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Wan He,1,* Changbu Wu,2,3,* Guanping Chen,2– 4 Guili Zhang,2,3 Zihan Zhao,2,3 Shu’an Wen,2,3 Yuan Zhou,2,3 Xue Deng,2,3 Yu Feng,2,3 Lan-Lan Zhong,2,3 Guo-Bao Tian,2– 4 Min Dai1 1School of Laboratory Medicine, Chengdu Medical College, Chengdu, 610500, People’s Republic of China; 2Department of Immunology and Microbiology, Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, People’s Republic of China; 3Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, 510080, People’s Republic of China; 4Department of Immunology, School of Medicine, Sun Yat-Sen University, Shenzhen, 518107, People’s Republic of China*These authors contributed equally to this workCorrespondence: Min Dai, School of Laboratory Medicine, Chengdu Medical College, Chengdu, Sichuan Province, People’s Republic of China, Tel +86 28-62739128, Email daimin1015@163.com Guo-Bao Tian, Department of Immunology and Microbiology, Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan 2nd Road, Guangzhou, 510080, People’s Republic of China, Tel/Fax +86 20 87335387, Email tiangb@mail.sysu.edu.cnBackground: The emergence and spread of hypervirulent carbapenem-resistant Klebsiella pneumoniae (hv-CRKP) is a potential epidemiological threat that needs to be monitored. However, the transmission and pathogenic characteristics of hv-CRKP in China remain unclear. We investigated the epidemiological characteristics of gut colonized hv-CRKP in a hospital in Guangdong Province, China.Methods: A total of 46 gut colonized hv-CRKP isolates were collected from Sun Yat-Sen Memorial Hospital (Guangzhou, China) from August 31st to December 31st, 2021. Minimum inhibitory concentrations (MICs) were obtained for 15 antibiotics for 46 hv-CRKP isolates. BALB/C mice infection model and mucoviscosity assay was used to evaluate the virulence of the isolates. The characteristics of genome, phylogenetic relationship and the structure of the plasmid of 46 gut colonized hv-CRKP isolates were compared with pathogenic isolates from GeneBank based on whole-genome data.Results: The hv-CRKP isolation rate of all gut colonized carbapenem-resistant Klebsiella pneumoniae was 17% (46/270), and the intestinal colonization rate of hv-CRKP was irrelevant to the sex, age, department of hospitalization, and history of antibiotic use of the host. The gut colonized hv-CRKP showed pandrug resistance and hypervirulence. The gut colonized hv-CRKP and pathogenic hv-CRKP prevalent in China were mainly ST11 hv-CRKP and had two major epidemic clades. The similarities in genomic characteristics between gut colonized hv-CRKP and pathogenic hv-CRKP were consistent. The gut colonized hv-CRKP carried an incomplete structure pK2044 virulence plasmid from hypervirulent K. pneumoniae NTUH-K2044 by analyzing the virulence plasmid structure.Conclusion: Our results suggest that the gut colonized ST11 hv-CRKP may serve as a reservoir for the clinical pathogenic ST11 HV-CRKP. It is necessary to further strengthen the monitoring of gut colonized hv-CRKP and research the potential mechanism of infection caused by gut colonized hv-CRKP.Keywords: K. pneumoniae, intestinal colonization, hypervirulent, genomic characterization, carbapenemase

Xiaoxue Liang,1,* Ping Chen,2,* Baoguo Deng,2,* Feng-Hui Sun,1,* Yongqiang Yang,3– 5 Yanxian Yang,3,4 Ruowen He,3,4 Mingyang Qin,2 Yiping Wu,3,4 Fan Yang,2 Guo-Bao Tian,3,4 Min Dai1 1School of Laboratory Medicine, Chengdu Medical College, Chengdu, Sichuan Province, People’s Republic of China; 2School of Basic Medical Science, Xinxiang Medical University, Xinxiang, Henan Province, People’s Republic of China; 3Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong Province, People’s Republic of China; 4Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, Guangdong Province, People’s Republic of China; 5School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Guangzhou, Guangdong Province, People’s Republic of China*These authors contributed equally to this workCorrespondence: Min Dai, School of Laboratory Medicine, Chengdu Medical College, Chengdu, Sichuan Province, People’s Republic of China, Tel +86 28-62739128, Email daimin1015@163.comPurpose: To compare antimicrobial resistance, virulence, clinical characteristics, and risk factors between carbapenem-resistant K. pneumoniae (CRKP) and carbapenem-susceptible K. pneumoniae (CSKP) isolates from patients with bloodstream infections (BSIs) in China.Patients and Methods: The clinical data of 103 patients with K. pneumoniae BSI from 10 hospitals were retrospectively analyzed. The minimum inhibitory concentrations of 15 antibiotics against the bacteria were determined. A Galleria mellonella infection model was used to evaluate virulence of the isolates. Kaplan–Meier curves were calculated to evaluate the 28-day and in-hospital survival rates of the isolates. The risk factors for CRKP and CSKP infection and respective mortality rate were evaluated by univariate analysis, and independent risk factors were evaluated using the multivariate logistic regression model.Results: Our results indicated that CRKP isolates were more resistant to most tested antibiotics than CSKP isolates. The G. mellonella infection model was used to demonstrate that CRKP isolates were more virulent than CSKP isolates. We found that in-hospital deaths occurred in 39.3% (22/56) of patients with CRKP BSIs and were significantly higher than those in patients with CSKP infections (19.1%, 9/47). Patients infected with CRKP isolates had poorer outcomes than those infected with the CSKP strains. For in-hospital mortality of CRKP BSIs, the independent risk factors included carbapenem-resistant Enterobacterales bacteremia and length of hospitalization after the onset of BSI.Conclusion: Our findings confirm that CRKP isolates are more drug-resistant than CSKP isolates and are associated with poorer outcomes. To prevent CRKP infection, strict infection control strategies and active surveillance should be implemented in hospitals.Keywords: Klebsiella pneumoniae, bloodstream infections, virulence, antimicrobial resistance

