Public health implications of Yersinia enterocolitica investigation: an ecological modeling and molecular epidemiology study.

BACKGROUND: Yersinia enterocolitica has been sporadically recovered from animals, foods, and human clinical samples in various regions of Ningxia, China. However, the ecological and molecular characteristics of Y. enterocolitica, as well as public health concerns about infection in the Ningxia Hui Autonomous Region, remain unclear. This study aims to analyze the ecological and molecular epidemiological characteristics of Y. enterocolitis in order to inform the public health intervention strategies for the contains of related diseases. METHODS: A total of 270 samples were collected for isolation [animals (n = 208), food (n = 49), and patients (n = 13)], then suspect colonies were isolated and identified by the API20E biochemical identification system, serological tests, biotyping tests, and 16S rRNA-PCR. Then, we used an ecological epidemiological approach combined with machine learning algorithms (general linear model, random forest model, and eXtreme Gradient Boosting) to explore the associations between ecological factors and the pathogenicity of Y. enterocolitis. Furthermore, average nucleotide identity (ANI) estimation, single nucleotide polymorphism (SNP), and core gene multilocus sequence typing (cgMLST) were applied to characterize the molecular profile of isolates based on whole genome sequencing. The statistical test used single-factor analysis, Chi-square tests, t-tests/ANOVA-tests, Wilcoxon rank-sum tests, and Kruskal-Wallis tests. RESULTS: A total of 270 isolates of Yersinia were identified from poultry and livestock (n = 191), food (n = 49), diarrhoea patients (n = 13), rats (n = 15), and hamsters (n = 2). The detection rates of samples from different hosts were statistically different (χ2 = 22.636, P < 0.001). According to the relatedness clustering results, 270 isolates were divided into 12 species, and Y. enterocolitica (n = 187) is a predominated species. Pathogenic isolates made up 52.4% (98/187), while non-pathogenic isolates made up 47.6% (89/187). Temperature and precipitation were strongly associated with the pathogenicity of the isolates (P < 0.001). The random forest (RF) prediction model showed the best performance. The prediction result shows a high risk of pathogenicity Y. enterocolitica was located in the northern, northwestern, and southern of the Ningxia Hui Autonomous Region. The Y. enterocolitica isolates were classified into 54 sequence types (STs) and 125 cgMLST types (CTs), with 4/O:3 being the dominant bioserotype in Ningxia. The dominant STs and dominant CTs of pathogenic isolates in Ningxia were ST429 and HC100_2571, respectively. CONCLUSIONS: The data indicated geographical variations in the distribution of STs and CTs of Y. enterocolitica isolates in Ningxia. Our work offered the first evidence that the pathogenicity of isolates was directly related to fluctuations in temperature and precipitation of the environment. CgMLST typing strategies showed that the isolates were transmitted to the population via pigs and food. Therefore, strengthening health surveillance on pig farms in high-risk areas and focusing on testing food of pig origin are optional strategies to prevent disease outbreaks.

Whole-genome sequencing-based prediction and analysis of antimicrobial resistance in Yersinia enterocolitica from Ningxia, China.

Focusing on resistance trends and transmission patterns of pathogenic microorganisms is a major priority for national surveillance programs. The use of whole-genome sequencing for antimicrobial susceptibility testing (WGS-AST) is a powerful alternative to traditional microbiology laboratory methods. Yersinia enterocolitica antimicrobial resistance (AMR) in the Ningxia Hui Autonomous Region has yet to be described thoroughly in current studies. We assessed and monitored the development of Y. enterocolitica AMR in the Ningxia Hui Autonomous Region during 2007-2019 based on WGS-AST. Resistance genotypes were predicted based on WGS. Antimicrobial resistance testing using classical microbiology determined resistance to 13 antimicrobial agents in 189 Y. enterocolitica isolates from Ningxia. The highest resistance level was 97.88% for cefazolin, followed by ampicillin (AMP) (44.97%), ciprofloxacin (CIP) (25.40%), streptomycin (STR) (11.11%), and tetracycline (TET) (10.58%). Isolates emerged as chloramphenicol (CHL) and trimethoprim/sulfamethoxazole (SXT) resistant. The primary plasmid types were IncFII(Y) and ColRNAI. The TET, STR, and SXT resistance were mediated by the tetA, aph(6)-Id, aph(3″)-Ib, and sul2 genes located on the IncQ1 plasmid. The resistant strains were predominantly biotype 4/O:3/ST429 and the hosts were pigs and patients. The number of multidrug-resistant (MDR) strains was of concern, at 27.51%. At present, the prediction of antimicrobial resistance based on WGS requires a combination of phenotypes. From 2007 to 2019, Y. enterocolitica isolates from the Ningxia Hui Autonomous Region showed a relatively high rate of resistance to cefazolin (CZO) and some resistance to AMP, CIP, STR, and TET. CIP, SXT, and TET showed a relatively clear trend of increasing resistance. Plasmids carrying multiple drug resistance genes are an important mechanism for the spread of antimicrobial resistance. Isolates with low pathogenicity were more likely to present an AMR phenotype than non-pathogenic isolates.

