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Article(id=1151881495099617730, tenantId=1146029695717560320, journalId=1149652044408987649, issueId=1151881493552394994, articleNumber=null, orderNo=null, doi=10.19812/j.cnki.jfsq11-5956/ts.20241204001, pmid=null, cstr=null, oa=null, hot=null, price=null, onlineType=0, articleFormat=0, articleType=null, articleTypeStr=null, receivedDate=1733241600000, receivedDateStr=2024-12-04, revisedDate=null, revisedDateStr=null, acceptedDate=null, acceptedDateStr=null, onlineDate=1752559549355, onlineDateStr=2025-07-15, pubDate=1748102400000, pubDateStr=2025-05-25, doiRegisterDate=null, doiRegisterDateStr=null, onlineIssueDate=1752559549355, onlineIssueDateStr=2025-07-15, onlineJustAcceptDate=null, onlineJustAcceptDateStr=null, onlineFirstDate=null, onlineFirstDateStr=null, sourceXml=null, magXml=null, createTime=1752559549355, creator=13701087609, updateTime=1752559549355, updator=13701087609, issue=Issue{id=1151881493552394994, tenantId=1146029695717560320, journalId=1149652044408987649, year='2025', volume='16', issue='10', pageStart='1', pageEnd='324', issueExtLink='null', onlineDate='null', pubDate='null', beforeIssueId=null, nextIssueId=null, price=null, status=1, issueComplete=1, articleOrder=1, issueType=-1, specialIssue=0, createTime=1752559548986, creator=13701087609, updateTime=1756202008453, updator=13701087609, preIssue=null, nextIssue=null, ext={EN=IssueExt(id=1167159075906265916, tenantId=1146029695717560320, journalId=1149652044408987649, issueId=1151881493552394994, language=EN, specialIssueTitle=, coverIllustrator=null, specialIssueEditor=, specialIssueAbout=), CN=IssueExt(id=1167159075906265917, tenantId=1146029695717560320, journalId=1149652044408987649, issueId=1151881493552394994, language=CN, specialIssueTitle=, coverIllustrator=null, specialIssueEditor=, specialIssueAbout=)}, issueFiles=null}, startPage=97, endPage=104, ext={EN=ArticleExt(id=1151923900624548689, articleId=1151881495099617730, tenantId=1146029695717560320, journalId=1149652044408987649, language=EN, title=Analysis of integrative and conjugative elements composition in contaminated microorganisms of cooked poultry products by metagenomic sequencing, columnId=1151923892655846010, journalTitle=Journal of Food Safety & Quality, columnName=Special Topic: Food Safety Risk Assessment and Risk Monitoring, runingTitle=null, highlight=null, articleAbstract=

Objective To investigate the distribution, sources, and gene cassette contents of integrative and conjugative elements in microorganisms contaminating cooked poultry meat products. Methods Cooked duck meat was purchased, and DNA extraction, sequencing, assembly, binning, and metagenome-assembled genome (MAG) acquisition were performed. These MAGs were then compared with an integron database. Results A total of 110 integrative and conjugative elements belonging to 65 distinct types were detected in the contaminating microbiota of cooked duck meat, primarily originating from 31 host microorganisms, including Mesorhizobium, Pseudomonas aeruginosa, and Klebsiella pneumoniae. Among these integrative and conjugative elements, there were 9 kinds of transposases, 1 kinds of virulence factor gene, and 19 resistance-related genes, including 10 tetracycline resistance genes. Additionally, 11 defense genes, all of which were phage-defense genes, were identified. Conclusion The discovery of various integrative and conjugative elements, virulence factors, resistance-related genes, and defense genes reveals the complex genetic diversity of microorganisms in food. This provides important clues for studying horizontal gene transfer and has significant implications for assessing food safety and preventing and controlling foodborne pathogens. The effective application of metagenomic technology in integron research also demonstrates its potential in the fields of food safety and public health.

, correspAuthors=Han GAO, authorNote=null, correspAuthorsNote=null, copyrightStatement=null, copyrightOwner=null, extLink=null, articleAbsUrl=null, sourceXml=null, magXml=null, pdfUrl=null, pdf=null, pdfFileSize=null, pdfExtLink=null, richHtmlUrl=null, mobilePdfUrl=null, reviewReport=null, pdfFirstPage=null, abstractGraph=null, abstractGraphContent=null, abstractVideo=null, citation=null, cebUrl=null, magXmlContent=null, mapNumber=null, authorCompany=null, fund=null, authors=null, authorsList=Sheng SONG, Kun-Peng GUO, Lu-Miao ZHANG, Qing-Wen LUO, Fang WANG, Han GAO), CN=ArticleExt(id=1151923900943315800, articleId=1151881495099617730, tenantId=1146029695717560320, journalId=1149652044408987649, language=CN, title=宏基因组测序分析熟制禽肉制品污染微生物中整合子组成, columnId=1151923892995109553, journalTitle=食品安全质量检测学报, columnName=专题：食品安全风险评估与风险监测, runingTitle=null, highlight=null, articleAbstract=

目的 研究熟制禽肉制品污染微生物中整合子的分布、来源及其携带的基因盒内容等相关情况。方法 采购熟制鸭肉, 对样品进行DNA提取, 测序、混合拼接、分箱, 获取宏基因组组装基因组, 整合子数据库比对。结果 熟制鸭肉污染微生物中检测到65种整合子, 共计110个, 主要来源于31种宿主微生物, 包括中生根瘤菌属、铜绿假单胞菌与肺炎克雷伯氏菌等; 整合子中共有9种转座酶, 1种毒力因子基因, 19个抗性相关基因, 其中四环素抗性基因10个, 防御基因11个, 均为防御噬菌体的基因。结论 多种整合子及毒力因子、抗性相关和防御基因的发现, 揭示了食品中微生物遗传多样性的复杂程度, 为研究基因的水平转移提供了重要线索, 对于评估食品安全性、预防和控制食源性病原体具有重要意义。

, correspAuthors=高晗, authorNote=null, correspAuthorsNote=
* 通信作者: 高晗(1982—), 男, 硕士, 高级工程师, 主要研究方向为食品质量安全研究与风险评估。E-mail:
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宋晟(1979—), 男, 硕士, 高级工程师, 主要研究方向为食品安全与食品微生物。E-mail:

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宋晟(1979—), 男, 硕士, 高级工程师, 主要研究方向为食品安全与食品微生物。E-mail:

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宋晟(1979—), 男, 硕士, 高级工程师, 主要研究方向为食品安全与食品微生物。E-mail:

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Analysis of molecular subtyping, drug sensitivity and virulence factors of 45 strains of Salmonella by whole genome sequencing[J]. Journal of Food Safety & Quality, 2024, 15(20): 79-88., articleTitle=Analysis of molecular subtyping, drug sensitivity and virulence factors of 45 strains of Salmonella by whole genome sequencing, refAbstract=null)], funds=[Fund(id=1167158455958774435, tenantId=1146029695717560320, journalId=1149652044408987649, articleId=1151881495099617730, awardId=2022JJ90028, language=CN, fundingSource=湖南省自然科学基金项目(2022JJ90028), fundOrder=null, country=null)], companyList=[AuthorCompany(id=1167158450778808857, tenantId=1146029695717560320, journalId=1149652044408987649, articleId=1151881495099617730, xref=null, ext=[AuthorCompanyExt(id=1167158450783003162, tenantId=1146029695717560320, journalId=1149652044408987649, articleId=1151881495099617730, companyId=1167158450778808857, language=EN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=1. Hunan Povincial Key Laboratory of Food Safety Monitoring and Early Warning, Changsha 410000, China), AuthorCompanyExt(id=1167158450808168987, tenantId=1146029695717560320, journalId=1149652044408987649, articleId=1151881495099617730, companyId=1167158450778808857, language=CN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=1.食品安全监测与预警湖南省重点实验室, 长沙 410000)]), AuthorCompany(id=1167158450933998108, tenantId=1146029695717560320, journalId=1149652044408987649, articleId=1151881495099617730, xref=null, ext=[AuthorCompanyExt(id=1167158450954969629, tenantId=1146029695717560320, journalId=1149652044408987649, articleId=1151881495099617730, companyId=1167158450933998108, language=EN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=2. Hunan Povincial Institute of Product and Goods Quality Inspection, Changsha 410000, China), AuthorCompanyExt(id=1167158450992718367, tenantId=1146029695717560320, journalId=1149652044408987649, articleId=1151881495099617730, companyId=1167158450933998108, language=CN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=2.湖南省产商品质量检验研究院, 长沙 410000)])], figs=[ArticleFig(id=1167158454515933829, tenantId=1146029695717560320, journalId=1149652044408987649, articleId=1151881495099617730, language=EN, label=Table 1, caption=

