Progress in research of 2019-nCoV Omicron variant / 中华流行病学杂志

2019-nCoV Omicron (B.1.1.529) variant, which has brought new challenges to the prevention and control of COVID-19 pandemic, has the characteristics of stronger transmissibility and more rapid transmission and more significant immune evasion. It took only two months to become a predominant strain worldwide after its identification in South Africa in November 2021. Local epidemics caused by Omicron variant have been reported in several provinces in China. However, the epidemiological characteristics of highly mutated Omicron variant remain unclear. This article summarizes the progress in the research of functional mutations, transmissibility, virulence, immune evasion and cross-reactive immune responses of Omicron variant, to provide references for the effective prevention and control of COVID-19 pandemic caused by Omicron variant.

Epidemiological and etiological characteristics of Vibrio parahaemolyticus strains causing foodborne disease outbreaks in Guangdong Province from 2017 to 2020 / 中华预防医学杂志

Objective: To study the epidemiological and pathogenic characteristics of Vibrio parahaemolyticus isolated from outbreaks cases in Guangdong Province, 2017-2020. Methods: Epidemiological characteristics of 87 outbreak events caused by Vibrio parahaemolyticus were analyzed. Strains were serotyped, and then analyzed by pulsed-field gel electrophoresis (PFGE). Results: The food-borne disease outbreak caused by Vibrio parahaemolyticus was found in 16 cities. 44.8% (39/87) and 37.9% (33/87) of the outbreaks occurred in hotels, restaurants and school canteens, respectively. Improper food processing and storage (40.2%, 35/87) and cross contamination caused by indiscriminate raw and cooked food (25.3%, 22/87) were the main causes of food-borne disease outbreaks of Vibrio parahaemolyticus. The main serotypes of patient derived strains were O3:K6 (87.5%) and O4:KUT (22.5%). The similarity value between O3:K6 type isolates was 65.5%-100.0%, and the PFGE pattern similarity value of O4:KUT type isolates was 66.5%-100.0%. Conclusion: Outbreaks caused by Vibrio parahaemolyticus are widely distributed in Guangdong province. It is necessary to strengthen the publicity and education on the correct handling of food in hotels, restaurants, schools, and unit canteens. O3:K6 and O4:KUT serotypes are the main serotypes of the outbreak. There is genetic diversity among the epidemic strains.

Identification and analysis of 2 Corynebacterium diphtheria strains in Guangdong Province / 中华预防医学杂志

Objective: To identify and analyze two strains of C. diphtheriae in Guangdong Province by combining whole genome sequencing with traditional detection methods. Methods: The C. diphtheriae was isolated from Guangzhou in 2010 and Zhuhai in 2020 respectively. Isolates were identified by API Coryne strips and MALDI-TOF-MS. Genomic DNA was sequenced by using Illumina. The assembly was performed for each strain using CLC software. J Species WS online tool was used for average nucleoside homology identification, then narKGHIJ and tox gene were detected by NCBI online analysis tool BLSATN. MEGA-X was used to build a wgSNP phylogenetic tree. Results: GD-Guangzhou-2010 was Belfanti and GD-Zuhai-2020 was Gravis. ANIb between GD-Guangzhou-2010 and C. belfantii was 99.61%. ANI between GD-Zhuhai-2020 and C. diphtheriae was 97.64%. BLASTN results showed that the nitrate reduction gene narKGHIJ and tox gene of GD-Guangzhou-2010 was negative, while GD-Zhuhai-2020 nitrate reduction gene narKGHIJ was positive. There were two obvious clades in wgSNP phylogenetic tree. The first clades included all Mitis and Gravis types strains as well as GD-Zhuhai-2020. The second clades contained all isolates of C.belfantii, C.diphtheriae subsp. lausannense and GD-guangzhou-2010. Conclusion: Two non-toxic C. diphtheriae strains are successfully isolated and identified. The phylogenetic tree suggests that GD-Guangzhou-2010 and GD-Zhuhai-2020 are located in two different evolutionary branches.

