Objective:To analyze the short-term hospital-based transmission characteristics and gene variation of Carbapenem-Resistant Klebsiella pneumoniae (CRKP) by genome-wide technique to provide evidence for transmission control. Methods:The experimental strain was derived from all the CRKP isolated in Affiliated Hospital of North China University of Science and Technology from October 2022 to December 2023. Strain identification and drug susceptibility were tested with VITEK 2-Compact automatic bacterial identification drug susceptibility analyzer or disk method, and the results were interpreted through whole genome sequencing. The ST type, carbapenem resistance gene, virulence factor, and O serotype of the collected strains were analyzed.Results:Among the 115 strains of CRKP, 94 strains were isolated from the intensive care unit (ICU), accounting for 81.7%, and 21 strains were isolated from the non-intensive care unit (NICU), accounting for 18.3%. The 115 strains of CRKP can be divided into 11 ST types, of which ST11 type was the most (54.8%, 63/115), followed by ST15 type (22.6%, 26/115) and ST5492 type (15.7%, 18/115). Type ST5492 was a new clonal group in the region. The 115 strains of CRKP could be divided into 7 O serotypes, most of which were O2a type(32.2%,37/115), followed by O5 type(30.4%,35/115) and O1 type(27.8%,32/115). The resistance genes of carbapenem antibiotics showed that there were 107 strains carrying the blaKPC-2 gene, one strain with the blaNDM-1 gene, and one strain with both the blaKPC-2 and blaNDM-13 genes. Virulence genes were detected in 55 CRKP strains (47.8%, 55/115), among which six strains detected peg-344, iucA, iroB, rmpA, and rmpA2 virulence genes (5.2%, 6/115). Four virulence genes ( peg-344, iucA, rmpA, and rmpA2) were detected in 34 strains (29.6%, 34/115). Three virulence genes ( iucA, iroB and rmpA) were detected in two strains (1.7%, 2/115). Three virulence genes ( peg-344, iucA and rmpA) were detected in one strain (0.8%, 1/115). IucA and rmpA virulence genes were detected in 12 strains (10.4%, 12/115). KPC-2_ST11_O2a, KPC-2_ST15_O1 and KPC-2_ST5492_O5 were dominant clones, and their distribution was mainly in the intensive care unit. The whole genome sequence analysis showed that there were three dominant clones, among which ST11 clones were subdivided into three dominant O serotypes, all of which were mainly in the intensive care unit. Conclusion:The popular strain in the hospital of CRKP is a KPC-2_ST11 clone group carrying iucA, rmpA/rmpA2, with cross-department transmission and mutation. ST5492 is a newly-launched clone type. The intensive care unit of hvKP carrying five virulence genes, including peg-344, should be alert to the epidemic risk of CR-hvKP outbreak.

Objective:To investigate the epidemiological dynamics and spatiotemporal diffusion trend of brucellosis in China from 2010 to 2024.Methods:Data on reported human brucellosis cases in mainland China from January 1, 2010, to December 31, 2024, were collected via the"China Information System for Disease Control and Prevention", including detailed information on the date of onset, gender, age, occupation, and residential address of the cases. The Joinpoint regression and spatial interpolation techniques were used to investigate the spatiotemporal dynamics and population distribution characteristics of human brucellosis in pastoral/semi-pastoral areas and other regions, as well as urban and rural areas, and explore the epidemic trends of the disease.Results:From 2010 to 2024, pastoral/semi-pastoral regions reported 252 094 brucellosis cases, with a mean annual incidence rate of 36.57±7.28 per 100 000. In contrast, other regions cumulatively recorded 519 748 cases during the same period, demonstrating a significantly lower mean annual incidence rate of 2.54±0.74 per 100 000. The incidence rate of human brucellosis in pastoral/semi-pastoral regions exhibited a declining-rebounding-declining trend. Specifically, the incidence rate decreased significantly from 2010 to 2017 (APC=-7.20; P<0.001) and increased notably from 2017 to 2021 (APC=18.00; P=0.015) with a decline again from 2021 to 2024 (APC=-7.53; P=0.027). In other regions, the incidence rate showed a fluctuating upward trend. Specifically, the incidence rate increased significantly from 2010 to 2015 (APC=20.37; P<0.001) and decreased notably from 2015 to 2018 (APC=-21.78; P<0.001), followed by an increase again from 2018 to 2024, a significant upward trend in incidence rate from 2018 to 2021 (APC=26.73; P<0.001) and a non-significant decline from 2021 to 2024 (APC=-0.99; P=0.735), resulting in the maintenance of a relatively high incidence level. Rural areas demonstrated significantly higher brucellosis incidence rates than urban settings (all P<0.001). Brucellosis exhibited a diffusion trend from the northern epidemic areas of China to neighboring regions, along with sporadic diffusion in southern regions between 2010 and 2024. The age structure of patients in pastoral/semi-pastoral areas differed significantly from that in other regions. Specifically, in pastoral/semi-pastoral areas, the incidence rate was higher among the 35-49 age groups, while in other regions, the incidence rate was higher among those aged 55-64. Conclusion:There are notable disparities in the incidence of human brucellosis between pastoral/semi-pastoral areas and other regions in China. Human brucellosis exhibits a diffusion trend from the northern epidemic areas of China to neighboring regions, along with sporadic diffusion in southern regions.

