Antimicrobial Susceptibility and Molecular Typing of Salmonella Senftenberg Isolated from Humans and Other Sources in Shanghai, China, 2005 to 2011

Clinical profiles and antimicrobial resistance patterns of invasive Salmonella infections in children in China

Invasive Salmonella infections result in a significant burden of disease including morbidity, mortality, and financial cost in many countries. Besides typhoid fever, the clinical impact of non-typhoid Salmonella infections is increasingly recognized with the improvement of laboratory detection capacity and techniques. A retrospective multicenter study was conducted to analyze the clinical profiles and antimicrobial resistance patterns of invasive Salmonella infections in hospitalized children in China during 2016–2018. A total of 130 children with invasive Salmonella infections were included with the median age of 12 months (range: 1–144 months). Seventy-nine percent of cases occurred between May and October. Pneumonia was the most common comorbidity in 33 (25.4%) patients. Meningitis and septic arthritis caused by nontyphoidal Salmonella (NTS) infections occurred in 12 (9.2%) patients and 5 (3.8%) patients. Patients < 12 months (OR: 16.04) and with septic shock (OR: 23.4), vomit (OR: 13.33), convulsion (OR: 15.86), C-reactive protein (CRP) ≥ 40 g/L (OR: 5.56), and a higher level of procalcitonin (PCT) (OR: 1.05) on admission were statistically associated to an increased risk of developing meningitis. Compared to 114 patients with NTS infections, 16 patients with typhoid fever presented with higher levels of CRP and PCT (P < 0.05). The rates of resistance to ampicillin, sulfamethoxazole/trimethoprim, ciprofloxacin, and ceftriaxone among Salmonella Typhi and NTS isolates were 50% vs 57.3%, 9.1% vs 24.8%, 0% vs 11.2%, and 0% vs 9.9%, respectively. NTS has been the major cause of invasive Salmonella infections in Chinese children and can result in severe diseases. Antimicrobial resistance among NTS was more common.

Whole-Genome Sequencing Provides Insight Into Antimicrobial Resistance and Molecular Characteristics of Salmonella From Livestock Meat and Diarrhea Patient in Hanzhong, China

Salmonella is a major zoonotic pathogen, which usually contaminates food resulting in salmonellosis in humans. Exploring the characteristics and origins of Salmonella is essential in formulating prevention and control measures for Salmonella infection. We used slide agglutination, antimicrobial susceptibility testing, and whole-genome sequencing to analyze and compare Salmonella’s phenotype, genotyping diversity, and genetic relatedness from livestock meat and diarrhea patients in Hanzhong, China, from 2018 to 2020. Totally 216 Salmonella enterica isolates were screened from frozen whole chicken carcasses (44.3%, 70/158), frozen raw ground pork (36.2%, 59/163), and diarrhea patients (4.4%, 87/1964). Salmonella Typhimurium was the dominant serotype. Notably, compared with other sources, isolates obtained from frozen whole chicken carcasses showed significant resistance to third-generation cephalosporin and fluoroquinolones (p < 0.05). All strains were assigned into 36 sequence types (STs) and two novel STs, and an excellent consistency was observed between ST and serotype. Genomic data revealed that extended-spectrum β-lactamase genes were responsible for third-generation cephalosporin resistance in 52 Salmonella strains, and the most predominant resistance determinant was bla_CTX–M. Furthermore, of the 60 ciprofloxacin-resistant isolates, five single-base mutations in quinolone resistance-determining regions were identified in gyrA or parC, and the plasmid-mediated quinolone resistance gene aac(6’)Ib-cr was most often detected. The cgMLST clusters show that five clusters among four serotypes (including S. Typhimurium, S. London, S. Derby, and S. Agona) cover samples from diarrhea patients and livestock meat pathway isolate, indicating a possibility of cross-host transmission. In conclusion, the livestock meat isolates have a higher level of resistance than diarrhea patients’ isolates and could be an essential source of human Salmonella infection.

Rapid Identification and Source Tracing of a Salmonella Typhimurium Outbreak in China by Metagenomic and Whole-Genome Sequencing

Salmonella spp. are among the most prevalent foodborne pathogens. Rapid identification of etiologic agents during foodborne outbreaks is of great importance. In this study, we report a traceback investigation of a Salmonella outbreak in China. Metagenomic sequencing of suspected food samples was performed on MinION and MiSeq platforms. Real-time nanopore sequencing analysis identified reads belonging to the Enterobacteriaceae family. MiSeq sequencing identified 63 reads specifically mapped to Salmonella. Conventional methods including quantitative-PCR and culture-based isolation confirmed as Salmonella enterica serovar Typhimurium. The foodborne outbreak of Salmonella Typhimurium was further recognized by whole-genome sequencing and pulsed-field gel electrophoresis analysis. Our study demonstrates the ability of metagenomic sequencing to rapidly identify enteric pathogens directly from food samples. These results highlight the capacity of metagenomic sequencing to deliver actionable information rapidly and to expedite the tracing and identification of etiologic agents during foodborne outbreaks.