Emerging Role of MicroRNAs and Long Noncoding RNAs in Healthy and Diseased Lung.

Pulmonary hypertension (PH) is a complex and multifactorial disease. An inability to fully unravel the molecular complexities has led to various clinical challenges in developing new therapies for this disease. Noncoding RNAs (ncRNAs) are RNA molecules with limited ability of coding proteins. The amount of ncRNAs is up to 98% of the whole genome's transcripts. Many ncRNAs with a regulatory function of genes have been identified to date and found to act at various steps along the protein biosynthetic process, which includes transcription, RNA maturation, translation, and protein degradation. These discoveries are fueling a new era in understanding the pathophysiology and therapeutic pathways of PH. In this chapter, we discuss the emerging role of noncoding RNAs in PH as well as other pulmonary diseases.

Ecology and geographic distribution of Yersinia enterocolitica among livestock and wildlife in China.

The results in this study show the prevalence of Yersinia enterocolitica varies in different animal species and regions of China. The highest prevalence is among pigs (12.91%), followed by dogs (9.80%), Ochotona curzoniae (plateau pica) (6.76%), chickens (4.50%), rodents (3.40%), cattle (2.78%) and sheep (0.89%). Pathogenic isolates comprised the majority of the Y. enterocolitica recovered from pigs (73.50%) and dogs (59.44%); whereas the nonpathogenic Y. enterocolitica made up most of poultry and wildlife recovered strains. A correlation analysis comparing the prevalence and geographic factors showed the isolation rate of Y. enterocolitica in pigs and dogs was negatively correlated with elevation (r=-0.50, P<0.05) and annual average air temperature (r=-0.43, P<0.05), but there was positive correlation with annual precipitation (r=0.43, P<0.05); conversely, the isolation rate from wildlife is positively correlated with elevation (r=0.3, P<0.05) contrary to the result seen in livestock. Twelve novel biotype 2 pathogenic Y. enterocolitica carried ail and ystB virulence genes, and one biotype 1A nonpathogenic strain positive with ail, ystB and ystA genes were isolated from Microtus fuscus (Qinghai vole) on plague foci of the Qinghai-Xizang plateau. The PFGE pattern K6GN11C30021 was predominant in pigs (44.25%) and patients (41.18%); K6GN11C30068 was predominant in dogs (40.16%). Animal isolates from the same region shared the same pattern (K6GN11C30021 and K6GN11C30012), indicating they may be from the same clone and arose through cross infection. Moreover, the identical PFGE pattern among local animals and diarrhea patients suggested that the animals may be the source of infections in these areas.

[Etiological study on cases with viral diarrhea in Ningxia during 2011].

OBJECTIVE: To investigate the etiological characteristics of human rotavirus (HRV), human calicivirus (HuCV), human astrovirus (HAstV) and human enteral adenovirus (HAdV) in Ningxia province during 2011. METHODS: Stool specimen was collected from acute diarrhea case of Ningxia during 2011. HRV was detected by ELISA and serotype/genotype identified on those RT-PCR positive specimens. HuCV, HAstV and HAdV were detected by RT-PCR. RESULTS: In this study, a total of 690 specimens were detected, with the infection rates of HRV, HuCV, HAstV and HAdV as 2.17%, 21.74%, 3.19% and 6.52%, respectively. Co-infections were found in 4.20% of all the samples being tested. Among 15 HRV positive cases, serotypes G1, G3 and P[4] were the most predominant strains. CONCLUSION: Children who were under 2 years of age were the majority among patients infected by diarrhea viruses while HuCV was recognized as the main pathogen responsible for the viral diarrhea cases in Ningxia, 2011.

Complete Genome Sequence of Acinetobacter baumannii ZW85-1.