Monitoring of diarrheagenic Escherichia coli infections in patients in Guangdong Province during 2013 to 2016 / 中华微生物学和免疫学杂志

Objective To investigate the infection status, serotype distribution, drug sensitivity and molecular characteristics of diarrheagenic Escherichia coli (DEC) in patients with diarrhea in Guangdong Province. Methods Fecal samples were collected, cultured and isolated by traditional methods. Suspected Escherichia coli isolates were confirmed by multiplex PCR used for detecting specific virulence genes and bio-chemical methods. Positive strains were serotyped, characterized for drug sensitivity and analyzed by pulsed-field gel electrophoresis ( PFGE). Results The total positive rate of DEC in patients with diarrhea was 6.26%. The positive rates of enteropathogenic Escherichia coli (EPEC), enterotoxigenic Escherichia coli (ETEC), enterohemorrhagic Escherichia coli (EHEC), enteroadherent Escherichia coli (EAEC) and en-teroinvasive Escherichia coli (EIEC) were 2. 47% , 1. 54% , 1. 32% , 0. 62% and 0. 09% , respectively, with infections primarily in children aged 0-<7 years. The total seropositive rate was 52. 54% , with EHEC accounting for 15. 00% . DEC showed high sensitivity to imipenem, ciprofloxacin, ceftazidime and cefo-taxime. The multidrug resistance rate of DEC was 58. 45% , with EPEC being the most serious for multidrug resistance. PFGE results showed that ETEC, EHEC, EPEC and EAEC had a high degree of polymorphism. Conclusion EPEC is the predominant type of DEC circulating in Guangdong Province. Third-generation cephalosporins are the first drugs of choice for treating infections in children. Ciprofloxacin can be used to treat adults. The problem of multiple drug resistance of DEC is severe and efforts to monitor DEC infections and drug resistance should be strengthened.

Analysis of the brucella pathogen and its molecular genotype in Guangdong province / 中国地方病学杂志

Objective To analysis the etiology and molecular classification of brucella strains isolated in Guangdong province in 2010.Methods The strains of 19 brucella were verified and identified by some methods including traditional biology phenotype confirmation,PCR amplification and pulsed field gel electrophoresis (PFGE).Results On phenotype level,4 strains were brucella melitensis biovar 1,2 strains were brucella suis biovar 3,and the rest were brucella melitensis biovar 3,which were specific B genes positive strains,and the PFGE typing similar values ranging from 67.9％ to 100％.In addition to the four strains from Zhuhai for the outbreak,the homology was 100％,and the rest were sporadic cases.Conclusions Brucella cases,in Guangdong province,are highly sporadic and dispersed outbreaks.Compared with a few years ago,it shows species diversification,and brucella melitensis biovar 3 is still the dominant serotype.PFGE can be used to distinguish the three species of brucella,but it can't effectively distinguish the allotypes.

Surveillance and analysis on the pathogenic features of Salmonella in Guangdong province in 2010 / 中华预防医学杂志