Statistical table of ICEs in samples

, figureFileSmall=null, figureFileBig=null, tableContent=
序号 ICE编号 ICE名称 大小/kb 宿主微生物 数量 占比/%
1 36 ICEVflInd1 114.20 河流弧菌Ind1 1 0.91
2 52 ICEPaeLESB58-1 111.10 铜绿假单胞菌LESB58 1 0.91
3 76 ICESde3396 63.70 乳酸乳球菌乳亚种NS3396 1 0.91
4 133 ICEMloMAF-1 61.00 百脉根中生根瘤菌MAFF303099 4 3.64
5 174 PAGI-2 105.00 铜绿假单胞菌C 1 0.91
6 195 ICE(Tn4371)6036 59.80 西瓜食酸菌AAC00-1 1 0.91
7 198 ICE(Tn4371)6039 53.50 食酸菌属JS42 1 0.91
8 200 ICE(Tn4371)6041 48.50 铜绿假单胞菌2192 6 5.45
9 219 ICE-GI1 255.50 彼得里氏鲍特氏菌DSM 12804 1 0.91
10 338 CMGI-3 97.00 耐重金属贪铜菌CH34 1 0.91
11 438 phn Island 240.80 代尔夫特菌属Cs1-4 1 0.91
12 827 ICESpy009 55.30 酿脓链球菌MB56Spyo009 1 0.91
13 941 CTnPi4 58.60 中间普雷沃氏菌17 1 0.91
14 1010 ICEPae690 86.20 铜绿假单胞菌FFUP_PS_690 1 0.91
15 1045 ICEValHN437 94.30 解藻酸弧菌HN437 2 1.82
16 1081 Pac_ICE1_cn 102.60 丁香假单胞菌猕猴桃科M7或CH2010-6 2 1.82
17 1097 ICEMcSym(1284)-α 477.10 鹰嘴豆中生根瘤菌WSM1284 2 1.82
18 1121 ICEKpn2_G_12-1 56.14 肺炎克雷伯氏菌2_G_12 1 0.91
19 1157 ICEKpnA_0125-1 58.05 肺炎克雷伯氏菌A_0125 5 4.55
20 1179 ICEKpnB12-AN-2 238.17 肺炎克雷伯氏菌B12(AN) 1 0.91
21 1253 ICEKpnINF249-2 210.25 肺炎克雷伯氏菌INF249 5 4.55
22 1378 ICEKpnJF999-1 80.22 肺炎克雷伯氏菌亚种.肺炎JF999 1 0.91
23 1459 ICE_FpA2-165_tNAleu 34.40 普氏栖粪杆菌A2-165菌株JCM 31915 1 0.91
24 1471 ICE_LspYL32_lysS 99.30 乳杆菌YL32 1 0.91
25 1563 ICE_SsuNSUI002_plL_1 71.60 猪链球菌NSUI002株 1 0.91
26 1576 ICE-2 73.20 多噬伯克霍尔德氏菌ATCC BAA-247 1 0.91
27 1585 ICEAac2 27.70 伴放线菌团聚杆菌VT1169 1 0.91
28 1587 ICE-ABAQ 71.80 丁香假单胞菌ES4326-D 1 0.91
29 1588 ICEAcap1 66.70 荚膜酸杆菌ATCC 51196 1 0.91
30 1629 ICE-DQ 83.60 丁香假单胞菌ES4326-D 1 0.91
31 1646 ICEEaI(4)_CSID3000516074 97.20 按蚊伊丽莎白金菌CSID3000516074 3 2.73
32 1651 ICEEaII(1)_0422 63.80 按蚊伊丽莎白金菌0422 1 0.91
33 1661 ICEEaII(7)_F3543 104.60 按蚊伊丽莎白金菌F3543 1 0.91
34 1743 ICEP33 211.20 铜绿假单胞菌P33 2 1.82
35 1763 ICEPgs6Chn1 116.00 鸽变形菌T60 1 0.91
36 1819 ICEPsy15 51.20 丁香假单胞菌CFBP6109 2 1.82
37 1844 ICEPvuChnBC22 148.80 普通变形菌BC22 1 0.91
38 1869 ICESpsH35-1 69.80 副猪链球菌H35 1 0.91
39 1870 ICESpsH35-2 62.30 副猪链球菌H35 1 0.91
40 1871 ICESpsSUT-286-1 123.90 副猪链球菌SUT-286 5 4.55
41 1872 ICESpsSUT-286-2 51.40 副猪链球菌SUT-286 9 8.18
42 1881 ICESsu1112S 74.40 猪链球菌1112S株 1 0.91
43 1974 ICEXfa1_9a5c 88.20 苛养木杆菌9a5c 1 0.91
44 2010 Tn6783_201330 72.00 铜绿假单胞菌201330 1 0.91
45 2011 Tn6783_1305E 72.00 铜绿假单胞菌1305E 1 0.91
46 2049 ICEMaB5P-1 129.80 澳大利亚中生根瘤菌B5P 2 1.82
47 2052 ICEMcSymWSM1497-α 443.50 鹰嘴豆中生根瘤菌WSM1497 2 1.82
48 2062 ICEMsp.SymAA22-α 766.80 中生根瘤菌属AA22 1 0.91
49 2070 ICEMsp.M1D 199.40 中生根瘤菌属M1D.F.Ca.ET.043.01.1.1 2 1.82
50 2071 ICEMsp.SymM1D-1 332.10 中生根瘤菌属M1D.F.Ca.ET.043.01.1.1 1 0.91
51 2073 ICEMsp.SymM1E-α 563.10 中生根瘤菌属M1E.F.Ca.ET.045.02.1.1 1 0.91
52 2076 ICEMsp.M2A.F.02 222.70 中生根瘤菌属M2A.F.Ca.ET.043.02.1.1 2 1.82
53 2080 ICEMsp.M2A.F.046 155.50 中生根瘤菌属M2A.F.Ca.ET.046.03.2.1 1 0.91
54 2083 ICEMsp.SymM3A 396.80 中生根瘤菌属M3A.F.Ca.ET.080.04.2.1 1 0.91
55 2084 ICEMsp.SymM4B 529.70 中生根瘤菌属M4B.F.Ca.ET.058.02.1.1 2 1.82
56 2086 ICEMsp.M7D 336.10 中生根瘤菌属M7D.美国联邦法规005.01.1.1 1 0.91
57 2088 ICEMsp.M8A-1 102.00 中生根瘤菌属M8A.F.Ca.ET.057.01.1.1 1 0.91
58 2089 ICEMsp.M8A-2 197.00 中生根瘤菌属M8A.F.Ca.ET.057.01.1.1 2 1.82
59 2094 ICEMlNZP2042 65.90 中生根瘤菌属NZP2042 1 0.91
60 2098 ICEMsp.NZP2077 508.30 中生根瘤菌属NZP2077NS 3 2.73
61 2100 ICEMsp.SymNZP2298 467.10 中生根瘤菌属NZP2298 1 0.91
62 2103 ICEMsp.SymSEMIA3007 480.90 中生根瘤菌属SEMIA 3007 2 1.82
63 2104 ICEMlSymTONO 508.60 中生根瘤菌属TONO 2 1.82
64 2105 ICEMlTONO 241.60 中生根瘤菌属TONO 1 0.91
65 2111 ICEMsNIBBAC000500504-3 95.80 土中慢生根瘤菌NIBBAC000500504 1 0.91
), ArticleFig(id=1167158454624985735, tenantId=1146029695717560320, journalId=1149652044408987649, articleId=1151881495099617730, language=CN, label=表1, caption=

