Background Salmonella enterica (S. enterica) causes tens of thousands of cases of diarrheal disease worldwide each year. However, our understanding of the genome and transmission dynamics of S. enterica in Minhang District in Shanghai, China is still insufficient. This study is aimed to better understand the population structure, antibiotic resistance patterns, and evolution dynamics of local strains. Methods We sequenced 458 S. enterica strains from outpatients at Minhang District Central Hospital in Shanghai, China, from 2012 to 2021. Bioinformatics analyses on antibiotic resistance genes, virulence factors, mobile genetic elements, pathogenic islands, and phylogenetic relationships were performed. Results Here we show that two dominant serovars are S. Enteritidis and S. Typhimurium isolated from outpatients in Minhang District in Shanghai, China. A total of 40 serovars and 53 sequence types (STs) are identified, two S. Montevideo strains isolated in 2013 belong to a newly identified ST10844, which is firstly identified in Minhang District in Shanghai, China. More than half of the isolates show resistance to fluoroquinolones and beta-lactams. Notably, 259 (56.6%) of the 458 isolates exhibit a multidrug-resistant pattern. Third-generation cephalosporin resistance gene bla_CTX-M-55 is identified in 15 (3.3%) isolates, and fluoroquinolone resistance gene qnrS1 is identified in 42 (9.2%) isolates, both of which are strongly correlated with IS26. Mutations of T57S in ParC and D87Y in GyrA are observed in 149 (32.5%) and 133 (29.0%) isolates, respectively. In addition, phylogenetic analysis confirms the presence of outbreaks caused by S. Enteritidis and S. Typhimurium, respectively. Conclusions These results suggest local expansion and evolution in Salmonella occurred in Shanghai, China, and the underlying emergence of the undefined multidrug-resistant clone. Our findings enlarge the knowledge of local epidemics of Salmonella, especially S. Enteritidis and S. Typhimurium in Shanghai, and provide a piece of useful baseline information for future whole-genome sequencing surveillance.

In the spring and summer of 2024, an unexpected large outbreak of pertussis hit China, with the annual incidence of pertussis (34.03/100,000) more than 12-fold higher than that of 2023 (2.71/100,000). We aimed to assess clinical and molecular epidemiological patterns and unravel the reasons behind the 2024 pertussis outbreak. PCR-confirmed pertussis cases were enrolled from five sentinel hospitals in Shanghai, Anhui, Hainan, Fujian, and Inner Mongolia between 1 January and 30 September 2024. The epidemiological data of PCR-confirmed cases, as well as the clinical data and vaccination history of hospitalized cases were collected. Nasopharyngeal swab samples were collected from partial pertussis cases and their household contacts for Bordetella pertussis culture during the local peak months. Antimicrobial susceptibility testing and whole genome sequencing were performed on all 394 isolates to evaluate six antibiotic susceptibility and characterize the antigenic, virulent, and phylogenetic characteristics of the circulating isolates. A total of 14,874 cases of pertussis were PCR-confirmed in the 5 sentinel hospitals, peaking in April to July. Infants represented 9.6% of cases and children aged 4–10 years represented 74.3% of cases in the five hospitals. Of the 7238 (48.7%) cases with vaccination data, 6563 (90.7%) were fully vaccinated. Breakthrough pertussis cases were mainly observed in fully vaccinated children since the age of 7 months. Among the 828 (5.6%) cases hospitalized for pertussis, 71.7% (594/828) cases had complications (pneumonia 69.7%, 577/828), 5.7% (47/828) were admitted to intensive care unit and 0.24% (2/828) cases died. Sixty-four per cent (403/630) of families had both the patient and at least one family member PCR-positive for B. pertussis. In total, 394 B. pertussis isolates were recovered from the 1921 nasopharyngeal swab samples. Ninety-nine point seven per cent (393/394) of isolates displayed high-level resistance to azithromycin (MIC range, 16–256 μg/ml), and 48.0% (189/394) isolates were susceptible to trimethoprim-sulfamethoxazole (MIC range, <0.008/0.152–0.5/9.5 μg/ml). All the isolates were susceptible to levofloxacin, doxycycline, ceftazidime, and cefoperazone/sulbactam. All the isolates were assigned to ST-2 and 99.5% (392/394) belonged to the MT28-Shanghai clone by SNP-based analysis, carrying ptxP3 AgST4, 23S rRNA-13 (with erythromycin resistance), and prn150. 23.4% (92/394) of isolates were predicted to be PRN-deficient. The waning vaccine-derived protection and the prevailing macrolide-resistant MT28 clone harboring non-vaccine type ptxP3 are responsible for the 2024 large outbreak of pertussis in China. Our findings highlight the urgent need for revising national pertussis vaccination strategies and traditional first-line antibiotic therapy. Booster vaccination for children aged 4–6 years is urgent to control the pertussis outbreak. This work is supported by Shanghai Municipal Sixth Round Three-Year Action Plan for Strengthening the Construction of the Public Health System (GWVI-11.1-07, GWVI-2.1.2) and 10.13039/501100001809 National Natural Science Foundation of China (82272381).

Evolution of ST4821 Meningococci

As an important foodborne bacterium, non-typhoidal Salmonella (NTS) is estimated to cause approximately 215,000 deaths worldwide each year. Globally, S. Mo

Background: The occurrence and dissemination of hypermucoviscous and hypervirulent Klebsiella pneumoniae (hm-hvKp) isolates in clinical settings are a critical public health problem in the world. However, the data on these isolates in community populations are limited. This study aims to understand the prevalence and molecular characteristics of hm-hvKp isolates in community patients in Shanghai, China. Methods: In 2018, an active surveillance system focused on hm-hvKp in community diarrhoeal cases was implemented in Pudong New Area, Shanghai, China, involving 12 sentinel hospitals. The antimicrobial susceptibility of hm-hvKp isolates from fecal samples was tested, and whole-genome sequencing (WGS) was performed to predict the serotypes and sequence types and to identify antimicrobial resistance determinants, virulence determinants, and phylogenetic clusters. Results: The overall prevalence of hm K. pneumoniae isolates was 2.48% (31/1252), with the proportions of 1.76% (22/1252) for hm-hvKp and 0.72% (9/1252) for hm not hv K. pneumoniae. The prevalence of hm-hvKp isolates among different age groups and different months was statistically significant. All the 22 hm-hvKp isolates were susceptible to 20 antimicrobial agents and only carried bla_SHV gene, and KL1 and KL2 accounted for eight (36.36%) cases and seven (31.82%) cases, respectively. The eight ST23/KL1 isolates belonged to the predominant CG23-I clade, which typically possessed the virulence determinants profile of rmpA/rmpA2-iro-iuc-ybt-irp-clb. The five ST86/KL2 isolates were assigned to the global clusters ST86/KL2-1 (n=2), ST86/KL2-2 (n=2), ST86/KL2-3 (n=1), all lack of the clb gene. Shanghai ST23/KL1 and ST86/KL2 isolates were closely related to the global isolates from liver abscesses, blood, and urine. Conclusion: Hm-hvKp is carried by the community population of Shanghai, with ST23/KL1 and ST86/KL2 isolates predominant. Hm-hvKp isolates of different continents, different sources, and different virulence levels were closely related. Ongoing surveillance of hm-hvKp isolates in the community population is warranted.