Objective:To identify candidate strains of Nontoxigenic Clostridioides difficile (NTCD) with potential for intervention in Clostridioides difficile infection (CDI) and analyze their phenotypic characteristics. Methods:A total of 713 Clostridioides difficile strains from various sources were systematically collected nationwide between 2015 and 2023. This included 649 strains isolated from human fecal samples and 64 strains isolated from the fecal samples of farmed animals. NTCD strains were preliminarily screened through toxin gene detection and antibiotic sensitivity test, and then NTCD candidate strains with potential for intervention in CDI were screened by a series of in vitro experiments, including MLST, sporulation, germination, adhesion, motility, and biofilm formation ability. Ultimately, the virulence genes and antimicrobial resistance genes of the candidate strains were comprehensively analyzed to rigorously assess their safety profiles. Results:Among 713 strains of C. difficile from different sources, 10 strains were initially screened out, which were non-toxin-producing and sensitive to antibiotics. MLST showed that seven strains were from the Clade1 branch and three strains were of a novel type. The results of sporulation and germination showed that SD59, SD178, SJZ17, and WZ142 had stronger sporulation and germination abilities. The adhesion of 10 strains was high, and the adhesion rate was between 72.93% and 99.32%. The motility of all strains was different, and the motility of SD178, SD59 and SJZ17 was stronger. The biofilm-forming ability of all strains was weak. SD59, SD178 and SJZ17 carried a limited number of virulence and resistance genes, thereby posing a relatively low safety risk. Conclusion:Three NTCD strains are successfully selected as potential effective NTCD strains to interfere with CDI.

Objective:To analyze the carriage status, subtype distribution and flanking gene sequence characteristics of oxacillinases (OXA enzyme) in 241 clinical strains of Pseudomonas aeruginosa, and assess their roles in the drug resistance of Pseudomonas aeruginosa and ability to horizontally transfer across species. Methods:Clinical P. aeruginosa isolates were collected from four hospitals in Sanya, Tangshan, Zhangjiakou, and Beijing. The prevalence of oxacillinases and their flanking gene sequences was analyzed by whole-genome sequencing (NGS) and bioinformatic approaches. Results:A total of 241 isolates of P. aeruginosa were gathered, and 35 blaOXA subtypes were identified through screening of 252 blaOXA genes. These genes were classified into three subfamilies: blaOXA-50-like (241, 95.6%), blaOXA-1-like (9, 3.6%) and blaOXA-10-like (2, 0.8%). Among these, 11 subtypes (11, 31.4%) were novel blaOXA subtypes. Nine of these belonged to the blaOXA-50-like subfamily and were designated as blaOXA-1244, blaOXA-1245, blaOXA-1246, blaOXA-1250, blaOXA-1252, blaOXA-1253, blaOXA-1254, blaOXA-1255, and blaOXA-1256. The remaining two belonged to the blaOXA-10-like subfamily and were named blaOXA-1247 and blaOXA-1248. Compared to the amino acid sequence of OXA-10, the newly identified subtype OXA-1247 exhibited a mutation at position 117, where a valine was replaced by a leucine. This change was thought to improve the enzyme′s ability to hydrolyze carbapenems. In the analysis of the flanking sequences of the blaOXA genes, Class I integrons were identified in four bacterial strains. The variable regions of these integrons carried three distinct patterns of resistance gene cassettes: aac( 6′) -Ib-blaOXA-1247-ant( 3′′) -Ia, aac( 6′) -Ib-blaOXA-1248 and aac( 6′) -Ib- blaIMP-45-blaOXA-1-catB3. Among these, the strain BJ2326 carried a class I integron that was connected to the downstream IS CR1 element to form a composite class I integron structure, additionally carrying the resistance gene blaPER-1. Out of the 223 non-wild-type P. aeruginosa strains, 127 strains exhibited non-wild-type profiles to the four beta-lactam antibiotics MEM, CAZ, FEP, and TZP, with the combination of MEM+CAZ+FEP being the most prevalent, representing 57.0% of the total. Conclusions:The blaOXA genes in 241 clinical P. aeruginosa strains showed diversity. Some blaOXA genes had a co-transfer risk with the metallo-β-lactamase resistance gene blaIMP-45. Among the 11 newly discovered blaOXA subtypes, the new subtype OXA-1247 may have carbapenemase activity and potential for horizontal transfer.

