China CDC
In August 2023, the Shanghai CDC laboratory received diarrheal stool specimens from two pediatric hospitals in close succession. These specimens were identified and serotyped as Salmonella enterica serotype Grumpensis (S. Grumpensis). The rarity of this serotype was confirmed upon consulting the local Chinese Salmonella genome database (1), which contains no recorded instances, suggesting that it is an infrequent occurrence in China. Commonly, symptoms of salmonellosis emerge anywhere from 6 hours to 6 days following infection. The discovery of two instances of this unusual serotype within a 24-hour period signals a red flag for a possible outbreak and underscores the pathogen’s transmission capability.
Two male children, aged 1 and 2 years, presented to the hospital on August 1and 2 with similar clinical symptoms of bloody diarrhea (>3 episodes in 24 hours) and abdominal pain (Table 1). Initially treated with cefdinir, patient G2’s symptoms persisted despite a 5-day course, leading to a switch to azithromycin, which resulted in gradual improvement and ful recovery.
Epidemiological investigations play a crucial role in managing cases related to uncommon pathogens. Despite the initial findings showing no evidence of typical sources of infection such as dining out, travel, contact with symptomatic individuals, consumption of raw water, undercooked foods, or owning pets, it posed a challenge in determining the origin of the infection.
CDC laboratory personnel collected specimens from the household of individual G2. Adhering to the procedures specified in GB4789.4-2016, a diverse set of samples, including stool from family members, uneaten food, and environmental swabs, were gathered. Maintaining sterility and a constant temperature of 4 ℃, samples were transported to the lab for pathogen examination within two hours. Despite these precautions, no Salmonella was detected in any of the samples. Additionally, there were no further cases involving this particular Salmonella serotype reported at the same hospital. In our continued investigation of the two S. Grumpensis strains, we conducted a comprehensive analysis that included both antimicrobial susceptibility testing (AST) and whole genome sequencing (WGS). The AST employed the broth microdilution technique to assess the resistance against 22 antibiotics encompassing 11 classes, as listed in Supplementary Table S1. This method was strictly in accordance with Clinical and Laboratory Standards Institute (CLSI) guidelines and the National Antimicrobial Resistance Monitoring System (NARMS) protocol, aiming to determine the Minimum Inhibitory Concentrations (MICs) for each antibiotic (2–3). The AST findings, as presented in Supplementary Table S1, indicated that the strains were susceptible to the full array of antibiotics tested.
Meanwhile, WGS results, detailed in Table 2, classified both isolates as Salmonella Grumpensis S.I (13, 23: d: 1,7). They shared multilocus sequence type (ST) 2060 and core genome multilocus sequence type (cgST) 175517, differing in only one allele, suggesting a strong genetic similarity. Their matching phenotypic and genotypic resistance patterns, absence of plasmid replicons, and common genetic features indicate a close genetic relationship, typical for strains involved in outbreaks, pointing to a common source or transmission chain.
The study analyzed the genomes of 51 S. Grumpensis available in the NCBI database (Supplementary Table S2), revealing its widespread across 11 countries and regions globally, with the highest numbers in Spain (n=20), the United Kingdom (n=15), and the United States (n=7). The strains were isolated between 2005 and 2023, with a surge from 2017 to 2023. Various sample types were identified, including human (n=42), food (n=2), plant (n=1), poultry (n=1), and unknown sources (n=7). Human samples primarily consisted of fecal specimens (n=39), as well as blood (n=2) and cerebrospinal fluid (n=1).
Phylogenetic analysis (Figure 1) identified ST2060 (n=37) and ST751 (n=13) as the predominant global STs among S. Grumpensis isolates. Most isolates harbored acc(6’)-Iaa (98.1%) and fosA7 (96.2%) genes. ST751 has been observed since 2016 in the UK, Canada, the USA, and Brazil, from both humans and poultry, notably lacks of multidrug resistance. Initially reported in 2006, ST2060 is mainly present in human samples (97.3%) and comprised of two genetic clades: 2060.1 and 2060.2, with the latter branching into three sub-clades (2060.2-1, 2060.2-2, 2060.2-3). The study conducted hierarchical single linkage clustering based on pairwise single nucleotide polymorphism (SNP) differences at different thresholds (100, 50, 25, 10, 5, 0). Two isolates from the study belonged to the 2060.2-1 sub-clade, genetically close (0–80 SNPs) to isolates from the UK, USA, and Senegal, and highly similar (0–4 SNPs) to a 2023 USA strain (SRR26351730). An intriguing finding was an isolate from Senegal, in the 2060.2-1 sub-clade, having 14 antibiotic resistance genes (ARGs) and originating from a cerebrospinal fluid sample.