样品中ICEs统计表

, figureFileSmall=null, figureFileBig=null, tableContent=
序号 ICE编号 ICE名称 大小/kb 宿主微生物 数量 占比/%
1 36 ICEVflInd1 114.20 河流弧菌Ind1 1 0.91
2 52 ICEPaeLESB58-1 111.10 铜绿假单胞菌LESB58 1 0.91
3 76 ICESde3396 63.70 乳酸乳球菌乳亚种NS3396 1 0.91
4 133 ICEMloMAF-1 61.00 百脉根中生根瘤菌MAFF303099 4 3.64
5 174 PAGI-2 105.00 铜绿假单胞菌C 1 0.91
6 195 ICE(Tn4371)6036 59.80 西瓜食酸菌AAC00-1 1 0.91
7 198 ICE(Tn4371)6039 53.50 食酸菌属JS42 1 0.91
8 200 ICE(Tn4371)6041 48.50 铜绿假单胞菌2192 6 5.45
9 219 ICE-GI1 255.50 彼得里氏鲍特氏菌DSM 12804 1 0.91
10 338 CMGI-3 97.00 耐重金属贪铜菌CH34 1 0.91
11 438 phn Island 240.80 代尔夫特菌属Cs1-4 1 0.91
12 827 ICESpy009 55.30 酿脓链球菌MB56Spyo009 1 0.91
13 941 CTnPi4 58.60 中间普雷沃氏菌17 1 0.91
14 1010 ICEPae690 86.20 铜绿假单胞菌FFUP_PS_690 1 0.91
15 1045 ICEValHN437 94.30 解藻酸弧菌HN437 2 1.82
16 1081 Pac_ICE1_cn 102.60 丁香假单胞菌猕猴桃科M7或CH2010-6 2 1.82
17 1097 ICEMcSym(1284)-α 477.10 鹰嘴豆中生根瘤菌WSM1284 2 1.82
18 1121 ICEKpn2_G_12-1 56.14 肺炎克雷伯氏菌2_G_12 1 0.91
19 1157 ICEKpnA_0125-1 58.05 肺炎克雷伯氏菌A_0125 5 4.55
20 1179 ICEKpnB12-AN-2 238.17 肺炎克雷伯氏菌B12(AN) 1 0.91
21 1253 ICEKpnINF249-2 210.25 肺炎克雷伯氏菌INF249 5 4.55
22 1378 ICEKpnJF999-1 80.22 肺炎克雷伯氏菌亚种.肺炎JF999 1 0.91
23 1459 ICE_FpA2-165_tNAleu 34.40 普氏栖粪杆菌A2-165菌株JCM 31915 1 0.91
24 1471 ICE_LspYL32_lysS 99.30 乳杆菌YL32 1 0.91
25 1563 ICE_SsuNSUI002_plL_1 71.60 猪链球菌NSUI002株 1 0.91
26 1576 ICE-2 73.20 多噬伯克霍尔德氏菌ATCC BAA-247 1 0.91
27 1585 ICEAac2 27.70 伴放线菌团聚杆菌VT1169 1 0.91
28 1587 ICE-ABAQ 71.80 丁香假单胞菌ES4326-D 1 0.91
29 1588 ICEAcap1 66.70 荚膜酸杆菌ATCC 51196 1 0.91
30 1629 ICE-DQ 83.60 丁香假单胞菌ES4326-D 1 0.91
31 1646 ICEEaI(4)_CSID3000516074 97.20 按蚊伊丽莎白金菌CSID3000516074 3 2.73
32 1651 ICEEaII(1)_0422 63.80 按蚊伊丽莎白金菌0422 1 0.91
33 1661 ICEEaII(7)_F3543 104.60 按蚊伊丽莎白金菌F3543 1 0.91
34 1743 ICEP33 211.20 铜绿假单胞菌P33 2 1.82
35 1763 ICEPgs6Chn1 116.00 鸽变形菌T60 1 0.91
36 1819 ICEPsy15 51.20 丁香假单胞菌CFBP6109 2 1.82
37 1844 ICEPvuChnBC22 148.80 普通变形菌BC22 1 0.91
38 1869 ICESpsH35-1 69.80 副猪链球菌H35 1 0.91
39 1870 ICESpsH35-2 62.30 副猪链球菌H35 1 0.91
40 1871 ICESpsSUT-286-1 123.90 副猪链球菌SUT-286 5 4.55
41 1872 ICESpsSUT-286-2 51.40 副猪链球菌SUT-286 9 8.18
42 1881 ICESsu1112S 74.40 猪链球菌1112S株 1 0.91
43 1974 ICEXfa1_9a5c 88.20 苛养木杆菌9a5c 1 0.91
44 2010 Tn6783_201330 72.00 铜绿假单胞菌201330 1 0.91
45 2011 Tn6783_1305E 72.00 铜绿假单胞菌1305E 1 0.91
46 2049 ICEMaB5P-1 129.80 澳大利亚中生根瘤菌B5P 2 1.82
47 2052 ICEMcSymWSM1497-α 443.50 鹰嘴豆中生根瘤菌WSM1497 2 1.82
48 2062 ICEMsp.SymAA22-α 766.80 中生根瘤菌属AA22 1 0.91
49 2070 ICEMsp.M1D 199.40 中生根瘤菌属M1D.F.Ca.ET.043.01.1.1 2 1.82
50 2071 ICEMsp.SymM1D-1 332.10 中生根瘤菌属M1D.F.Ca.ET.043.01.1.1 1 0.91
51 2073 ICEMsp.SymM1E-α 563.10 中生根瘤菌属M1E.F.Ca.ET.045.02.1.1 1 0.91
52 2076 ICEMsp.M2A.F.02 222.70 中生根瘤菌属M2A.F.Ca.ET.043.02.1.1 2 1.82
53 2080 ICEMsp.M2A.F.046 155.50 中生根瘤菌属M2A.F.Ca.ET.046.03.2.1 1 0.91
54 2083 ICEMsp.SymM3A 396.80 中生根瘤菌属M3A.F.Ca.ET.080.04.2.1 1 0.91
55 2084 ICEMsp.SymM4B 529.70 中生根瘤菌属M4B.F.Ca.ET.058.02.1.1 2 1.82
56 2086 ICEMsp.M7D 336.10 中生根瘤菌属M7D.美国联邦法规005.01.1.1 1 0.91
57 2088 ICEMsp.M8A-1 102.00 中生根瘤菌属M8A.F.Ca.ET.057.01.1.1 1 0.91
58 2089 ICEMsp.M8A-2 197.00 中生根瘤菌属M8A.F.Ca.ET.057.01.1.1 2 1.82
59 2094 ICEMlNZP2042 65.90 中生根瘤菌属NZP2042 1 0.91
60 2098 ICEMsp.NZP2077 508.30 中生根瘤菌属NZP2077NS 3 2.73
61 2100 ICEMsp.SymNZP2298 467.10 中生根瘤菌属NZP2298 1 0.91
62 2103 ICEMsp.SymSEMIA3007 480.90 中生根瘤菌属SEMIA 3007 2 1.82
63 2104 ICEMlSymTONO 508.60 中生根瘤菌属TONO 2 1.82
64 2105 ICEMlTONO 241.60 中生根瘤菌属TONO 1 0.91
65 2111 ICEMsNIBBAC000500504-3 95.80 土中慢生根瘤菌NIBBAC000500504 1 0.91
), ArticleFig(id=1167158454801146506, tenantId=1146029695717560320, journalId=1149652044408987649, articleId=1151881495099617730, language=EN, label=Table 2, caption=