<p><b>OBJECTIVE</b>In order to better understand the nature of Salmonella infection in diarrheal patients in Guangdong province, the study analyzed the serum types, antibiotic resistance and molecular determinants of the isolated Salmonella strains.</p><p><b>METHODS</b>In year 2010, 8405 diarrhea patients from 16 surveillant hospital in Guangzhou, Zhongshan, Dongguan, Zhuhai, Maoming, Yangjiang and Jiangmen cities in Guangdong province, were recruited in the study. A total of 8405 fecal specimen were collected and subjected to Salmonella isolation and culture. The isolated Salmonella strains were further analyzed via serotyping, antimicrobial susceptibility testing, and PFGE. The χ(2) test was applied to compare the differences between the isolated Salmonella strains in different seasons and districts. BioNumerics software was used to analyze the PFGE results in order to determine the correlation between different Salmonella strains.</p><p><b>RESULTS</b>The positive rate of the surveillant Salmonella in Guangdong province was 3.58% (301/8405) in 2010; with the gender ratio at 1.34:1 (166/124). Salmonella infection was found in all age groups, and most in infants, accounting for 57.48% (173/301). The isolated rates of Salmonella were separately 3.48% (61/1751), 4.97% (134/2695), 3.08% (73/2370) and 2.08% (33/1589) in the four seasons; and the difference was statistically significant (χ(2) = 27.29, P < 0.01). The isolated rates of Salmonella in different regions were as follows: Zhuhai 15.43% (25/162), Maoming 7.53% (18/239), Dongguan 6.51% (39/599), Yangjiang 3.64% (14/385), Zhongshan 3.03% (70/2309), Guangzhou 2.90% (126/4349) and Jiangmen 2.49% (9/362). The difference between regions was statistically significant (χ(2) = 100.75, P < 0.01). Except one strain of the isolated Salmonella cannot be serotyped, the other 300 strains were divided into 42 serotypes, of which Salmonella typhimurium and Salmonella enteritidis were dominant, account for 45.18% (136/301) and 10.96% (33/301) respectively. Although over 85% of Salmonella were sensitive to cephalosporin, ACSSuT resistance patterns (defined as resistance to at least ampicillin, chloramphenicol, streptomycin, sulfamethoxazole and tetracycline) reached 34.88% (105/301), the highest resistant rate was found in serotype Salmonella typhimurium, as high as 65.44% (89/136). 136 strains of Salmonella typhimurium were divided into 51 PFGE types, showed great genetic diversity. 33 strains of Salmonella enteritidis were divided into 18 PFGE types. The strains with same PFGE pattern may have different drug-resistant patterns, and vice versa.</p><p><b>CONCLUSION</b>Salmonella typhimurium and Salmonella enteritidis were the dominant serotypes causing infectious diarrhea in Guangdong province. Cephalosporin was the primary choice in clinical medicine. However, Salmonella typhimurium was resistant to drug most seriously in Guangdong province. There was no significant correlation between Salmonella resistance patterns and PFGE type.</p>

Automated ribotyping of Salmonella and Staphylococcus aureus in food poisoning of Guangdong province / 中华流行病学杂志

Objective To understand the genetic polymorphism of Salmonella and Staphylococcus aureus in Guangdong province, as well as to explore methods for identifying and tracing the source of these two foodbome pathogens. Methods Using the automated ribotyping system, two foodbome pathogens were tested with either EcoR Ⅰ or Pvu Ⅱ restriction enzymes. BioNumerics software was then applied for image analysis, database establishment and other corresponding analysis. Results Digestion of 32 Salmonella isolates with Pvu Ⅱ yielded 19 different ribotypes,and digestion of 14 Salmonella isolates with EcoR Ⅰ yielded 2 different ribotypes. Staphyloccus aureus isolates showed greater genetic diversity, whereas EcoR Ⅰ digestion of 49 different isolates yielded 31 different ribotypes. Conclusion Unique Salmonella and Staphylococcus aureus isolates could be identified through ribotyping. Although Salmonella serotyping and ribotyping were not strongly correlated, the combination of both restriction enzymes could be used to more effectively identify the genetic relationship among different strains as well as the source of food poisoning. Thus, not only could the genetic relationships amongst the different strains be inferred through ribotyping skills, the source of food poisoning and mode of transmission could also be determined under the use of this method.

