonstrated complete resistance to ampicillin (100%) and tetracycline (100%) and exhibited multiple drug resistance patterns, with a high multiple antibiotic resistance index ranging from 0.45 to 0.55. The prevalence of Salmonella was significantly associated with the absence of foot baths (p = 0.0096) and the presence of other animal species on the farm (p = 0.026). The demonstrable emergence of multidrug-resistant Salmonella Enteritidis and Salmonella Typhimurium serotypes, alongside key factors driving the prevalence of nontyphoidal salmonellosis on poultry farms in northwestern Ethiopia, underscores the need for improved intervention strategies and ongoing large-scale One Health genomic surveillance to accurately monitor temporal dynamics of Salmonella infections and mitigate the rise of multidrug resistance.

Salmonellosis remains one of the most frequently reported foodborne diseases globally, with the highest burden in low-resource areas. The millions of deaths caused by Nontyphoidal Salmonella (NTS) infections emphasize the urgent need for timely, detailed, and evidence-based interventions to effectively manage and monitor NTS burdens. This study retrospectively analyzed 1,028 NTS isolates from animals, the environment, and food products in South Africa, collected between 1960 and 2023. Among the 102 serotypes identified, S . Heidelberg, isolated only between 2000−2009 and 2020−2023, accounted for 94.3% of isolations during the latter period, suggesting a recent shift in Salmonella epidemiology in the region. The highest resistance rates were observed for cefoxitin (65.7%), cephalothin (62.8%), and tetracycline (59.8%), with a significant increase in resistance to several antibiotics, including ceftriaxone and aztreonam, from 2010−2023. Genetic analysis revealed that S . Gallinarium had the highest prevalence of antibiotic resistance genes, such as tetA (71.4%), qnrA (64.3%), cat 1 (64.3%), bla PSE (57.1%), and both bla CMY-2 and qnrB at 50%. The bla PSE and bla SHV genes were strongly associated with ceftriaxone resistance in S . Dublin isolates, while bla PSE and qnrS were linked to chloramphenicol resistance in S . Enteritidis and S . Dublin isolates. Additionally, 87% of the virulence genes screened were present in over 50% of the serotypes, indicating increased adaptability and potential shifts in disease dynamics. The rise in antimicrobial resistance, driven by antimicrobial misuse, horizontal gene transfer, and biofilm formation, could alter serotype dynamics and changing disease epidemiology. This trend underscores the urgent need for effective antimicrobial stewardship and surveillance to combat the spread of antibiotic resistance in Salmonella populations.

In 2020, an outbreak of Salmonella Hadar illnesses was linked to contact with non-commercial, privately owned (backyard) poultry including live chickens, turkeys, and ducks, resulting in 848 illnesses. From late 2020 to 2021, this Salmonella Hadar strain caused an outbreak that was linked to ground turkey consumption. Core genome multilocus sequence typing (cgMLST) analysis determined that the Salmonella Hadar isolates detected during the outbreak linked to backyard poultry and the outbreak linked to ground turkey were closely related genetically (within 0–16 alleles). Epidemiological and traceback investigations were unable to determine how Salmonella Hadar detected in backyard poultry and ground turkey were linked, despite this genetic relatedness. Enhanced molecular characterization methods, such as analysis of the pangenome of Salmonella isolates, might be necessary to understand the relationship between these two outbreaks. Similarly, enhanced data collection during outbreak investigations and further research could potentially aid in determining whether these transmission vehicles are truly linked by a common source and what reservoirs exist across the poultry industries that allow Salmonella Hadar to persist. Further work combining epidemiological data collection, more detailed traceback information, and genomic analysis tools will be important for monitoring and investigating future enteric disease outbreaks.