Statistics table of host micobial

, figureFileSmall=null, figureFileBig=null, tableContent=
序号 宿主微生物 数量 占比/%
1 中生根瘤菌属 17 26.15
2 铜绿假单胞菌 7 10.77
3 肺炎克雷伯氏菌 4 6.15
4 副猪链球菌 4 6.15
5 按蚊伊丽莎白金菌 3 4.62
6 丁香假单胞菌 3 4.62
7 鹰嘴豆中生根瘤菌 2 3.08
8 猪链球菌 2 3.08
9 澳大利亚中生根瘤菌 1 1.54
10 百脉根中生根瘤菌 1 1.54
11 伴放线菌团聚杆菌 1 1.54
12 彼得里氏鲍特氏菌 1 1.54
13 代尔夫特菌属 1 1.54
14 丁香假单胞菌猕猴桃科 1 1.54
15 多噬伯克霍尔德氏菌 1 1.54
16 肺炎克雷伯氏菌亚种.肺炎 1 1.54
17 鸽变形菌 1 1.54
18 河流弧菌 1 1.54
19 荚膜酸杆菌 1 1.54
20 解藻酸弧菌 1 1.54
21 苛养木杆菌 1 1.54
22 耐重金属贪铜菌 1 1.54
23 酿脓链球菌 1 1.54
24 普氏栖粪杆菌 1 1.54
25 普通变形菌 1 1.54
26 乳杆菌 1 1.54
27 乳酸乳球菌乳亚种 1 1.54
28 食酸菌属 1 1.54
29 土中慢生根瘤菌 1 1.54
30 西瓜食酸菌 1 1.54
31 中间普雷沃氏菌 1 1.54
), ArticleFig(id=1167158454935364237, tenantId=1146029695717560320, journalId=1149652044408987649, articleId=1151881495099617730, language=CN, label=表2, caption=

宿主微生物统计表

, figureFileSmall=null, figureFileBig=null, tableContent=
序号 宿主微生物 数量 占比/%
1 中生根瘤菌属 17 26.15
2 铜绿假单胞菌 7 10.77
3 肺炎克雷伯氏菌 4 6.15
4 副猪链球菌 4 6.15
5 按蚊伊丽莎白金菌 3 4.62
6 丁香假单胞菌 3 4.62
7 鹰嘴豆中生根瘤菌 2 3.08
8 猪链球菌 2 3.08
9 澳大利亚中生根瘤菌 1 1.54
10 百脉根中生根瘤菌 1 1.54
11 伴放线菌团聚杆菌 1 1.54
12 彼得里氏鲍特氏菌 1 1.54
13 代尔夫特菌属 1 1.54
14 丁香假单胞菌猕猴桃科 1 1.54
15 多噬伯克霍尔德氏菌 1 1.54
16 肺炎克雷伯氏菌亚种.肺炎 1 1.54
17 鸽变形菌 1 1.54
18 河流弧菌 1 1.54
19 荚膜酸杆菌 1 1.54
20 解藻酸弧菌 1 1.54
21 苛养木杆菌 1 1.54
22 耐重金属贪铜菌 1 1.54
23 酿脓链球菌 1 1.54
24 普氏栖粪杆菌 1 1.54
25 普通变形菌 1 1.54
26 乳杆菌 1 1.54
27 乳酸乳球菌乳亚种 1 1.54
28 食酸菌属 1 1.54
29 土中慢生根瘤菌 1 1.54
30 西瓜食酸菌 1 1.54
31 中间普雷沃氏菌 1 1.54
), ArticleFig(id=1167158455048610448, tenantId=1146029695717560320, journalId=1149652044408987649, articleId=1151881495099617730, language=EN, label=Table 3, caption=

Statistical table of proteases in gene cassettes

, figureFileSmall=null, figureFileBig=null, tableContent=
序号 ICE编号 ICE名称 大小/kb 宿主微生物 转座酶或整合酶注释
1 198 ICE(Tn4371)6039 53.50 食酸菌属JS42 转座酶IS66
2 827 ICESpy009 55.30 酿脓链球菌MB56Spyo009 转座酶
3 1819 ICEPsy15 51.20 丁香假单胞菌CFBP6109 插入序列元件IS629的转座酶; 转座酶, IS51
4 1763 ICEPgs6Chn1 116.00 鸽变形菌T60 ISAba14转座酶; ve
5 1844 ICEPvuChnBC22 148.80 普通变形菌BC22 IS30样元件ISAba125家族转座酶; 转座酶, ISAba125
6 1869 ICESpsH35-1 69.80 副猪链球菌H35 IS6样元件IS1216家族转座酶; 转座酶, IS1216V
7 1121 ICEKpn2_G_12-1 56.14 肺炎克雷伯氏菌2_G_12 IS5样元件ISKpn26家族转座酶; 转座酶
8 1819 ICEPsy15 51.20 丁香假单胞菌CFBP6109 插入序列元件IS629的转座酶; 转座酶, IS51
9 1881 ICESsu1112S 74.40 猪链球菌1112S株 IS6样元件ISS1S家族转座酶; 转座酶
10 1563 ICE_SsuNSUI002_plL_1 71.60 猪链球菌NSUI002株 整合酶; ve
11 195 ICE(Tn4371)6036 59.80 西瓜食酸菌AAC00-1 整合酶, 催化区
12 1587 ICE-ABAQ 71.80 丁香假单胞菌ES4326-D 复制DNA解旋酶
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基因盒中蛋白酶统计表

, figureFileSmall=null, figureFileBig=null, tableContent=
序号 ICE编号 ICE名称 大小/kb 宿主微生物 转座酶或整合酶注释
1 198 ICE(Tn4371)6039 53.50 食酸菌属JS42 转座酶IS66
2 827 ICESpy009 55.30 酿脓链球菌MB56Spyo009 转座酶
3 1819 ICEPsy15 51.20 丁香假单胞菌CFBP6109 插入序列元件IS629的转座酶; 转座酶, IS51
4 1763 ICEPgs6Chn1 116.00 鸽变形菌T60 ISAba14转座酶; ve
5 1844 ICEPvuChnBC22 148.80 普通变形菌BC22 IS30样元件ISAba125家族转座酶; 转座酶, ISAba125
6 1869 ICESpsH35-1 69.80 副猪链球菌H35 IS6样元件IS1216家族转座酶; 转座酶, IS1216V
7 1121 ICEKpn2_G_12-1 56.14 肺炎克雷伯氏菌2_G_12 IS5样元件ISKpn26家族转座酶; 转座酶
8 1819 ICEPsy15 51.20 丁香假单胞菌CFBP6109 插入序列元件IS629的转座酶; 转座酶, IS51
9 1881 ICESsu1112S 74.40 猪链球菌1112S株 IS6样元件ISS1S家族转座酶; 转座酶
10 1563 ICE_SsuNSUI002_plL_1 71.60 猪链球菌NSUI002株 整合酶; ve
11 195 ICE(Tn4371)6036 59.80 西瓜食酸菌AAC00-1 整合酶, 催化区
12 1587 ICE-ABAQ 71.80 丁香假单胞菌ES4326-D 复制DNA解旋酶
), ArticleFig(id=1167158455342211733, tenantId=1146029695717560320, journalId=1149652044408987649, articleId=1151881495099617730, language=EN, label=Table 4, caption=