Coronavirus is the largest RNA virus with known genome so far,among which porcine coronavirus is an important pathogen causing acute diarrhea in piglets.Due to its highly mutable RNA nature,this virus poses a substantial challenge for disease prevention and control,leading to substantial annual economic losses within China's swine industry.The analysis of the mechanism of RNA synthesis of coronaviruses is helpful for understanding the genetic variation of coronaviruses and screening antiviral drugs.At present,more in-depth studies mainly focus on Murine coronavir-us(MHV)and human Severe acute respiratory syndrome coronavirus 2(SARS-CoV-2).In order to investigate the replication mechanism of porcine coronaviruses,this article takes MHV,SARS-CoV-2 and other coronaviruses as references to summarises the mechanism of regulating viral rep-lication in the non-coding region of porcine coronaviruses such as Porcine epidemic diarrhea virus(PEDV),Transmissible gastroenteritis virus(TGEV),Porcine deltacoronavirus(PDCoV),and Swine acute diarrhea syndrome coronavirus(SADS-CoV).Placed a specific emphasis on the func-tional roles of conserved motifs and secondary structures within the 5'UTR in facilitating viral rep-lication,elucidated how conserved structures in the 3'UTR regulate the same process.The signifi-cance of the interaction between the non-coding region of the virus and the host were discussed,and variations in the viral 5'UTR and 3'UTR were scrutinized,thereby establishing a solid theoret-ical foundation for the development of antiviral drugs that target UTRs and high titer vaccine can-didate strains.

Objective:To investigate the epidemiological dynamics and spatiotemporal diffusion trend of brucellosis in China from 2010 to 2024.Methods:Data on reported human brucellosis cases in mainland China from January 1, 2010, to December 31, 2024, were collected via the"China Information System for Disease Control and Prevention", including detailed information on the date of onset, gender, age, occupation, and residential address of the cases. The Joinpoint regression and spatial interpolation techniques were used to investigate the spatiotemporal dynamics and population distribution characteristics of human brucellosis in pastoral/semi-pastoral areas and other regions, as well as urban and rural areas, and explore the epidemic trends of the disease.Results:From 2010 to 2024, pastoral/semi-pastoral regions reported 252 094 brucellosis cases, with a mean annual incidence rate of 36.57±7.28 per 100 000. In contrast, other regions cumulatively recorded 519 748 cases during the same period, demonstrating a significantly lower mean annual incidence rate of 2.54±0.74 per 100 000. The incidence rate of human brucellosis in pastoral/semi-pastoral regions exhibited a declining-rebounding-declining trend. Specifically, the incidence rate decreased significantly from 2010 to 2017 (APC=-7.20; P<0.001) and increased notably from 2017 to 2021 (APC=18.00; P=0.015) with a decline again from 2021 to 2024 (APC=-7.53; P=0.027). In other regions, the incidence rate showed a fluctuating upward trend. Specifically, the incidence rate increased significantly from 2010 to 2015 (APC=20.37; P<0.001) and decreased notably from 2015 to 2018 (APC=-21.78; P<0.001), followed by an increase again from 2018 to 2024, a significant upward trend in incidence rate from 2018 to 2021 (APC=26.73; P<0.001) and a non-significant decline from 2021 to 2024 (APC=-0.99; P=0.735), resulting in the maintenance of a relatively high incidence level. Rural areas demonstrated significantly higher brucellosis incidence rates than urban settings (all P<0.001). Brucellosis exhibited a diffusion trend from the northern epidemic areas of China to neighboring regions, along with sporadic diffusion in southern regions between 2010 and 2024. The age structure of patients in pastoral/semi-pastoral areas differed significantly from that in other regions. Specifically, in pastoral/semi-pastoral areas, the incidence rate was higher among the 35-49 age groups, while in other regions, the incidence rate was higher among those aged 55-64. Conclusion:There are notable disparities in the incidence of human brucellosis between pastoral/semi-pastoral areas and other regions in China. Human brucellosis exhibits a diffusion trend from the northern epidemic areas of China to neighboring regions, along with sporadic diffusion in southern regions.