Surveillance on Salmonella infection in Guangdong province, 2008-2009 / 中华流行病学杂志

Objective To understand the infection of Salmonella (S.) in patients with diarrhea and outbreaks caused by Salmonella to identify the serotypes, resistance to antibiotics and PFGE types of the strains from the surveillance program in Guangdong province. Methods S. strains from patients with diarrhea were detected, and all the positive strains collected in routine and outbreak surveillance programs, were tested by serum agglutination, antibiotic susceptibility and PFGE.Results 71 S. strains were isolated from 1922 stool samples in 2008, with positive rate as 3.7%.85 S. strains were isolated from 2110 stool samples in 2009, with positive rate as 4.0%. All the 156 strains were divided into 37 serotypes, with S. serotype typhimurium and enteritidis as the most common serotypes. 10 incidents of food poisoning were detected, of which 4 were caused by enteritidis and 3 by typhimurium. A suspected outbreak by enteritidis was discovered and under epidemiological investigation. The findings indicated that 2 of the 4 patients from this outbreak were infected with identical enteritidis isolates. 80% of the 229 isolates were found susceptible to cephalosporins and quinoione and 59.3% of them were muitiresistant to the antibiotics. Conclusion S. enteritidis and S. typhimurium were the most common serotypes that caused infectious diarrhoea and food poisoning in Guangdong province.

Surveillance and pathogenic analysis on non-typhoidal Salmonella in Guangdong province, 2007 / 中华流行病学杂志

Objective To understand non-typhoid Salmonella in diarrhea patients from Guangdong province in order to timely discover the outbreaks caused by them as well as to grasp the serotypes, antibiotic resistance and pulse-field gel electrophoresis (PFGE) types of those strains isolated from this surveillance program. Methods Salmonella strains from diarrhea patients were detected and all the positive strains were tested by serum agglutination, antibiotic susceptibility and PFGE. Results 71 nontyphoid Salmonella strains were isolated from 1128 stoop samples, with a positive rate of 6.29 %. All the strains were divided into 29 serotypes, with Salmonella serotype enteritidis and typhimurium showing the most common serotypes. Most of the strains were sensitive to cephalosporins and quinolones. The antibiotic resistance rates of S. typhimurium were higher than S. enteritidis and S. stanley. Other than S. enteritidis, all the serotype strains did not have the same type of PFGE. 17 S. enteritidis strains digested by Xba Ⅰ were divided to 8 PFGE types while the PFGE 4 type appeared the most common one. 12 S. enteritidis strains were typed again by Sfi Ⅰ and Not Ⅰ , and there were still 3 groups of strains showing the same PFGE pattern. Conclusion Most of the infection caused by non-typhoidal Salmonella was sporadic in Guangdong province in 2007. Cephalosporins and quinolones seemed the best in curing the infection of non-typhoidal Salmonella at the clinics.

The etiologic characteristics of Vibrio cholerae in Guangdong province in 2007 / 中华流行病学杂志

Objective To analyze the etiologic characteristics of Vibrio cholerae in Guangdong province in 2007.Genetic relationship was observed including among predominated biotype isolates from different areas within the province and among same biotypes isolates from cholera cases and regular surveillance.Methods Isolates from cholera cases and through environmental surveillance were typed by sero-and phage-typings.Similarity of molecular fingerprinting was analyzed through comparing the pulsed field gel electrophoresis(PFGE)pattern of predominated biotype isolates,and those of the same biotype isolates from cholera cases and environment surveillance,respectively.In addition,genetic relationship was determined by clustering analysis,using bionumerics software.Results In total,31 isolates from cholera cases were collected and subtyped for 3 serogroups.V.cholerae O1 El Tor Inaba phage 1d was the predominant biotype which causing most of the cases in Guangdong province in 2007.Data from cluster analysis showed that the similarity among Inaba phage 1d strains from different areas were from 94.5% to 100%.However.16 isolates were collected from environment surveillance programs and the predominated biotype could not be found.Additionally,the biotype distribution of cases isolates was not consistent with those isolates through surveillance.High phylogenetic diversity was observed for the same biotypes isolates from cases and surveillance samples.Conclusion Our data showed that V.cholerae O1 El Tor Inaba phage 1d was the predominated biotype with multi-clone coexisting and circulating in Guangdong province in 2007.It also appeared to be the characteristics of cholera in the non-epidemic period,suggesting that it was necessary to enhance the alert surveillance programs for cholera epidemic based on the molecular typing techniques.