Statistical table of resistance proteases in gene cassettes

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序号 ICE编号 ICE名称 大小/kb 来源微生物 基因盒功能 功能蛋白说明
1 1872 ICESpsSUT-286-2 51.40 副猪链球菌SUT-286 四环素 分子伴侣DnaK
2 1872 ICESpsSUT-286-2 51.40 副猪链球菌SUT-286 四环素 分子伴侣DnaK
3 1872 ICESpsSUT-286-2 51.40 副猪链球菌SUT-286 四环素 分子伴侣DnaK
4 1872 ICESpsSUT-286-2 51.40 副猪链球菌SUT-286 四环素 分子伴侣DnaJ
5 1872 ICESpsSUT-286-2 51.40 副猪链球菌SUT-286 四环素 分子伴侣DnaK
6 1872 ICESpsSUT-286-2 51.40 副猪链球菌SUT-286 四环素 分子伴侣DnaK
7 1872 ICESpsSUT-286-2 51.40 副猪链球菌SUT-286 四环素 分子伴侣DnaK
8 1872 ICESpsSUT-286-2 51.40 副猪链球菌SUT-286 四环素 分子伴侣DnaK
9 1872 ICESpsSUT-286-2 51.40 副猪链球菌SUT-286 四环素 分子伴侣DnaK
10 1870 ICESpsH35-2 62.30 副猪链球菌H35 四环素 3-磷酸丝氨酸/磷酸羟苏氨酸转氨酶
11 1010 ICEPae690 86.20 铜绿假单胞菌FFUP_PS_690 氨基糖苷、β-内酰胺、消毒剂、磺胺 S-(羟甲基)谷胱甘肽脱氢酶/III类醇脱氢酶
12 1743 ICEP33 211.20 铜绿假单胞菌P33 氨基糖苷、β-内酰胺、消毒剂、苯尼考、磺胺G降解M金属抗性D限制性修改 异丁酰辅酶A脱氢酶
13 1743 ICEP33 211.20 铜绿假单胞菌P33 氨基糖苷、β-内酰胺、消毒剂、苯尼考、磺胺G降解M金属抗性D限制性修改 辅酶A酰化甲基丙二酸半醛脱氢酶
14 1253 ICEKpnINF249-2 210.25 肺炎克雷伯氏菌INF249 氨基糖苷、β-内酰胺、磺胺M金属抗性 铜转运P型ATP酶
15 1253 ICEKpnINF249-2 210.25 肺炎克雷伯氏菌INF249 氨基糖苷、β-内酰胺、磺胺M金属抗性 糖原磷酸化酶
16 1253 ICEKpnINF249-2 210.25 肺炎克雷伯氏菌INF249 氨基糖苷、β-内酰胺、磺胺M金属抗性 糖原磷酸化酶
17 1253 ICEKpnINF249-2 210.25 肺炎克雷伯氏菌INF249 氨基糖苷、β-内酰胺、磺胺M金属抗性 ATP依赖性Clp蛋白酶ATP结合亚基
18 1253 ICEKpnINF249-2 210.25 肺炎克雷伯氏菌INF249 氨基糖苷、β-内酰胺、磺胺M金属抗性 糖原磷酸化酶
19 36 ICEVflInd1 114.20 河流弧菌Ind1 氨基糖苷、叶酸途径拮抗剂、苯尼考、磺胺 ATP依赖性RNA解旋酶SrmB
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基因盒中抗性蛋白酶统计表

, figureFileSmall=null, figureFileBig=null, tableContent=
序号 ICE编号 ICE名称 大小/kb 来源微生物 基因盒功能 功能蛋白说明
1 1872 ICESpsSUT-286-2 51.40 副猪链球菌SUT-286 四环素 分子伴侣DnaK
2 1872 ICESpsSUT-286-2 51.40 副猪链球菌SUT-286 四环素 分子伴侣DnaK
3 1872 ICESpsSUT-286-2 51.40 副猪链球菌SUT-286 四环素 分子伴侣DnaK
4 1872 ICESpsSUT-286-2 51.40 副猪链球菌SUT-286 四环素 分子伴侣DnaJ
5 1872 ICESpsSUT-286-2 51.40 副猪链球菌SUT-286 四环素 分子伴侣DnaK
6 1872 ICESpsSUT-286-2 51.40 副猪链球菌SUT-286 四环素 分子伴侣DnaK
7 1872 ICESpsSUT-286-2 51.40 副猪链球菌SUT-286 四环素 分子伴侣DnaK
8 1872 ICESpsSUT-286-2 51.40 副猪链球菌SUT-286 四环素 分子伴侣DnaK
9 1872 ICESpsSUT-286-2 51.40 副猪链球菌SUT-286 四环素 分子伴侣DnaK
10 1870 ICESpsH35-2 62.30 副猪链球菌H35 四环素 3-磷酸丝氨酸/磷酸羟苏氨酸转氨酶
11 1010 ICEPae690 86.20 铜绿假单胞菌FFUP_PS_690 氨基糖苷、β-内酰胺、消毒剂、磺胺 S-(羟甲基)谷胱甘肽脱氢酶/III类醇脱氢酶
12 1743 ICEP33 211.20 铜绿假单胞菌P33 氨基糖苷、β-内酰胺、消毒剂、苯尼考、磺胺G降解M金属抗性D限制性修改 异丁酰辅酶A脱氢酶
13 1743 ICEP33 211.20 铜绿假单胞菌P33 氨基糖苷、β-内酰胺、消毒剂、苯尼考、磺胺G降解M金属抗性D限制性修改 辅酶A酰化甲基丙二酸半醛脱氢酶
14 1253 ICEKpnINF249-2 210.25 肺炎克雷伯氏菌INF249 氨基糖苷、β-内酰胺、磺胺M金属抗性 铜转运P型ATP酶
15 1253 ICEKpnINF249-2 210.25 肺炎克雷伯氏菌INF249 氨基糖苷、β-内酰胺、磺胺M金属抗性 糖原磷酸化酶
16 1253 ICEKpnINF249-2 210.25 肺炎克雷伯氏菌INF249 氨基糖苷、β-内酰胺、磺胺M金属抗性 糖原磷酸化酶
17 1253 ICEKpnINF249-2 210.25 肺炎克雷伯氏菌INF249 氨基糖苷、β-内酰胺、磺胺M金属抗性 ATP依赖性Clp蛋白酶ATP结合亚基
18 1253 ICEKpnINF249-2 210.25 肺炎克雷伯氏菌INF249 氨基糖苷、β-内酰胺、磺胺M金属抗性 糖原磷酸化酶
19 36 ICEVflInd1 114.20 河流弧菌Ind1 氨基糖苷、叶酸途径拮抗剂、苯尼考、磺胺 ATP依赖性RNA解旋酶SrmB
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Statistical table of defense-related proteases in gene cassettes

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序号 ICE编号 ICE名称 大小/kb 来源微生物 基因盒功能 功能蛋白说明
1 1179 ICEKpnB12-AN-2 238.17 肺炎克雷伯氏菌B12(AN) 噬菌体防御系统 伸长因子
2 1157 ICEKpnAR_0125-1 58.05 肺炎克雷伯氏菌AR_0125 噬菌体防御系统 顺乌头酸酶1
3 1157 ICEKpnAR_0125-1 58.05 肺炎克雷伯氏菌AR_0125 噬菌体防御系统 顺乌头酸酶1
4 1157 ICEKpnAR_0125-1 58.05 肺炎克雷伯氏菌AR_0125 噬菌体防御系统 顺乌头酸酶1
5 1157 ICEKpnAR_0125-1 58.05 肺炎克雷伯氏菌AR_0125 噬菌体防御系统 顺乌头酸酶1
6 1157 ICEKpnAR_0125-1 58.05 肺炎克雷伯氏菌AR_0125 噬菌体防御系统 顺乌头酸酶1
7 2088 ICEMsp.M8A-1 102.00 中生根瘤菌属M8A.F.Ca.ET.057.01.1.1 噬菌体防御系统 假想蛋白质
8 2100 ICEMsp.SymNZP2298 467.10 中生根瘤菌属NZP2298 噬菌体排出系统 甲硫氨酸腺苷转移酶
9 2071 ICEMsp.SymM1D-1 332.10 中生根瘤菌属M1D.F.Ca.ET.043.01.1.1 噬菌体排出系统 甲硫氨酸腺苷转移酶
10 2103 ICEMsp.SymSEMIA3007 480.90 中生根瘤菌属SEMIA 3007 噬菌体降解系统 4-氨基丁酸转氨酶
11 2103 ICEMsp.SymSEMIA3007 480.90 中生根瘤菌属SEMIA 3007 噬菌体降解系统 乙酰辅酶A乙酰转移酶
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基因盒中防御相关蛋白酶统计表

