Bo Pang

Background: The misuse of antibiotics in aquaculture and clinical settings promotes drug resistance in food-related microbes. Vibrio parahaemolyticus, a global pathogen linked to diarrheal disease and food safety concerns, warrants a systematic assessment of its resistance. Methods: We analyzed 9757 high-quality V. parahaemolyticus genomes retrieved from NCBI (1950–2023). ARGs, mobile genetic elements (MGEs), plasmid replicons, sequence types, and virulence genes were identified. Associations between ARGs and genomic/macro-level factors were assessed, and strain-level resistance risk was evaluated using arg_ranker. Results: Among all sequenced strains, 99.59% were pathogenic, and 23.57% were food and aquatic animal sources. Furthermore, pan-resistome analysis indicated that ARGs carried by the V. parahaemolyticus population are expanding. Notably, most ARG types were enriched in strains from food and aquatic animals. In terms of temporal trends, shifts in resistance categories highlight tetracyclines, penams, and phosphonic acid antibiotics as priority surveillance targets, given that their associated ARGs have recently increased. Consistent with these findings, a positive correlation was found between ARG abundance and mobile genetic element (MGE) count per strain, specifically with tnpA as the most frequently co-occurring MGE. In addition, dynamic changes in predominant plasmid replicon types were documented, among which IncA/C2 and Col3M show co-occurrence with high-risk ARGs. Finally, risk assessment classified 95.18% of strains as Risk Level IV (lowest). Conclusions: Although the overall global resistance risk remains low, strains from food and aquatic animals contained the highest proportion of higher-risk (Rank I and II) strains among all sources. This study provides updated insights into antimicrobial resistance trends in V. parahaemolyticus and offers a theoretical foundation for guiding future resistance management strategies.

Background: Aeromonas species are ubiquitous aquatic bacteria that have emerged as significant foodborne enteric pathogens worldwide, yet their genomic landscape in clinical settings remains poorly delineated, particularly in Beijing. Methods: To address this gap, we performed active surveillance for Aeromonas among 691 consecutive diarrheal outpatients in a Beijing district from January to December 2024. Isolates were recovered using enrichment culture coupled with PCR screening and identified by MALDI-TOF MS. Antimicrobial susceptibility was tested against 17 agents. Whole-genome sequencing was conducted on all isolates, enabling average nucleotide identity (ANI) analysis, comprehensive annotation of antimicrobial resistance and virulence genes, multilocus sequence typing (MLST), and core-genome SNP (cgSNP)-based phylogenetics. Results: Aeromonas was detected in 3.3% (23/691) of patients, with Aeromonas veronii (56.52%, 13/23) and Aeromonas caviae (26.09%, 6/23) predominating. Co-infections with other enteric pathogens occurred in 65.2% of positive cases. Resistance rates were notably high for ampicillin/ampicillin-sulbactam (78.26%), nalidixic acid (56.52%), and ertapenem (21.73%), and 65.21% of isolates were multidrug-resistant. Genotypic–phenotypic concordance was robust, with β -lactamase genes ampS (60.87%) and blaCEPH-A3 (47.83%) being most prevalent. Strikingly, mcr-3.25 and mcr-3.3 , which belong to the mcr family (originally described as mobile colistin resistance genes), were identified in 8.70% of isolates, exhibiting perfect correlation with phenotypic resistance. Plasmer analysis suggested both mcr genes to be chromosomally encoded. Comparative genomic analysis of virulence-associated genes revealed striking species-specific specialization: A. veronii predominantly carried complete T3SS clusters (61.5%), A. caviae and Aeromonas enteropelogenes were enriched in T6SS genes, and a single A. dhakensis isolate possessed an extensive arsenal including T3SS, T6SS, and a full RTX toxin cluster. MLST resolved the 23 isolates into 22 sequence types, 18 of which were novel. Phylogenetic reconstruction identified a tight monophyletic cluster of three A. veronii isolates (9–27 SNP differences) recovered within a 96-h window, suggestive of a potential cluster that warrants further epidemiological investigation. Comparative genomic analysis of the rare species Aeromonas allosaccharophila demonstrated that the Beijing clinical isolate S14 differs from the U.S. clinical strain ATCC 35942 by 42,099 SNPs, confirming its distinct genetic lineage. Conclusion: Collectively, this study delineates high genetic diversity, emerging chromosomal colistin resistance, and species-specific virulence specialization among Aeromonas isolates from diarrheal patients in Beijing. The detection of a potential outbreak cluster and a rare clinical isolate underscores the power of genomics-based surveillance for detecting and mitigating foodborne pathogen thre ats .

