Jay C D Hinton | Search PubMed

PubMed2025

Diversity of Salmonella enterica isolates from urban river and sewage water in Blantyre, Malawi.

BACKGROUND: Salmonella enterica encompasses over 2,600 serovars, including several commonly associated with severe infection in humans. Salmonella is a major cause of sepsis in Africa; however, diagnosis requires clinical microbiology facilities. Environmental surveillance has the potential to play a role in Salmonella surveillance. METHODS: We undertook water-based environmental surveillance in Blantyre, Malawi, from 2018-2020, taking samples from rivers (87.9%), a sewage plant (8.85%) and other water sources (3.24%), isolating and storing 1,042 non-typhoidal Salmonella (NTS) isolates in this period. Of these, 341 NTS isolates were whole genome sequenced, genome quality was checked, duplicate genomes from any given sample were removed and core genome phylogeny was reconstructed. AMRFinder, PathogenWatch and SISTR were used to further investigate serovar, sequence type and antimicrobial resistance determinants. RESULTS: After quality checks, and removal of duplicate genomes, 270 NTS genomes remained for further analysis. Multiple Salmonella serovars associated with human infection were detected, of which S. Typhimurium (55/270 isolates) was the most common, including 44 of Sequence Type (ST) 313, a serovar commonly associated with severe invasive disease (iNTS). Six lineage 2 ST313 genomes possessed AMR genes predicting multidrug resistance (MDR), while 29 lineage 3 isolates contained no AMR predictive genes. PCR based detection of staG has been proposed as a diagnostic marker of S. Typhi; however, all eight genomes that contained staG identified as Salmonella enterica serovar Orion, raising concerns about the specificity of this marker as a monoplex for environmental surveillance of S. Typhi. DISCUSSION: The study identified diverse Salmonella serovars in the environment, including those reported to cause invasive disease, emphasizing the complex but potentially valuable contribution of implementing environmental surveillance for Salmonella in high burden areas lacking diagnostic microbiology capacity.

Sewage↗

PubMed2025

Global diversity and evolution of Salmonella enterica serovar Panama: a genomic epidemiology study.

BACKGROUND: Non-typhoidal Salmonella is a globally important bacterial pathogen, typically associated with foodborne gastrointestinal infection. Some non-typhoidal Salmonella serovars can also colonise typically sterile sites in people to cause invasive non-typhoidal Salmonella disease. Salmonella enterica serovar Panama is responsible for a substantial number of cases of human bloodstream infection, but despite its global dissemination, numerous outbreaks, and a reported association with invasive non-typhoidal Salmonella disease, S enterica serovar Panama (S Panama) is understudied. We aimed to describe the genomic epidemiology and evolutionary history of S Panama to provide a vital baseline of understanding for this globally important serovar. METHODS: In this genomic epidemiology study, we analysed S Panama genomes derived from historical collections, national surveillance datasets, and publicly available epidemiological and whole-genome sequencing data which span the years 1931-2019. Maximum likelihood and Bayesian phylodynamic approaches were used to investigate population structure and evolutionary history and to infer geotemporal dissemination. A combination of different bioinformatic approaches with short-read and long-read data were used to characterise geographical and clade-specific trends in antimicrobial resistance (AMR) and genetic markers for invasiveness. FINDINGS: We analysed 836 S Panama genomes, of which 559 (67%) were sequenced as part of this study. The collection represents all inhabited continents and includes isolates collected between 1931 and 2019. We identified the presence of four geographically linked S Panama clades (C1 [ie, the Latin America and the Caribbean clade; n=338], C2 [ie, the European clade; n=124], C3 [ie, the Martinique clade; n=131], and C4 [ie, the Asia and Oceania clade; n=104]) and regional trends in AMR profiles. Most isolates (715 [86%] of 836) were pan-susceptible to antibiotics and belonged to clades circulating in Latin America and the Caribbean (64%, n=458). Most antibiotic-resistant isolates in our collection (113 [93%] of 121) fell within clades C4 (ie, the Asia and Oceania clade) and C2 (ie, the European clade), the latter of which had the highest invasiveness index values based on the conservation of 196 extraintestinal predictor genes. INTERPRETATION: This first large-scale phylogenetic analysis of S Panama has revealed important information about the population structure, AMR, global ecology, and genetic markers of invasiveness of the identified genomic subtypes. Our findings provide an important baseline for understanding S Panama infection. The presence of multidrug-resistant clades with elevated invasiveness index values should be monitored through ongoing surveillance, as such clades could pose an increased public health risk. FUNDING: UK Research and Innovation Global Challenges Research Fund and Biotechnology and Biological Sciences Research Council, UK Medical Research Council, Wellcome Trust, John Lennon Memorial Scholarship, Institut Pasteur, Santé publique France, Fondation Le Roch-Les Mousquetaires, Investissement d'Avenir Programme, and Australian National Health and Medical Research Council.

Humans↗

PubMed2025

Microbe Profile: Salmonella Typhimurium: the master of the art of adaptation.

Salmonella Typhimurium is a major Salmonella serovar that is found globally. It is responsible for outbreaks of self-limiting gastroenteritis that are broadly linked to the industrialization of food production. S. Typhimurium is a pathogen with a broad host range and remarkable metabolic versatility. The ∼5 Mb genome includes the pSLT virulence plasmid and has a characteristic prophage repertoire. The major virulence determinants are encoded by a variety of pathogenicity islands. Emerging multidrug-resistant lineages of epidemics of S. Typhimurium are currently causing bloodstream infections in sub-Saharan Africa. The versatility and adaptability of S. Typhimurium pose an important public health challenge.

Salmonella typhimurium↗