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序号 ICE编号 ICE名称 大小/kb 来源微生物 基因盒功能 功能蛋白说明
1 1179 ICEKpnB12-AN-2 238.17 肺炎克雷伯氏菌B12(AN) 噬菌体防御系统 伸长因子
2 1157 ICEKpnAR_0125-1 58.05 肺炎克雷伯氏菌AR_0125 噬菌体防御系统 顺乌头酸酶1
3 1157 ICEKpnAR_0125-1 58.05 肺炎克雷伯氏菌AR_0125 噬菌体防御系统 顺乌头酸酶1
4 1157 ICEKpnAR_0125-1 58.05 肺炎克雷伯氏菌AR_0125 噬菌体防御系统 顺乌头酸酶1
5 1157 ICEKpnAR_0125-1 58.05 肺炎克雷伯氏菌AR_0125 噬菌体防御系统 顺乌头酸酶1
6 1157 ICEKpnAR_0125-1 58.05 肺炎克雷伯氏菌AR_0125 噬菌体防御系统 顺乌头酸酶1
7 2088 ICEMsp.M8A-1 102.00 中生根瘤菌属M8A.F.Ca.ET.057.01.1.1 噬菌体防御系统 假想蛋白质
8 2100 ICEMsp.SymNZP2298 467.10 中生根瘤菌属NZP2298 噬菌体排出系统 甲硫氨酸腺苷转移酶
9 2071 ICEMsp.SymM1D-1 332.10 中生根瘤菌属M1D.F.Ca.ET.043.01.1.1 噬菌体排出系统 甲硫氨酸腺苷转移酶
10 2103 ICEMsp.SymSEMIA3007 480.90 中生根瘤菌属SEMIA 3007 噬菌体降解系统 4-氨基丁酸转氨酶
11 2103 ICEMsp.SymSEMIA3007 480.90 中生根瘤菌属SEMIA 3007 噬菌体降解系统 乙酰辅酶A乙酰转移酶
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宏基因组测序分析熟制禽肉制品污染微生物中整合子组成
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宋晟 1, 2 , 郭焜鹏 1, 2 , 张露苗 1, 2 , 罗青雯 1, 2 , 王芳 1, 2 , 高晗 1, 2, *
食品安全质量检测学报 | 专题：食品安全风险评估与风险监测 2025,16(10): 97-104
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食品安全质量检测学报 | 专题：食品安全风险评估与风险监测 2025, 16(10): 97-104
宏基因组测序分析熟制禽肉制品污染微生物中整合子组成
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宋晟1, 2 , 郭焜鹏1, 2, 张露苗1, 2, 罗青雯1, 2, 王芳1, 2, 高晗1, 2, *
作者信息
  • 1.食品安全监测与预警湖南省重点实验室, 长沙 410000
  • 2.湖南省产商品质量检验研究院, 长沙 410000

    • 宋晟(1979—), 男, 硕士, 高级工程师, 主要研究方向为食品安全与食品微生物。E-mail:

通讯作者:

* 通信作者: 高晗(1982—), 男, 硕士, 高级工程师, 主要研究方向为食品质量安全研究与风险评估。E-mail:
Analysis of integrative and conjugative elements composition in contaminated microorganisms of cooked poultry products by metagenomic sequencing
Sheng SONG1, 2 , Kun-Peng GUO1, 2, Lu-Miao ZHANG1, 2, Qing-Wen LUO1, 2, Fang WANG1, 2, Han GAO1, 2, *
Affiliations
  • 1. Hunan Povincial Key Laboratory of Food Safety Monitoring and Early Warning, Changsha 410000, China
  • 2. Hunan Povincial Institute of Product and Goods Quality Inspection, Changsha 410000, China
出版时间: 2025-05-25 doi: 10.19812/j.cnki.jfsq11-5956/ts.20241204001
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摘要
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目的 研究熟制禽肉制品污染微生物中整合子的分布、来源及其携带的基因盒内容等相关情况。方法 采购熟制鸭肉, 对样品进行DNA提取, 测序、混合拼接、分箱, 获取宏基因组组装基因组, 整合子数据库比对。结果 熟制鸭肉污染微生物中检测到65种整合子, 共计110个, 主要来源于31种宿主微生物, 包括中生根瘤菌属、铜绿假单胞菌与肺炎克雷伯氏菌等; 整合子中共有9种转座酶, 1种毒力因子基因, 19个抗性相关基因, 其中四环素抗性基因10个, 防御基因11个, 均为防御噬菌体的基因。结论 多种整合子及毒力因子、抗性相关和防御基因的发现, 揭示了食品中微生物遗传多样性的复杂程度, 为研究基因的水平转移提供了重要线索, 对于评估食品安全性、预防和控制食源性病原体具有重要意义。

熟制禽肉制品  /  宏基因组  /  整合子

Objective To investigate the distribution, sources, and gene cassette contents of integrative and conjugative elements in microorganisms contaminating cooked poultry meat products. Methods Cooked duck meat was purchased, and DNA extraction, sequencing, assembly, binning, and metagenome-assembled genome (MAG) acquisition were performed. These MAGs were then compared with an integron database. Results A total of 110 integrative and conjugative elements belonging to 65 distinct types were detected in the contaminating microbiota of cooked duck meat, primarily originating from 31 host microorganisms, including Mesorhizobium, Pseudomonas aeruginosa, and Klebsiella pneumoniae. Among these integrative and conjugative elements, there were 9 kinds of transposases, 1 kinds of virulence factor gene, and 19 resistance-related genes, including 10 tetracycline resistance genes. Additionally, 11 defense genes, all of which were phage-defense genes, were identified. Conclusion The discovery of various integrative and conjugative elements, virulence factors, resistance-related genes, and defense genes reveals the complex genetic diversity of microorganisms in food. This provides important clues for studying horizontal gene transfer and has significant implications for assessing food safety and preventing and controlling foodborne pathogens. The effective application of metagenomic technology in integron research also demonstrates its potential in the fields of food safety and public health.