Wastewater surveillance has rapidly emerged as an innovative, population-level monitoring tool that does not rely on healthcare-seeking behaviors and can systematically capture cryptic infections t...

Cholera outbreaks are prevalent in coastal regions, where hydroclimatic factors play a critical role. However, evidence on their associations with different genotypes remains limited, and global projection remains lacking. We compiled cholera data from EnteroBase and WHO weekly reports covering 110 coastal countries from 1980 to 2022. A generalized additive model was used to examine the associations between hydroclimatic factors and different cholera serotypes and genotypes. We further projected future cholera occurrences for each coastal country under three climate change scenarios from 2025 to 2100. During the study period, Wave 3 of O1 replaced Wave 1 as the predominant genotype of cholera, while cholera O139 remained at low levels and only occurred in Asia. At the country–year level, each 1 °C increase in sea surface temperature (SST) was significantly associated with cholera occurrence (OR: 1.032, 95% CI: 1.023 to 1.040) and Wave 3 of O1 (OR: 1.149, 95% CI: 1.097 to 1.203). Drainage density (m/km²) and coastline ratio (%) were positively related to cholera, with ORs of 1.067 (95% CI: 1.046 to 1.087) and 1.022 (95% CI: 1.019 to 1.027). For future projections, five trend patterns were identified under different emission scenarios, with most countries showing increased cholera risk due to global hydroclimatic changes, peaking under the SSP585 scenario. Our findings reveal associations between hydroclimatic factors and different cholera genotypes and project future cholera risk across coastal countries, thereby providing evidence to inform genotype-specific surveillance and targeted prevention strategies at the global scale.

Background: A novel lineage of serogroup O1 El Tor V. cholerae, genetically distinct from the seventh pandemic strain, has recently been identified in China and linked to diarrheal outbreaks. Investigations were conducted to examine the inflammation in the intestines of mice infected with V. cholerae strains including the new lineage strains VC6050 (ctxAB +) and VC6055 (ctxAB -), as well as the seventh pandemic strains of V. cholerae N16961.Results: The result showed that the colonization abilities of V. cholerae in the intestines of mice infected with VC6050 and N16961 was significantly higher than that of the VC6055 group. Histological sections of the small intestine revealed a few inflammatory cell infiltrations in the muscularismucosa, with inflammation being the primary form of tissue damage. The transcript changes in the neonatal mouse intestine were primarily associated with immune and inflammation-related genes after V. cholerae infection, including CCL7, CCL17, CCL21, CXCL9, and CXCL10. In comparison to the seventh pandemic strain N16961, the new lineage strains exhibited significant up-regulation of carboxyesterase and genes involved in aquaporin-mediated transport, whereas some inflammation-related genes were down-regulated. When compared to the nontoxigenic strain VC6055, the toxigenic strains N16961 and VC6050 demonstrated significant up-regulation of inflammation related genes and alpha-defensin gene (Defa). Conclusions: The results suggest that, in comparison to the seventh pandemic strains of V. cholerae, the new lineage strains exhibit lower levels of inflammatory cytokines and chemokines. Furthermore, CTX-positive strains, when contrasted with CTX-negative strains, not only activate a greater number of inflammatory factors but also stimulate the host to generate more antimicrobial peptides.

The El Tor biotype of Vibrio cholerae caused the seventh cholera pandemic (7CP). Although V. cholerae variants of this biotype frequently emerge, studies on their microevolution and spatiotemporal transmission in epidemics caused by a single clone are limited. During the cholera outbreak in Sichuan Province, China, in the 1990s, strains belonging to phage type 6 (PT6) but resistant to typing phage VP5 due to a deletion mutation in ompW, which is the gene associated with the VP5 receptor were identified. In this study, we analyzed PT6 strains using genome sequencing to reveal the genomic and transmission characteristics of such a transient phage type in China’s cholera epidemic history. The findings revealed that the PT6 strains formed an independent clone during the four-year epidemic and emerged in wave 2. Most of them carried multiple CTX^classΦ genome copies on chromosome 2 (Chr. 2) and two copies each of RS1^ET and RS1-4** on chromosome 1 (Chr. 1). Frequent cross-regional transmission and local outbreaks within Sichuan Province, China, were revealed for this clone. A variety of spontaneous mutations in the ompW gene, conferring resistance to the VP5 phage, were observed under VP5 infection pressure, showing the incident mutation of OmpW for the survival adaptation of V. cholerae to phage pressure. Therefore, this genomic epidemiological revisit of these distinct phage-resistant phenotype strains reveals their clonal genetic structure, improves our understanding of the spread of V. cholerae by tracking their variation, and assists in epidemic source tracing and disease control.

