Carbapenem-resistant Klebsiella pneumoniae (CRKP) has recently emerged as a notable public health concern, while the underlying drivers of CRKP transmission among patients across different healthcare facilities have not been fully elucidated. To explore the transmission dynamics of CRKP, 45 isolates were collected from both the intensive care unit (ICU) and non-ICU facilities in a teaching hospital in Guangdong, China, from March 2020 to August 2023. The collection of clinical data and antimicrobial resistance phenotypes was conducted, followed by genomic data analysis for these isolates. The mean age of the patients was 75.2 years, with 18 patients (40.0%) admitted to the ICU. The predominant strain in hospital-acquired CRKP was sequence type 11 (ST11), with k-locus type 64 and serotype O1/O2v1 (KL64:O1/O2v1), accounting for 95.6% (43/45) of the cases. The CRKP ST11 isolates from the ICU exhibited a low single nucleotide polymorphism (SNP) distance when compared to isolates from other departments. Genome-wide association studies identified 17 genes strongly associated with SNPs that distinguish CRKP ST11 isolates from those in the ICU and other departments. Temporal transmission analysis revealed that all CRKP isolates from other departments were genetically very close to those from the ICU, with fewer than 16 SNP differences. To further elucidate the transmission routes among departments within the hospital, we reconstructed detailed patient-to-patient transmission pathways using hybrid methods that combine TransPhylo with an SNP-based algorithm. A clear transmission route, along with mutations in potential key genes, was deduced from genomic data coupled with clinical information in this study, providing insights into CRKP transmission dynamics in healthcare settings.

Black-headed gulls have been confirmed as the natural hosts of Deltacoronavirus (δ-CoV) and Gammacoronavirus (γ-CoV). A total of 59 CoV-PCR-positive fecal samples were identified among 509 fecal samples collected from overwintering black-headed gulls in Yunnan Province, China. The prevalence of black-headed gull deltacoronavirus (BHG-DCoV) was 3.54% (18/509), while that of black-headed gull gammacoronavirus (BHG-GCoV) was 8.06% (41/509). The prevalence of BHG-GCoV was significantly higher than that of BHG-DCoV (χ² = 9.518, p < 0.01). Two complete genome sequences of BHG-GCoVs were obtained, with lengths of 27,358 bp and 27,355 bp, respectively, from the fecal samples of black-headed gulls. The nucleotide similarity between the two complete genomes is 98.75%. Phylogenetic analysis based on the whole genome has confirmed that the two strains of BHG-GCoVs clustered into the species Gammacoronavirus anatis. Although BHG-GCoVs belong to the species Gammacoronavirus anatis, they are distantly related to the representative strain Duck_CoV 2714 and exhibit a closer genetic relationship with GCoVs from Xenus cinereus (AvXc-GCoV) and Numenius phaeopus (AvNp-GCoV). Similarity analysis of the five conserved domains revealed a high amino acid similarity not only with AvXc-GCoV and AvNp-GCoV but also with GCoVs from common gulls detected in Poland and those from ruddy turnstones identified in Australia. Additionally, we found that, except for the common gull, the amino acid sequences of the S protein of BHG-GCoVs showed a 88.69% to 96.44% similarity with those of GCoVs carried by Charadriiformes, while the similarity with GCoVs carried by Anseriformes ranged from 31.15% to 54.81%. Furthermore, recombination events were detected in BHG-GCoVs, suggesting that these strains are likely recombinant strains of common gull GCoV and the GCoV of Arenaria interpres (AvAi-GCoV), indicating that recombination events may occur frequently among GCoVs.

Black-headed gulls have been confirmed to be the natural hosts of Deltacoronavirus (δ-CoV) and Gammacoronavirus (γ-CoV). A total of 59 coronaviruses (CoVs) were detected in 509 fecal samples collected from overwintering black-headed gulls in Yunnan Province, China. Among them, the prevalence of black-headed gull Deltacoronavirus (BHG-DCoV) was 3.54% (18/509), and that of black-headed gull Gammacoronaviru (BHG-GCoV) was 8.06% (41/509). The prevalence of BHG-GCoV was higher than that of BHG-DCoV (χ² = 9.518, P < 0.01). It was obtained that two complete genome sequences of BHG-GCoVs with lengths of 27,358 nt and 37,355 nt respectively from the fecal samples of black-headed gulls. The nu-cleotide similarity between the two complete genomes is 98.75%. Phylogenetic analysis based on the whole genome has confirmed that the two stains of BHG-GCoVs clustered into the species Gammacoronavirus anatis. Although BHG-GCoVs belong to the species Gammacoronavirus anatis, they are distantly related to the representative strain Duck_CoV 2714, and have a relatively close genetic relationship with the GCoV from Xenus cinereus (AvXc-GCoV) and the GCoV from Numenius phaeopus (AvNp-GCoV). Based on the similar-ity analysis of the five conserved domains, there is a high amino acid similarity not only with AvXc-GCoV and AvNp-GCoV, but also with the GCoV of the common gull detected in Poland and the GCoV from ruddy turnstone detected in Australia. We also found that the amino acids of the S protein of BHG-GCoVs had a relatively high similarity with GCoV from most of the Charadriiformes except for the common gull, while having a rela-tively low amino acid similarity with that from the Anseriformes. Meanwhile, we also de-tected recombination events in BHG-GCoVs, indicating that recombination events might occur frequently during the viral evolution process.