Objective:To identify candidate strains of Nontoxigenic Clostridioides difficile (NTCD) with potential for intervention in Clostridioides difficile infection (CDI) and analyze their phenotypic characteristics. Methods:A total of 713 Clostridioides difficile strains from various sources were systematically collected nationwide between 2015 and 2023. This included 649 strains isolated from human fecal samples and 64 strains isolated from the fecal samples of farmed animals. NTCD strains were preliminarily screened through toxin gene detection and antibiotic sensitivity test, and then NTCD candidate strains with potential for intervention in CDI were screened by a series of in vitro experiments, including MLST, sporulation, germination, adhesion, motility, and biofilm formation ability. Ultimately, the virulence genes and antimicrobial resistance genes of the candidate strains were comprehensively analyzed to rigorously assess their safety profiles. Results:Among 713 strains of C. difficile from different sources, 10 strains were initially screened out, which were non-toxin-producing and sensitive to antibiotics. MLST showed that seven strains were from the Clade1 branch and three strains were of a novel type. The results of sporulation and germination showed that SD59, SD178, SJZ17, and WZ142 had stronger sporulation and germination abilities. The adhesion of 10 strains was high, and the adhesion rate was between 72.93% and 99.32%. The motility of all strains was different, and the motility of SD178, SD59 and SJZ17 was stronger. The biofilm-forming ability of all strains was weak. SD59, SD178 and SJZ17 carried a limited number of virulence and resistance genes, thereby posing a relatively low safety risk. Conclusion:Three NTCD strains are successfully selected as potential effective NTCD strains to interfere with CDI.

Objective:To analyze the carriage status, subtype distribution and flanking gene sequence characteristics of oxacillinases (OXA enzyme) in 241 clinical strains of Pseudomonas aeruginosa, and assess their roles in the drug resistance of Pseudomonas aeruginosa and ability to horizontally transfer across species. Methods:Clinical P. aeruginosa isolates were collected from four hospitals in Sanya, Tangshan, Zhangjiakou, and Beijing. The prevalence of oxacillinases and their flanking gene sequences was analyzed by whole-genome sequencing (NGS) and bioinformatic approaches. Results:A total of 241 isolates of P. aeruginosa were gathered, and 35 blaOXA subtypes were identified through screening of 252 blaOXA genes. These genes were classified into three subfamilies: blaOXA-50-like (241, 95.6%), blaOXA-1-like (9, 3.6%) and blaOXA-10-like (2, 0.8%). Among these, 11 subtypes (11, 31.4%) were novel blaOXA subtypes. Nine of these belonged to the blaOXA-50-like subfamily and were designated as blaOXA-1244, blaOXA-1245, blaOXA-1246, blaOXA-1250, blaOXA-1252, blaOXA-1253, blaOXA-1254, blaOXA-1255, and blaOXA-1256. The remaining two belonged to the blaOXA-10-like subfamily and were named blaOXA-1247 and blaOXA-1248. Compared to the amino acid sequence of OXA-10, the newly identified subtype OXA-1247 exhibited a mutation at position 117, where a valine was replaced by a leucine. This change was thought to improve the enzyme′s ability to hydrolyze carbapenems. In the analysis of the flanking sequences of the blaOXA genes, Class I integrons were identified in four bacterial strains. The variable regions of these integrons carried three distinct patterns of resistance gene cassettes: aac( 6′) -Ib-blaOXA-1247-ant( 3′′) -Ia, aac( 6′) -Ib-blaOXA-1248 and aac( 6′) -Ib- blaIMP-45-blaOXA-1-catB3. Among these, the strain BJ2326 carried a class I integron that was connected to the downstream IS CR1 element to form a composite class I integron structure, additionally carrying the resistance gene blaPER-1. Out of the 223 non-wild-type P. aeruginosa strains, 127 strains exhibited non-wild-type profiles to the four beta-lactam antibiotics MEM, CAZ, FEP, and TZP, with the combination of MEM+CAZ+FEP being the most prevalent, representing 57.0% of the total. Conclusions:The blaOXA genes in 241 clinical P. aeruginosa strains showed diversity. Some blaOXA genes had a co-transfer risk with the metallo-β-lactamase resistance gene blaIMP-45. Among the 11 newly discovered blaOXA subtypes, the new subtype OXA-1247 may have carbapenemase activity and potential for horizontal transfer.