Characterization of the emerging multidrug-resistant Salmonella enterica serotype Kentucky ST314 in China

Salmonella enterica serotype Kentucky (S. Kentucky) is an important Salmonella serotype with multiple sequence types (ST) with a worldwide incidence. We identified 8 STs from 180 strains of S. Kentucky, and ST314 emerged as the most commonly encountered ST. Drug susceptibility testing revealed that ST314 had multiple resistance properties, and 75.5% of the strains were resistant to three or more classes of antimicrobials. The rate of resistance to chloramphenicol, florfenicol, sulfafurazole and tetracycline were greater than 60%. The rates of ST314 resistance to quinolones were as follows: ciprofloxacin, 32.1%; nalidixic acid, 16%; and ofloxacin, 7.5%. Investigating the mechanism of quinolone resistance of ST314 revealed that mutations in the quinolone resistance-determining regions were rare, and resistance mainly occurred due to the resistance genes carried by plasmids. Only 1.9% (2/106) of ST314 strains had mutations in the quinolone resistance-determining regions (QRDR). The drug resistance genes of ST314 were primarily of plasmid-mediated quinolone resistance (PMQR). The detection rate of Salmonella genomic island 1 (SGI1) in ST314 was 12.3%. XbaI-pulsed-field gel electrophoresis revealed that S. enterica Kentucky ST314 was capable of cross-regional and cross-host transmission in China. We found ST314 to be the dominant S. Kentucky ST in China, and it carried multidrug resistance. This is the first report about the emergence of quinolone-resistant S. enterica Kentucky ST314 in China, which is different from previous reports, and the findings of the present study suggest that the mechanism of quinolone resistance in these strains are plasmid-mediated. Notably, plasmids carrying resistance genes may promote the rapid spread of ciprofloxacin resistance.

Rapid Emergence of Florfenicol-Resistant Invasive Non-Typhoidal Salmonella in China: A Potential Threat to Public Health

Infection caused by invasive Salmonella occurs when Salmonella bacteria, which normally cause diarrhea, enter the bloodstream and spread through the body. We report the dramatic increase in florfenicol-resistant invasive non-typhoidal Salmonella (iNTS) in China between 2007 and 2016. Of the 186 iNTS strains isolated during the study period, 34 were florfenicol resistant, most of which harbored known resistance genes. Florfenicol is exclusively used in veterinary medicine in China, but now florfenicol-resistant iNTS is found in clinical patients. This finding indicates that antimicrobial resistance produced in veterinary medicine can be transmitted to humans, which poses a severe threat to public health.

Molecular epidemiology and antimicrobial resistance of invasive non-typhoidal Salmonella in China, 2007-2016

Purpose

Human infections caused by invasive non-typhoidal Salmonella (iNTS) are highly prevalent worldwide. However, data for such infections in China are scarce. This study reports the epidemiology of iNTS in China.

Methods

INTS isolates were recovered from blood and other clinical specimens collected during 2007-2016 across five provinces (Shanghai, Xinjiang, Fujian, Guangxi, and Chongqing) in China. Antimicrobial susceptibility was performed using the agar dilution method and molecular epidemiology was performed using standard microbiological techniques.

Results

A total of 178 iNTS isolates were recovered from approximately 9700 patient specimens during 2007-2016. The predominant serovars were Salmonella Enteritidis (57/178, 32%), Salmonella Choleraesuis (47/178, 26.4%), and Salmonella Typhimurium (24/178, 13.5%). Up to 50 isolates (28.1%) were from patients who were ≤1 year of age, while 28 (15.7%) were from patients who were ≥60 years. Among these isolates, high rates of resistance to nalidixic acid (114/178, 64%), sulfisoxazole (59%), ciprofloxacin (15.2%), and cefotaxime (8.4%) were found. Moreover, 53.4% (95/178) exhibited multidrug resistance, and 3.9% (7/178) showed co-resistance to third-generation cephalosporins and ciprofloxacin. Steadily increasing numbers of nalidixic acid, cefotaxime, and ciprofloxacin-resistant isolates, but decreasing numbers of multidrug resistance isolates were detected during the study period. Detection of quinolone genes in 114 nalidixic acid-resistant isolates showed that 58.3% (67/114) harbored plasmid-mediated quinolone resistance (PMQR) genes [aac(6´)-Ib-cr, qnrA, qnrB, oqxAB, qepA, qnrS, and qnrD] and 98.2% (112/114) exhibited mutations in quinolone resistance determining regions [gyrA, parC, and parE]. Furthermore, we detected beta-lactamases genes in the ceftriaxone-resistant isolates. The most common were bla_TEM-1 (93.3%), followed by bla_CTX-M-55 (40%), bla_CMY-2 (33.3%), and bla_OXA-1 (33.3%). Finally, a range of pulsed-field gel electrophoresis patterns were detected among the Salmonella Enteritidis and Salmonella Typhimurium isolates.

Conclusion

High rates of multidrug resistance and steadily increasing cefotaxime and ciprofloxacin-resistant iNTS could pose a significant challenge for the effective treatment of salmonellosis in China.