cooked poultry meat products  /  metagenomics  /  integrative and conjugative elements
宋晟, 郭焜鹏, 张露苗, 罗青雯, 王芳, 高晗. 宏基因组测序分析熟制禽肉制品污染微生物中整合子组成. 食品安全质量检测学报, 2025 , 16 (10) : 97 -104 . DOI: 10.19812/j.cnki.jfsq11-5956/ts.20241204001
Sheng SONG, Kun-Peng GUO, Lu-Miao ZHANG, Qing-Wen LUO, Fang WANG, Han GAO. Analysis of integrative and conjugative elements composition in contaminated microorganisms of cooked poultry products by metagenomic sequencing[J]. Journal of Food Safety & Quality, 2025 , 16 (10) : 97 -104 . DOI: 10.19812/j.cnki.jfsq11-5956/ts.20241204001
正文
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0 引言
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整合子(integrative and conjugative elements, ICEs)是在细菌进化过程中发挥重要作用的移动DNA原件, 具有完整的接合机制, 可整合到细菌染色体中, 稳定遗传, 并能在细菌之间自我传播[1-2]; 其携带的不同基因盒, 可赋予宿主不同的表型特征, 如抗生素抗性、毒力机制、防御系统、金属抗性、化合物降解和共生等, 对细菌的多样性和适应性有重要贡献[3-4]。ICEs通常由5端和3端两个保守区以及一个基因盒可变区组成, 具有整合酶基因和初始整合位点, 可通过整合酶捕获外源基因, 并对外源基因进行启动和表达[5-6]。研究ICEs有利于深入了解基因在细菌中的水平转移, 并可对目标基因进行溯源。这对于了解细菌耐药性、致病性对于的产生、发展和传播机制以及指导临床用药具有重要意义。
ICEs的研究方法包括聚合酶扩增法、多重聚合酶扩增法和宏基因测序法[7]。聚合酶扩增法, 即通过设计特异引物对ICEs可变区进行扩增, 检测ICEs及其携带的基因盒, 张亚茹等[8]采用聚合酶链反应法鉴定稻蛙共养系统样品, 有14株菌检出ICEs且携带基因盒; 多重聚合酶扩增法, 即针对多种类型的ICEs设计多对特异引物, 实现1类、2类或3类ICEs的同时检测, 黄靖宇等[9]采用多重聚合酶链式法对临床领域48株亚胺培南耐药铜绿假单胞菌进行整合酶基因检测, 其中5株为1类整合酶; 24株为2类整合酶; 宏基因组测序法, 即不采用任何参照序列, 通过高通量测序获得基因组序列[10-12], 并与ICEs数据库比对, 实现一次测序, 测定样本中细菌所携带的所有ICEs的技术手段, 较聚合酶链式反应更为全面真实[13-14], 郑鑫洱[15]采用宏基因组法分析生猪屠宰环节样品, 1型ICEs检出率为78.26%, 基因盒所含的耐药基因类型包括甲氧苄胺嘧啶类、氯霉素类、磺胺类等。宏基因测序法提供的信息量最大, 能够覆盖整个微生物组; 多重聚合酶扩增法次之, 可以同时扩增多个目标序列; 聚合酶扩增法提供的信息量最有限, 只能扩增特定区域的DNA, 由此可知, 宏基因组测序法分析范围最广最全面, 可实现ICEs的一次测序, 全部鉴定。
课题组组前期已采集包括生鲜鸡鸭肉、肉制品半成品、鸡鸭肉熟制品样品进行宏基因组分析, 在各样品中鉴定出多种致病菌以及多种致病基因与耐药基因, 为更深入研究致病基因、耐药基因的来源与传播方式, 及与ICEs的关系。本研究从市场上再次购入熟制禽肉制品, 通过宏基因测序, 序列拼接, 分箱归类后, 获取样本宏基因组组装基因组, 与ICEbeg 3.0数据库比对等, 得到样本中所有ICEs, 并对其携带的基因盒信息进行识别与功能基因注释。该研究对于熟制禽肉制品中ICEs的统计分析, 有助于提高禽肉制品微生物中基因水平转移的认识, 以及致病基因与耐药基因的可能来源分析。
1 材料与方法
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1.1 材料与试剂
五香卤鸭掌由国内知名大厂生产, 生产日期为2024年8月15日, 为山东产90 d龄麻鸭, 经添加八角、茴香、桂皮、食盐、酱油等卤制, 二次加热杀菌后包装, 采购自京东商城。
磁珠法DNA提取试剂盒(货号M1257-01, 美国欧米加生命技术有限公司); Qubit3.0 DNA检测试剂盒(货号Q33226, 美国英杰生命技术有限公司)。
1.2 仪器与设备
PL602E电子天平(精度0.01 g, 瑞士梅特勒托利多公司); Qubit®3.0荧光仪(美国英杰生命技术有限公司); ETC 811 PC扩增仪(北京东胜创新生物科技有限公司); F980A生物电泳图像分析系统(上海复日科技有限公司)。
1.3 样品中细菌DNA的提取与浓度测定
在100 g样品中加入液氮, 研磨至粉末状, 混合均匀后, 在2 mL灭菌离心管中称入0.25 g样品, 加入缓冲液振荡混匀后, 加入蛋白酶K, 65 ℃裂解10 min后, 4 ℃ 10000 r/min离心5 min, 转移上清液, 加入磁珠吸附5 min后, 加入500 μL磁珠清洗液, 混匀磁珠, 放置5 min, 弃上清, 重复清洗一次, 分离磁珠, 加入50 μL DNA洗脱液到离心管中, 充分振荡混匀, 65 °C水浴10 min。小心吸取上清DNA液体到新的1.5 mL离心管中, 用Qubit3.0 DNA检测DNA样本浓度。
1.4 样品的宏基因组分析
样本DNA经Illumina Miseq™/Hiseq™测序后, 将原始数据进行质量评估与过滤, 去除宿主基因组污染数据, 混合拼接, 分箱重新归类后, 获取宏基因组组装基因组。选择大于长度大于100 bp的基因, 翻译成氨基酸序列, 采用非比对和比对两种方式分析基因集丰度; 将基因集比对ICEbeg3.0数据库得到ICEs基因注释信息。
1.5 数据处理
将重复测试3次的数据结果, 采用WPS Office (12.1.0.19302)统计模块对数据进行分类统计分析。
2 结果与分析
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2.1 样本中整合子的统计分析
样本中共检测到65种共计110个ICEs, 其中ICE1872最多, 共有9个, 占比为8.18%, 来源于副猪链球菌SUT-286; ICE200共6个, 占比为5.45%, 来源于铜绿假单胞菌2192; ICE1157共5个, 占比为4.55%, 来源于肺炎克雷伯氏菌A_0125; ICE1253共5个, 占比为4.55%, 来源于肺炎克雷伯氏菌INF249; ICE1871共5个, 占比为4.55%, 来源于副猪链球菌SUT-286; ICE133共4个, 占比为3.64%, 来源于百脉根中生根瘤菌MAFF303099; ICE1646共3个, 占比为2.7%, 来源于按蚊伊丽莎白金菌CSID3000516074; ICE1045、ICE1081、ICE1097、ICE1743、ICE1819、ICE2049、ICE2052、ICE2070、ICE2076、ICE2084、ICE2089、ICE2103、ICE2104均为2个, 占比均为1.8%, 其他ICEs数量均为1(表1)。
ICEs来源于31种宿主微生物, 有17种ICEs来源于中生根瘤菌属, 占比为26.15%; 有7种ICEs来源于铜绿假单胞菌, 占比为10.77%; 有4种ICEs来源于肺炎克雷伯氏菌, 占比为6.15%; 有4种ICEs来源于副猪链球菌, 占比为6.15%; 有3种ICEs来源于按蚊伊丽莎白金菌, 占比为4.62%; 有3种ICEs来源于丁香假单胞菌, 占比为4.62%; 有2种ICEs来源于鹰嘴豆中生根瘤菌, 占比为3.08%; 有2种ICEs来源于猪链球菌, 占比为3.08%(表2)。宿主微生物, 如: 中生根瘤菌和丁香假单胞菌, 主要来自于土壤或水等, 肺炎克雷伯氏菌、副猪链球菌等均为畜禽养殖中常见致病菌, 因此ICEs的传播极有可能是通过养殖环境。
