Abstract：
BACKGROUND: Carbapenem-resistant Klebsiella pneumoniae (CRKP) is a great public health problem and is associated with many disease outbreaks and high mortality rates. Alarmingly, K. pneumoniae has been isolated from food in several recent studies. This study aimed to investigate the prevalence and characteristics of CRKP in food samples from Egypt.
METHODS: A total of 311 food samples (including 116 minced meat, 92 chicken meat, 75 diced meat, and 28 mutton) were collected from local markets in Egypt and were screened for CRKP with the determination of their antimicrobial resistance profiles. The whole genome sequence was done for 23 CRKP isolates to clarify the relationship between CRKP from food and human cases in Egypt using the SNP core genome. The conjugation probability of the blaNDM-5 harboring plasmid was identified using oriTfinder RESULTS: CRKP was isolated from 11% (35/311) of the samples, with 45.71% (16/35) of them showing resistance to colistin, one of the last-resort options for treating CRKP-mediated infections. In addition to the carbapenem and colistin resistance, the CRKP isolates frequently exhibited resistance to multiple antimicrobials including β-lactams, fluoroquinolones, aminoglycosides, tetracyclines, and chloramphenicol. In addition, most of the CRKP were potentially hypervirulent K. pneumoniae (HvKP) identified as phylogroup Kp1 and of high-risk groups as detected in STs reported in many human outbreaks globally, such as ST383 and ST147. The core-genome phylogeny showed similarities between the isolates from this study and those previously isolated from clinical human samples in Egypt. In addition, analysis of the plasmid on which blaNDM is encoded revealed that several antimicrobial resistance genes such as blaOXA-9, blaCTX-M-15, aac(6\')-Ib, qnrS1, and several virulence genes are encoded on the same plasmid.
CONCLUSIONS: This study is significant for food safety and public health and is important to further identify the change in the epidemiology of CRKP infections, especially the consumption of contaminated food products.
METHODS: A total of 311 food samples (including 116 minced meat, 92 chicken meat, 75 diced meat, and 28 mutton) were collected from local markets in Egypt and were screened for CRKP with the determination of their antimicrobial resistance profiles. The whole genome sequence was done for 23 CRKP isolates to clarify the relationship between CRKP from food and human cases in Egypt using the SNP core genome. The conjugation probability of the blaNDM-5 harboring plasmid was identified using oriTfinder RESULTS: CRKP was isolated from 11% (35/311) of the samples, with 45.71% (16/35) of them showing resistance to colistin, one of the last-resort options for treating CRKP-mediated infections. In addition to the carbapenem and colistin resistance, the CRKP isolates frequently exhibited resistance to multiple antimicrobials including β-lactams, fluoroquinolones, aminoglycosides, tetracyclines, and chloramphenicol. In addition, most of the CRKP were potentially hypervirulent K. pneumoniae (HvKP) identified as phylogroup Kp1 and of high-risk groups as detected in STs reported in many human outbreaks globally, such as ST383 and ST147. The core-genome phylogeny showed similarities between the isolates from this study and those previously isolated from clinical human samples in Egypt. In addition, analysis of the plasmid on which blaNDM is encoded revealed that several antimicrobial resistance genes such as blaOXA-9, blaCTX-M-15, aac(6\')-Ib, qnrS1, and several virulence genes are encoded on the same plasmid.
CONCLUSIONS: This study is significant for food safety and public health and is important to further identify the change in the epidemiology of CRKP infections, especially the consumption of contaminated food products.
摘要：
背景：耐碳青霉烯类肺炎克雷伯菌（CRKP）是一个严重的公共卫生问题，与许多疾病暴发和高死亡率有关。令人震惊的是,在最近的几项研究中，肺炎克雷伯菌已从食物中分离出来。本研究旨在调查埃及食品样品中CRKP的患病率和特征。
方法:共311份食物样本(包括116份肉末,92鸡肉，75块肉丁，和28只羊肉）是从埃及当地市场收集的，并通过确定其抗菌素耐药性来筛选CRKP。对23个CRKP分离株进行了全基因组测序，以使用SNP核心基因组阐明埃及食物中CRKP与人类病例之间的关系。使用oriTfinder鉴定blaNDM-5携带质粒的接合概率结果：CRKP从11％（35/311）的样品中分离，其中45.71％（16/35）对粘菌素具有抗性，治疗CRKP介导的感染的最后选择之一。除了碳青霉烯类和粘菌素的耐药性，CRKP分离株经常表现出对包括β-内酰胺类在内的多种抗菌药物的耐药性，氟喹诺酮类药物,氨基糖苷类,四环素,和氯霉素.此外,大多数CRKP是潜在的高毒力肺炎克雷伯菌（HvKP），被确定为系统组Kp1，并且是在全球许多人类暴发中报告的STs中检测到的高危人群，例如ST383和ST147。核心基因组系统发育表明，本研究的分离株与先前从埃及临床人类样本中分离的分离株之间存在相似性。此外,对blaNDM编码的质粒的分析表明，几种抗微生物抗性基因，如blaOXA-9，blaCTX-M-15，aac（6'）-Ib，qnrS1和几个毒力基因在同一质粒上编码。
结论：这项研究对食品安全和公共卫生具有重要意义，对进一步确定CRKP感染的流行病学变化具有重要意义。特别是食用受污染的食品。
方法:共311份食物样本(包括116份肉末,92鸡肉，75块肉丁，和28只羊肉）是从埃及当地市场收集的，并通过确定其抗菌素耐药性来筛选CRKP。对23个CRKP分离株进行了全基因组测序，以使用SNP核心基因组阐明埃及食物中CRKP与人类病例之间的关系。使用oriTfinder鉴定blaNDM-5携带质粒的接合概率结果：CRKP从11％（35/311）的样品中分离，其中45.71％（16/35）对粘菌素具有抗性，治疗CRKP介导的感染的最后选择之一。除了碳青霉烯类和粘菌素的耐药性，CRKP分离株经常表现出对包括β-内酰胺类在内的多种抗菌药物的耐药性，氟喹诺酮类药物,氨基糖苷类,四环素,和氯霉素.此外,大多数CRKP是潜在的高毒力肺炎克雷伯菌（HvKP），被确定为系统组Kp1，并且是在全球许多人类暴发中报告的STs中检测到的高危人群，例如ST383和ST147。核心基因组系统发育表明，本研究的分离株与先前从埃及临床人类样本中分离的分离株之间存在相似性。此外,对blaNDM编码的质粒的分析表明，几种抗微生物抗性基因，如blaOXA-9，blaCTX-M-15，aac（6'）-Ib，qnrS1和几个毒力基因在同一质粒上编码。
结论：这项研究对食品安全和公共卫生具有重要意义，对进一步确定CRKP感染的流行病学变化具有重要意义。特别是食用受污染的食品。