Objective:To analyze the short-term hospital-based transmission characteristics and gene variation of Carbapenem-Resistant Klebsiella pneumoniae (CRKP) by genome-wide technique to provide evidence for transmission control. Methods:The experimental strain was derived from all the CRKP isolated in Affiliated Hospital of North China University of Science and Technology from October 2022 to December 2023. Strain identification and drug susceptibility were tested with VITEK 2-Compact automatic bacterial identification drug susceptibility analyzer or disk method, and the results were interpreted through whole genome sequencing. The ST type, carbapenem resistance gene, virulence factor, and O serotype of the collected strains were analyzed.Results:Among the 115 strains of CRKP, 94 strains were isolated from the intensive care unit (ICU), accounting for 81.7%, and 21 strains were isolated from the non-intensive care unit (NICU), accounting for 18.3%. The 115 strains of CRKP can be divided into 11 ST types, of which ST11 type was the most (54.8%, 63/115), followed by ST15 type (22.6%, 26/115) and ST5492 type (15.7%, 18/115). Type ST5492 was a new clonal group in the region. The 115 strains of CRKP could be divided into 7 O serotypes, most of which were O2a type(32.2%,37/115), followed by O5 type(30.4%,35/115) and O1 type(27.8%,32/115). The resistance genes of carbapenem antibiotics showed that there were 107 strains carrying the blaKPC-2 gene, one strain with the blaNDM-1 gene, and one strain with both the blaKPC-2 and blaNDM-13 genes. Virulence genes were detected in 55 CRKP strains (47.8%, 55/115), among which six strains detected peg-344, iucA, iroB, rmpA, and rmpA2 virulence genes (5.2%, 6/115). Four virulence genes ( peg-344, iucA, rmpA, and rmpA2) were detected in 34 strains (29.6%, 34/115). Three virulence genes ( iucA, iroB and rmpA) were detected in two strains (1.7%, 2/115). Three virulence genes ( peg-344, iucA and rmpA) were detected in one strain (0.8%, 1/115). IucA and rmpA virulence genes were detected in 12 strains (10.4%, 12/115). KPC-2_ST11_O2a, KPC-2_ST15_O1 and KPC-2_ST5492_O5 were dominant clones, and their distribution was mainly in the intensive care unit. The whole genome sequence analysis showed that there were three dominant clones, among which ST11 clones were subdivided into three dominant O serotypes, all of which were mainly in the intensive care unit. Conclusion:The popular strain in the hospital of CRKP is a KPC-2_ST11 clone group carrying iucA, rmpA/rmpA2, with cross-department transmission and mutation. ST5492 is a newly-launched clone type. The intensive care unit of hvKP carrying five virulence genes, including peg-344, should be alert to the epidemic risk of CR-hvKP outbreak.

Coronavirus is the largest RNA virus with known genome so far,among which porcine coronavirus is an important pathogen causing acute diarrhea in piglets.Due to its highly mutable RNA nature,this virus poses a substantial challenge for disease prevention and control,leading to substantial annual economic losses within China's swine industry.The analysis of the mechanism of RNA synthesis of coronaviruses is helpful for understanding the genetic variation of coronaviruses and screening antiviral drugs.At present,more in-depth studies mainly focus on Murine coronavir-us(MHV)and human Severe acute respiratory syndrome coronavirus 2(SARS-CoV-2).In order to investigate the replication mechanism of porcine coronaviruses,this article takes MHV,SARS-CoV-2 and other coronaviruses as references to summarises the mechanism of regulating viral rep-lication in the non-coding region of porcine coronaviruses such as Porcine epidemic diarrhea virus(PEDV),Transmissible gastroenteritis virus(TGEV),Porcine deltacoronavirus(PDCoV),and Swine acute diarrhea syndrome coronavirus(SADS-CoV).Placed a specific emphasis on the func-tional roles of conserved motifs and secondary structures within the 5'UTR in facilitating viral rep-lication,elucidated how conserved structures in the 3'UTR regulate the same process.The signifi-cance of the interaction between the non-coding region of the virus and the host were discussed,and variations in the viral 5'UTR and 3'UTR were scrutinized,thereby establishing a solid theoret-ical foundation for the development of antiviral drugs that target UTRs and high titer vaccine can-didate strains.