2.2 样本中整合相关蛋白酶的统计分析
样本中共检测到9种转座酶, 分别来源于8种宿主微生物, 其中丁香假单胞菌有两个转座酶, 其他宿主微生物均只携带一种转座酶, 来源于酿脓链球菌MB56Spyo009的转座酶与大环内酯类、大环内酯、链菌素B抗性有关, 来源于副猪链球菌H35的转座酶与大环内酯、林可酰胺、链菌素B、恶唑烷酮、苯尼考抗性有关; 样本中共检测到2种整合酶, 分别来源于猪链球菌与西瓜食酸菌, 其中来源于猪链球菌NSUI002株的整合酶与四环素抗性有关, 样本中共检测到1种解旋酶, 来源于丁香假单胞菌(表3), 转座酶能携带抗性基因的基因盒从一个位置移动到另一个位置, 甚至在不同的细菌之间转移。整合酶则负责将基因盒整合到ICEs的特定位置。由此可知, 转座酶和整合酶通过促进抗性基因的水平转移和稳定整合, 共同在微生物耐药性的形成和传播中发挥了关键作用。这种作用不仅影响了个体微生物, 还对整个微生物群体和生态系统的抗生素耐药性产生了深远的影响。
2.3 基因盒功能注释与统计分析
样本中主要的毒力因子基因为多药ABC转运蛋白ATP结合和渗透酶蛋白, 来源于副猪链球菌SUT-286, 它是一种ATP结合和水解的跨膜转运蛋白, 通过水解ATP释放的能量来驱动底物的跨膜转运, 其转运的底物包括毒素或代谢产物; 且参与病原体对宿主细胞的黏附、入侵和定殖等过程, 从而增强病原体的致病能力。
样本中抗性相关基因共有19个, 其中四环素抗性基因最多, 共计10个, 主要来源于副猪链球菌, 功能蛋白主要为分子伴侣DnaK; 氨基糖苷、β-内酰胺、消毒剂、苯尼考、磺胺G降解M金属抗性D限制性修改基因共计5个, 主要来源于铜绿假单胞菌, 功能蛋白主要为脱氢酶; 氨基糖苷、β-内酰胺、磺胺M金属抗性共计5个, 主要来源于肺炎克雷伯氏菌, 功能蛋白分别为铜转运P型ATP酶或糖原磷酸化酶; 氨基糖苷、叶酸途径拮抗剂、苯尼考与磺胺抗性基因, 主要来源于河流弧菌, 功能蛋白为ATP依赖性RNA解旋酶SrmB(表4)。这一发现有助于理解抗性基因如何在微生物之间传播, 从而增加微生物对抗生素的耐药性。这对于制定有效的抗生素使用策略和控制细菌耐药性的传播具有重要意义。
样本中防御基因共有11个, 均为防御噬菌体的基因, 其中噬菌体防御系统基因最多为7个, 主要来源于肺炎克雷伯氏菌与中生根瘤菌, 主要功能蛋白为伸长因子、顺乌头酸酶1与假想蛋白质; 噬菌体排出系统基因2个, 来源于中生根瘤菌, 功能蛋白为甲硫氨酸腺苷转移酶; 噬菌体降解系统基因2个, 来源于中生根瘤菌, 功能蛋白为乙酰辅酶A乙酰转移酶和4-氨基丁酸转氨酶(表5)。这些防御基因的存在和分布揭示了微生物在面对噬菌体侵袭时所采取的多种防御策略, 如噬菌体防御系统、噬菌体排出系统和噬菌体降解系统等。
3 讨论与结论
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随着聚合酶链式反应扩增技术、多重聚合酶链式反应扩增技术以及高通量测序技术的飞速发展, 科研人员得以更深入地探究畜禽肉中微生物的抗性基因与毒力因子基因[16-18]。由于畜禽养殖业中抗生素的普遍且广泛使用, 鸡鸭肉中的抗性基因检出率不断攀升, 且这些基因呈现出多样化的趋势, 涵盖了β-内酰胺类、氨基糖苷类、大环内酯类等多种类型耐药基因, 而这些耐药基因的多样性与高检出率, 极有可能与基因的水平转移有关[19-21]。与此同时, 不良的饲养环境, 包括卫生条件不达标、通风不良、饮水质量低劣以及高密度饲养等因素, 也加剧了病原菌的传播风险, 并推动了其适应性进化。在这种环境下, 毒力因子基因更容易发生变异和重组, 从而赋予病原菌更强的致病能力和耐药性[22-25]。
为了深入探索熟制禽肉制品中抗性基因与毒力因子基因在微生物群落中的潜在传播途径, 本研究采用了一种先进的策略, 即结合宏基因组测序技术与生物信息学分析方法, 对这类产品中的ICEs进行了详尽的统计分析。在熟制鸭肉样本中, 成功鉴定出65种共计110个ICEs, 其中ICE1872 ICEs数量最多, 达到了9个, 这些ICEs广泛分布于31种不同的宿主微生物中, 如中生根瘤菌属、铜绿假单胞菌、肺炎克雷伯氏菌、副猪链球菌等[26-27], 有17种ICEs直接来源于中生根瘤菌属。这一发现不仅证实了ICEs在熟制禽肉制品中的普遍存在, 还揭示了其主要源自几种关键的病原菌, 进一步凸显了其在微生物抗性基因传播中的重要性。
通过对ICEs及其携带的基因盒进行深入剖析, 本研究发现了9种转座酶, 它们源自8种不同的宿主微生物, 同时鉴定出2种整合酶和1种解旋酶, 这些酶的存在为基因的水平转移提供了强有力的证据。在毒力因子方面, 本研究仅检测到1种, 即多药ABC转运蛋白ATP结合和渗透酶蛋白, 它来源于副猪链球菌SUT-286, 这表明在熟制禽肉制品中毒力因子基因的水平传播相对有限[28-29]。然而, 在抗性相关基因方面, 发现了多达19个基因, 其中四环素抗性基因最为丰富, 共计10个, 主要来源于副猪链球菌。此外, 还鉴定出11个防御噬菌体的防御基因, 它们主要源自肺炎克雷伯氏菌与中生根瘤菌。这些发现不仅展示了宏基因组测序技术在解析复杂微生物群落结构及其基因组成方面的强大能力, 还揭示了抗性基因与防御基因在微生物间的复杂交互作用。
本研究发现的大量抗性相关基因主要来源于病原菌, 且大多通过ICEs的方式进行传播, 这强烈暗示了ICEs在微生物群体抗性形成中的关键作用[30]。这一发现不仅加深了对抗性基因传播机制的理解, 还为制定有效的策略以阻断抗性基因在食品链中的传播提供了科学依据。未来计划进一步采集饲养、屠宰以及生产环境样品, 运用高通量测序技术对ICEs进行纵向追踪研究, 以期更深入地揭示毒力因子基因与抗性基因的传播机制。
基金
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  • 湖南省自然科学基金项目(2022JJ90028)
文献
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2025年第16卷第10期
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doi: 10.19812/j.cnki.jfsq11-5956/ts.20241204001
  • 接收时间：2024-12-04
  • 首发时间：2025-07-15
  • 出版时间：2025-05-25
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  • 收稿日期：2024-12-04
基金
湖南省自然科学基金项目(2022JJ90028)
作者信息
    1.食品安全监测与预警湖南省重点实验室, 长沙 410000
    2.湖南省产商品质量检验研究院, 长沙 410000

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* 通信作者: 高晗(1982—), 男, 硕士, 高级工程师, 主要研究方向为食品质量安全研究与风险评估。E-mail:
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2种不同金属材料的力学参数
科
Family		 属数
Number of
genus		 种数
Number of
species		 占总种数比例
Percentage of
total species (%)		 属
Genus		 种数
Number of
species		 占总种数比例
Percentage of total
species (%)
鹅膏菌科Amanitaceae 2 11 5.26 鹅膏菌属 Amanita 10 4.78
小菇科 Mycenaceae 2 12 5.74 丝盖伞属 Inocybe 5 2.39
多孔菌科 Polyporaceae 8 14 6.70 蜡蘑属 Laccaria 5 2.39
红菇科 Russulaceae 3 23 11.00 小皮伞属 Marasmius 6 2.87
小菇属 Mycena 11 5.26
光柄菇属 Pluteus 5 2.39
红菇属 Russula 17 8.13
栓菌属 Trametes 5 2.39
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