Acinetobacter baumannii is an aerobic, nonmotile Gram-negative bacterium that causes nosocomial infections worldwide. Here, we report the complete genome sequence of Acinetobacter baumannii strain ZW85-1 and its two plasmids. One of the plasmids carries genes for NDM-1, which can hydrolyze a wide range of antibiotics.

Prevalence of Yersinia enterocolitica in pigs slaughtered in Chinese abattoirs.

The distribution of Yersinia enterocolitica in slaughtered pigs in China was studied. A total of 8,773 samples were collected and examined from different pig abattoirs in 11 provinces from 2009 to 2011. Of these, 4,495 were oral-pharyngeal swab (tonsils) samples from pigs, 1,239 were from intestinal contents, and 3,039 were feces samples from abattoirs or local pigpens. The data showed that 1,132 strains were obtained, from which the isolation rate for Yersinia enterocolitica was 19.53% (878/4,495) from the tonsil samples, 7.51% (93/1,239) from intestinal contents, and 5.30% (161/3,039) from feces. Of the 850 pathogenic Yersinia strains, except for three of bioserotype 2/O:9 and three of bioserotype 4/O:3, most (844/850) were of bioserotype 3/O:3. Interestingly, pathogenic Y. enterocolitica accounted for the majority of the isolated strains from most provinces (85.17% to 100%), whereas from Heilongjiang, 96.52% (111/115) were classified as nonpathogenic biotype 1A with various serotypes, and only 3.48% of the strains (4/115) were pathogenic 3/O:3. All of the pathogenic strains were analyzed using pulsed-field gel electrophoresis (PFGE), and 49 patterns were obtained for the O:3 pathogenic strains; most of them were K6GN11C30021 (53.13%: 450/847) and K6GN11C30012 (21.37%: 181/847). Several strains from diarrhea patient samples revealed PFGE patterns identical to that from samples of local pigs, suggesting a possible link between porcine isolates and human infection. The results above suggested that Yersinia enterocolitica in slaughtered pigs from Chinese abattoirs was characterized by region-specific PFGE patterns and confirmed that strains isolated from pigs are closely related to those from human infections.

[Analysis of the variation and changes of Yersinia enterocolitica in Ningxia area from 1984 to 2011].

OBJECTIVE: To analyze the genetic evolution and bacterial type changes of Yersinia enterocolitica in the Ningxia area between year 1984 and 2011. METHODS: A total of 296 strains of Yersinia enterocolitica was collected from diarrhea patients, pig, rodents, sheep and dogs between year 1984 and 2011. The serotype, biotype, ail, ystA, ystB, yadA, virF and other toxic genes were detected. The PFGE subtypes of serotype O:3 and O:9 strains and the cluster features were analyzed. RESULTS: Out of 296 Yersinia enterocolitica strains, pig was the main host, accounting for 65.20% (193/296), followed by rodents, accounting for 32.43% (96/296). Serotype and biotype had their own respective dominant types in different periods. During 1984 and 1985, 2 strains of serotype O:3 and 3 strains of serotype O:9 were isolated, all belonged to biotype 3. Because of lack of strains, there were no obvious dominant types found. Between 1997 and 1999, 177 strains of serotype O:9 Yersinia enterocolitica were isolated as the dominant strain; and there were 178 strains of biotype 2 Yersinia enterocolitica were found. During 2007 and 2011, 54 strains of serotype O:3 Yersinia enterocolitica were isolated as dominant strain; followed by 26 strains of serotype O:5. There were separately 44 and 59 strains of biotype 1A and biotype 3. The PCR test divided the 248 strains into 4 types, including pathogenic strains as type I (ail(+), ystA(+), ystB(-), yadA(+), virF(+)). The PFGE divided the serotype O:3 into 12 types, in which K6GN11C30021 and K6GN11C30012 were the dominant types, accounting for 63.64% (42/66). The serotype O:9 were divided into 14 types, in which K6GN11C90010, K6GN11C90008, K6GN11C30018 and K6GN11C90003 were the dominant types, accounting for 89.01% (162/182). CONCLUSION: The different serotypes of isolated strains in Ningxia district showed different dominant bacteria in different periods; while the biotypes also changed with serotypes. The Yersinia enterocolitica isolated from different years showed great variation.

[Characteristics of Yersinia enterocolitica genes isolated in Ningxia Hui autonomous region from 1997 to 2010].

