Genome Mining of Novel Targets and Construction of Ladder-shaped melting temperature isothermal amplification Assays for the Identification of Cronobacter sakazakii and Cronobacter malonaticus.

Cronobacter species are potential pathogens that can contaminate powdered infant formula. C. sakazakii and C. malonaticus are the most common species of Cronobacter associated with infections. This study mined new molecular targets for the detection of C. sakazakii and C. malonaticus by using comparative genome approaches. Specific target genes mngB and ompR were obtained and used to detect C. sakazakii and C. malonaticus, respectively. A novel detection method, termed ladder-shape melting temperature isothermal amplification (LMTIA), was developed and evaluated. The detection limit for pure C. sakazakii DNA was 1 pg per reaction and 1 fg per reaction for C. malonaticus. The C. sakazakii, C. malonaticus, and the reference stains were all correctly identified. The amplicons can be successfully visualized and identified by naked eyes when hydroxy naphthol blue dye (HNB dye) was used in the reaction. Therefore, the LMTIA assays developed in this study showed potential application for microorganism identification and detection.

Comparison of Antibiotic Resistance Profiles of Salmonella Isolates from Retail Meats in Nanchang, China, in Two Periods.

Salmonella is one of the most important foodborne pathogens. In this article, a total of 160 Salmonella isolates recovered from retail meats in June-July 2018 (before COVID-19 outbreak) and December 2020-April 2021 (after COVID-19 outbreak) in Nanchang, China, were characterized for serotyping, antimicrobial susceptibility, and specific resistance gene screening. The prevalence of Salmonella Typhimurium increased from 5.4% in 2018 to 19.1% in 2021, and Salmonella Enteritidis increased from 3.3% in 2018 to 8.8% in 2021. Compared with those in June-July 2018, Salmonella isolates in December 2020-April 2021 demonstrated a significant increase in resistance to 13 tested antibiotics except for doxycycline and nitrofurantoin (p < 0.05). The Salmonella isolates in December 2020-April 2021 showed a higher presence of plasmid-mediated quinolone resistance genes (qnrA, qnrB, and qnrS), and mutations in the quinolone resistance-determining region (gyrA Asp87Asn, gyrA Asp87Tyr, parC Thr57Ser, and parC Ser80Ile). Whole-genome sequencing was used to analyze four polymyxin B-resistant strains. Some common mutation sites in eptC and micA were found in the four strains. Based on the data in this article, it indicated that antibiotic resistance was facilitated and more gene mutations related to quinolone resistance were developed.

Whole-genome sequencing analysis of a rare Salmonella diarizonae clinical strain carrying multiple plasmids and novel gene cassettes.

OBJECTIVES: Human infection caused by an uncommon Salmonella enterica subsp. diarizonae (hereafter S. diarizonae) is rising. However, knowledge concerning S. diarizonae is still limited. This study aimed to investigate the genomic features of S. diarizonae S499 isolated from a child patient with gastroenteritis symptom in China. METHODS: The antimicrobial susceptibility of S. diarizonae S499 was determined by microdilution broth assay. Whole genome was sequenced using Illumina HiSeq X-10 and PacBio RS II platforms and was de novo assembled using Unicycler and SPAdes. Conjugation experiment was performed by a broth mating method. RESULTS: S. diarizonae S499 was a multi-drug resistant (MDR) isolate and showed resistance to all cephalosporin drugs tested. Six plasmids (pS0499A, pS0499B, pS0499C, pS0499D, pS0499E and pS0499F) were identified. A rare gene cassette IS26-blaCTX-M-55-wbuc-△blaTEM-1-IS26-intI1 was repeatedly inserted into pS0499A three times in one locus and reversely inserted into plasmid pS0499D. That enhanced cephalosporin resistance. To the best of our knowledge, this finding has not been reported previously. Both pS0499A and pS0499B contained multiple resistance genes and could transfer to recipient strain E. coli EC600. CONCLUSION: This article reported the genome features of S. diarizonae S499, which contained four resistant plasmids including a novel plasmid pS0499A with a novel gene cassette rearrangement. These data could contribute to a better understanding of the antimicrobial resistance mechanisms and transmission dynamics of S. diarizonae.