Whole Genome Sequencing, Antibiotic Resistance, and Epidemiology Features of Nontyphoidal Salmonella Isolated From Diarrheic Children: Evidence From North China

Genomic analyses reveal presence of extensively drug-resistant Salmonella enterica serovars isolated from clinical samples in Guizhou province, China, 2019-2023

Background

The emergence of extensively drug-resistant (XDR) Salmonella in humans poses a significant public health and therapeutic challenge. However, limited data are available on XDR Salmonella isolates from Guizhou province, China. This study aimed to investigate the molecular epidemiology and resistance patterns of XDR Salmonella isolates from clinical samples in this region.

Methods

A total of 931 Salmonella isolates were screened for XDR isolates through antimicrobial susceptibility testing. These XDR isolates were subjected to whole-genome sequencing (WGS) and bioinformatic analysis to further systematically investigating the molecular epidemiology and resistance patterns of XDR Salmonella isolates.

Results

Between 2019 and 2023, 931 Salmonella isolates were collected from clinical samples in Guizhou. Of these isolates, 51 (5.5%) were identified as XDR and classified into 16 serovars. Among the serovars, 15 corresponded to a specific sequence type, except for S. Typhimurium serovars. The predominant serovars, S. 1,4,[5],12:i:-, S. Enteritidis, and S. Kentucky, were divided into ST34, ST11, and ST198, respectively. Genomic analysis showed that all XDR isolates harbored at least eight antimicrobial resistance genes (ARGs) and multidrug efflux pumps. Highly prevalent point mutations in gyrA (D87 and S83) and parC (S80I) were detected, along with eight plasmid-mediated quinolone resistance (PMQR) genes. The qnrS1 gene was the most common (43.1%), followed by oqxA, aac-(6')-lb-cr variant, qnrB4, qnrS2, qnrA1, qepA2, and oqxB. The predominant β-lactamase gene was blaTEM-1 (54.9%), and blaCTX-M-55 (35.3%) was the most prevalent extended-spectrum β-lactamase subtype. Notably, blaNDM-1 gene was identified for the first time in Salmonella from Guizhou, and one S. 1,4,[5],12:i:- isolate contained the mcr-1.1 gene. ARGs profiles varied by serovars, with S. 1,4,[5],12:i:- isolates carrying the highest number. Ten plasmid types were identified, predominantly IncHI2/IncHI2A (47.5%). Key resistance genes such as tetA, PMQR, blaCTX-M , mcr-1.1, and blaNDM-1 were located on IncHI2/IncHI2A plasmids. Notably, 75.0% of the conjugative plasmids belonged to IncHI2/IncHI2A, indicating that horizontal gene transfer through conjugation facilitates ARGs dissemination. Core genome multilocus sequence typing (cgMLST) analysis revealed significant genetic diversity, with 39 core genome sequence types (cgSTs) identified and no evidence of outbreaks.

Conclusion

The rising prevalence of XDR Salmonella in Guizhou province is concerning. Initial whole-genome sequencing (WGS) data provide critical insights for understanding and controlling XDR Salmonella infections, aiding public health officials in identifying emerging threats and trends.

Interpretable machine learning-derived nomogram model for early detection of persistent diarrhea in Salmonella typhimurium enteritis: a propensity score matching based case-control study

BACKGROUND

Salmonella typhimurium infection is a considerable global health concern, particularly in children, where it often leads to persistent diarrhea. This condition can result in severe health complications including malnutrition and cognitive impairment.

METHODS

A comprehensive retrospective study was conducted involving 627 children diagnosed with Salmonella typhimurium enteritis. These children were hospitalized for Salmonella typhimurium enteritis between January 2010 and December 2022 at the Second Affiliated Hospital of Wenzhou Medical University. Propensity score matching was used to explore the potential risk factors and predictors of persistent diarrhea following S. typhimurium infection.

RESULTS

The study identified body temperature, C-reactive protein (CRP) levels, alanine aminotransferase (ALT) levels, white blood cell count, and lactose intolerance were significant predictors of persistent diarrhea. Nomogram models developed based on these predictors demonstrated robust performance in predicting persistent diarrhea risk, with an accuracy of > 90%.

CONCLUSION

The developed nomogram models provide a practical tool for the early identification of children at high risk of persistent diarrhea, facilitating intervention, potentially preventing serious sequelae, and improving the prognosis of children with S. typhimurium enteritis.

Genotypic Antimicrobial Resistance Profiles of Diarrheagenic Escherichia coli and Nontyphoidal Salmonella Strains Isolated from Children with Diarrhea and Their Exposure Environments in Ethiopia

Background

Antimicrobial resistance (AMR) poses a significant global threat, particularly in low- and middle-income countries, such as Ethiopia, where surveillance is limited. This study aimed to predict and characterize the AMR profiles of diarrheagenic Escherichia coli (DEC) and nontyphoidal Salmonella (NTS) strains isolated from human, animal, food, and environmental samples using whole genome sequencing.

Methods

A total of 57 NTS and 50 DEC isolates were sequenced on an Illumina NextSeq 550. The ResFinder and PointFinder tools were employed to identify antimicrobial resistance genes (ARGs) and point mutations. Salmonella serotypes were determined using SeqSero.