OBJECTIVE: To investigate the distribution of virulent genes of Yersinia enterocolitica (Y. enterocolitica) in Ningxia Hui autonomous region and the characteristics of the molecular patterns of Y. enterocolitica. METHODS: 283 strains of Y. enterocolitica were isolated in Ningxia Hui autonomous region between year 1997 and 2010. The genes ail, ystA, ystB, yadA and virF were analyzed by PCR method; the chromosomal DNA of Y. enterocolitica was digested by restriction endonucleases NotI and processed by pulsed-field gel electrophoreses (PFGE); and then the cluster analysis were conducted by BioNumeric computer software towards the above results. RESULTS: Of all, 209 strains of serotypes O:3 and O:9 Y.enterocolitica showed positive virulence of genes ail, ystA, yadA and virF; 97.6% (204/209) of which, the ystB virulence were negative. The virulence of all genes in serotype O:8 and serum-unclassified strains were negative. 9 out of 11 strains of serotype O:5 Y. enterocolitica showed negative virulence of the above five genes. By PFGE, according to the NotI Macrorestriction Map on chromosomal DNA, the 29 strains of serotype O:3 Y. enterocolitica were divided into 12 PFGE patterns, 2 of which were dominant patterns which could be found in over 5 strains; and the 180 strains of serotype O:9 Y. enterocolitica were divided into 13 patterns, 4 of which were dominant patterns which existed in over 10 strains; which were isolated individually from pigs and house mouse, pigs and dogs as well as pigs and wild rabbits. CONCLUSION: Y.enterocolitica serotypes O:3 and O:9 were pathogenic in Ningxia, and serotype O:3 becomes predominant gradually. O:5, O:8 and serum-unclassified serotypes were non-pathogenic.

[Genetic characteristics of entervirus 71 isolated in Ningxia Hui Autonomous region in 2009].

OBJECTIVE: To analyze the genetic characteristics of EV71 strains isolated from HFMD cases in Ningxia Hui Autonomous Region in 2009. METHODS: In 2009, totally 385 specimens from 344 HFMD cases were collected from Ningxia. Enterovirus isolation was performed in RD cell line from all the specimens. EV71 isolates were identified by specific RT-PCR from the positive cultures, and sequences of complete EV71 VP1 encoding region were determined for farther analyses. RESULTS: Totally from 126 EV strains isolated in this study, 58 EV71 strains (46%) were identified. And complete VP1 sequences of 46 EV71 strains were determined, and genetic analyses were performed. It was showed that the nucleotide identity of 46 Ningxia strains with the representatives of A and B genotypes were 81.7%-82.8% and 83.1%-85.2%, and the amino acid identity were 93.9%-95.9% and 96. 2%-97.9% respectively. The nucleotide identity of NingXia EV71 isolates with representatives of subgenotype C1, C2, C3, C4a, C4b, and C5 were 88.3%-90.6% (97.9%-99.6%), 88.3%-90.1% (97.9%-99.3%), 87.8%-89.0% (97.6%-98.9%), 94.2%-98.9% (97.9%-100%), 91.8%-94.1% (98.6%-99.6%), and 86.7%-89.1% (97.9%-98.9%). Phylogenetic tree analysis revealed that 46 stains were clustered with reference stains of subgenotype C4 and the Ningxia EV71 isolates were belonged to subgenotype C4a. CONCLUSION: EV71 of subgenotype C4a had spread widely in Ningxia in 2009, which was absolutely predominant type in Ningxia in 2009 and also as the predominant type in China mainland since 2005.

[Genetic characterization of enterovirus 71 stains isolated in Ningxia province in 2008].

OBJECTIVE: To study the genetic characterization of enterovirus 71 (EV71) strains isolated from specimens of patients with hand-foot-mouth disease (HFMD) in Ningxia province in 2008. METHODS: All the stool, throat swab and vesicle samples that collected from patients with HFMD were cultured. The positive isolates were identified by reverse transcriptase PCR (RT-PCR) with specific primers of EV71. Complete VP1 gene sequences (891 nucleotides) of 29 strains (part of 93 EV71 strains) were determined and compared with A, B and C genotype reference EV71 strains while EV71 China isolates by homogeneity and phylogenetic tree analyses. RESULTS: 215 strains of EV were isolated from 439 specimens. Results from RT-PCR indicated that 93 strains belong to EV71. Phylogenetic tree analysis revealed that the selected 29 stains were clustered with reference strains of C4 subgenotype. The nucleotide identity with C4 reference strains was 91.7%-99.4%. The amino acid homogeneity was 96.6%-100.0%. CONCLUSION: The recently identified EV71 strains in Ningxia province belonged to subgenotype C4 which resembled to most of the isolates in China.