We investigated the molecular epidemiology of Vibrio cholerae O1 in Fujian Province, China, during 2009--2023. Sequence type (ST) 75 clonal complex has emerged continuously since 2020, and ST1480 and ST182 have dominated. ST1480 strains appear to have widespread transmission. To monitor V. cholerae evolution, continued global genomic surveillance is needed.

Introduction: Shewanella is an important opportunistic pathogen distributed in marine environments that has caused an increasing number of clinical infections. However, there are few reports on the distribution and characteristics of Shewanella in the diarrheal pathogen spectrum. In this study, we have systematically described the prevalence of Shewanella infections in diarrhea patients in Beijing, China 2017–2019, and genome characteristics and antimicrobial susceptibility of Shewanella isolates.Methods: Stool samples were collected from diarrhea patients in a surveillance project from 2017 to 2019. Shewanella strains were isolated, and identified using VITEKR 2 COMPACT and MALDI-TOF MS. Average nucleotide identity (ANI) analysis, multi-locus sequence typing (MLST), phylogenetic analysis, virulence-associated genes and antimicrobial resistance genes analysis were used for genome characteristics description. The antibiotic susceptibility test was performed with microbroth dilution method.Results: 1104 fecal samples were collected, and the Shewanella detection rate was 2.36% (26/1104). The main manifestations of infection caused by Shewanella spp. were diarrhea (100%, 26/26), abdominal pain (65.38%, 17/26), and vomiting (38.46%, 10/26). The 26 isolates were classified into 3 species (S. algae (n = 18), S. indica (n = 5), and S. chilikensis (n = 3)) and 22 sequence types. Core genome single nucleotide polymorphism-based evolutionary tree identified three clone groups corresponding to three infection events in the same months in 2017 and 2019. The putative virulence-associated gene pool consisted of 56 potential virulence genes, including 19 virulence gene factors. The resistance rates of the 26 isolates to 17 antibiotics from high to low were as follows: polymyxin E (76.92%), cefotaxime (57.69%), ampicillin (50%), ampicillin-sulbactam (34.62%), nalidixic acid (15.38%), ciprofloxacin (11.54%), selectrin (3.846%,1/26), and tetracycline (3.846%, 1/26). The rate of multidrug resistance was 38.46% (10/26).Discussion: Monitoring for Shewanella spp. should be added to the routine surveillance of infectious diarrhea during the epidemic season.

In 2020, a new serotype of Vibrio parahaemolyticus O10:K4 emerged and caused several outbreaks and sporadic cases in Guangxi, China. Phylogenetic analysis indicated that those strains are new variants of the sequence type 3 pandemic clone. The new serotype may become dominant, warranting enhanced investigations and surveillance.

There is a growing demand for rapid, sensitive, field-deployable nucleic acid tests for cholera, which usually occurs in rural areas. In this study, we developed a Cas12a-assisted rapid isothermal detection (CARID) system for the detection of toxigenic V. cholerae serogroups O1 and O139 by combining recombinase-aided amplification and CRISPR-Cas (clustered regularly interspaced short palindromic repeats and CRISPR-associated proteins). The results can be determined by fluorescence signal and visualized by lateral flow dipstick. We identified 154 V. cholerae strains and 129 strains of other intestinal diarrheagenic bacteria with a 100% coincidence rate. The limit of detection of CARID was 20 copies/reaction of V. cholerae genomic DNA, which is comparable to that of polymerase chain reaction (PCR) and qPCR. Multiple-CARID was also established for efficiency and economic considerations with an acceptable decrease in sensitivity. Simulated sample tests showed that CARID is suitable for complex samples. In conclusion, CARID is a rapid, sensitive, economically efficient, and portable method for the detection of V. cholerae, which makes it suitable for field responses to cholera.