Results

The analysis identified at least one ARG in every NTS sample and 78% of the DEC isolates, with 22 distinct ARGs in the NTS samples and 40 in the DEC samples. The most prevalent ARGs were aac(6')-Iaa and aph(3')-Ib, which predict aminoglycoside resistance in 100% of NTS and 54% of DEC isolates, respectively. Other commonly identified ARGs include sul2, aph(6)-Id, blaTEM-1B , and tet(A), which confer resistance to folate inhibitors, aminoglycosides, β-lactams, and tetracycline. Some ARGs predicted phenotypic multidrug resistance in both DEC and NTS isolates. All identified β-lactam ARGs, except for blaTEM -1D, conferred resistance to more than three antibiotics. Interestingly, blaCTX- M-15 was found to confer resistance to nine antibiotics, including third-generation cephalosporins, in 18% of DEC and 3.5% of NTS isolates. DEC isolates from children exhibited the highest ARG diversity. Notably, genes such as aph(3″)-Ib, aph(6)-Id, sul2, and tet(A) were detected across all sample types, including water sources, although some ARGs were exclusive to specific sample types. Point mutations mediating AMR were detected in several genes, with mutations associated with nucleotide substitution being the most frequent.

Conclusion

This genotypic AMR profiling revealed the presence of widespread drug-resistant NTS and DEC strains in Ethiopia. Robust and sustained AMR surveillance is essential for monitoring the emergence and spread of these resistant pathogens.

Antimicrobial resistance and genomic investigation of Salmonella isolated from retail foods in Guizhou, China

Introduction

Salmonella is a major foodborne pathogen worldwide that causes severe morbidity and mortality. It is mainly caused by consuming contaminated food, with retail food considered the primary source.

Methods

In Guizhou, China, 102 Salmonella strains isolated from 2016 to 2021 underwent phenotypic antimicrobial resistance testing and whole-genome sequencing (WGS) to understand Salmonella diversity, including serotypes, sequencing types (STs), antimicrobial genes, virulence genes, plasmid types, multi-locus sequence types (MLST), and core genome MLST (cgMLST).

Results and discussion

S.Typhimurium was the dominant serotype, and O:4(B) was the leading serogroup. The most prevalent genotype was ST40. Phenotypic antimicrobial resistance identified 66.7% of the sampled isolates as multi-drug resistant (MDR). S.Enteritidis (n = 7), S.Typhimurium (n = 1), S.Indiana (n = 1), S.Kentucky (n = 1), S.Uganda (n = 1), all of which were MDR, were resistant to Colistin. Resistance rates varied significantly across different strains and food types, particularly meat products exhibiting higher resistance. Notably, significant increases in resistance were observed from 2016 to 2021 for the following: ≥ 1 resistant (P = 0.001), MDR (P = 0.001), ampicillin (P = 0.001), tetracycline (P < 0.001), chloramphenicol (P = 0.030), and trimethoprim/sulfamethoxazole (P = 0.003). The marked escalation in drug resistance over the recent years, coupled with the varying resistance rates among food sources, underscores the growing public health concern. Our findings highlight the need for a coordinated approach to effectively monitor and respond to Salmonella infections in Guizhou, China.

Salmonella Enteritidis activates inflammatory storm via SPI-1 and SPI-2 to promote intracellular proliferation and bacterial virulence

Salmonella Enteritidis is an important intracellular pathogen, which can cause gastroenteritis in humans and animals and threaten life and health. S. Enteritidis proliferates in host macrophages to establish systemic infection. In this study, we evaluated the effects of Salmonella pathogenicity island-1 (SPI-1) and SPI-2 to S. Enteritidis virulence in vitro and in vivo, as well as the host inflammatory pathways affected by SPI-1 and SPI-2. Our results show that S. Enteritidis SPI-1 and SPI-2 contributed to bacterial invasion and proliferation in RAW264.7 macrophages, and induced cytotoxicity and cellular apoptosis of these cells. S. Enteritidis infection induced multiple inflammatory responses, including mitogen-activated protein kinase (ERK-mediated) and Janus kinase-signal transducer and activator of transcript (STAT) (STAT2-mediated) pathways. Both SPI-1 and SPI-2 were necessary to induce robust inflammatory responses and ERK/STAT2 phosphorylation in macrophages. In a mouse infection model, both SPIs, especially SPI-2, resulted in significant production of inflammatory cytokines and various interferon-stimulated genes in the liver and spleen. Activation of the ERK- and STAT2-mediated cytokine storm was largely affected by SPI-2. S. Enteritidis ΔSPI-1-infected mice displayed moderate histopathological damage and drastically reduced bacterial loads in tissues, whereas only slight damage and no bacteria were observed in ΔSPI-2- and ΔSPI-1/SPI-2-infected mice. A survival assay showed that ΔSPI-1 mutant mice maintained a medium level of virulence, while SPI-2 plays a decisive role in bacterial virulence. Collectively, our findings indicate that both SPIs, especially SPI-2, profoundly contributed to S. Enteritidis intracellular localization and virulence by activating multiple inflammatory pathways.