Minmin Lin,1,* Yongqiang Yang,2– 4,* Yanxian Yang,2,3,* Guanping Chen,5 Ruowen He,2,3 Yiping Wu,2,3 Lan-Lan Zhong,2,3 Mohamed Abd El-Gawad El-Sayed Ahmed,2,3,6 Siyuan Feng,2,3 Cong Shen,2,3 Xin Wen,2,3 Jin Huang,1 Hongyu Li,7 Xiaobin Zheng,1 Guo-Bao Tian2,3 1Department of Respiratory Medicine, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai 519000, People’s Republic of China; 2Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, People’s Republic of China; 3Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, People’s Republic of China; 4School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Guangzhou 510006, People’s Republic of China; 5Sun Yat-sen University School of Medicine, Guangzhou 510006, People’s Republic of China; 6Department of Microbiology and Immunology, Faculty of Pharmaceutical Sciences and Drug Manufacturing, Misr University for Science and Technology (MUST), Cairo, 6th of October City, Egypt; 7Department of Laboratory, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, People’s Republic of China*These authors contributed equally to this workCorrespondence: Guo-Bao Tian; Xiaobin Zheng Email tiangb@mail.sysu.edu.cn; zhxbin@mail.sysu.edu.cnBackground: Bloodstream infection (BSI) caused by carbapenem-resistant Enterobacteriaceae are potentially life-threatening related to poorer outcomes. Colistin is considered one of the last-resort treatments against human infections caused by multidrug-resistant (MDR) Gram-negative bacteria. Therefore, emergence of strains from the blood that co-harboring mcr and carbapenem resistance genes were considered as a serious problem.Purpose: In this study, two mcr-9-harboring MDR Enterobacter cloacae isolates BSI034 and BSI072 recovered from BSI patients were identified, one of which co-harbored mcr-9 and blaNDM-1. The genetic characteristics of the MDR plasmid needed to be clarified.Methods: S1-PFGE and Southern blotting were conducted to determine the location of mcr-9. Whole-genome sequencing was performed to obtain the complete genome and plasmid sequences. The resistome and virulence genes of the strains, accompanied by the genetic characteristics of mcr-9- and blaNDM-1-harboring plasmids, were analyzed.Results: Whole-genome sequencing showed that BSI034 harbored mcr-9-carrying IncHI2-type pBSI034-MCR9 and blaNDM-1-carrying IncX3-type pBSI034-NDM1. The 278,517 bp pBSI034-MCR9 carried mcr-9 along with the other 19 resistance genes. mcr-9 was flanked by IS 903B (1057 bp) and IS 26 (820 bp) in the same orientation. In addition to resistance genes, strain BSI034 also carried a chromosome-located Yersinia high-pathogenicity island, which harbored genes of yersiniabactin biosynthesis operon ybtSXQPAUTE, irp1/2, and fyuA.Conclusion: We described the complete genome and mcr-9/blaNDM-1-co-harboring plasmid of E. cloacae from a BSI patient. Notable differences were observed within mosaic modules between pBSI034-MCR9 and other mcr-9-harboring plasmids due to extensive recombination via horizontal gene transfer.Keywords: MDR, mcr-9, colistin, virulence genes

Lan-Lan Zhong,1,2,* Qian Zhou,3,* Cui-Yan Tan,3,* Adam P Roberts,4,5 Mohamed Abd El-Gawad El-Sayed Ahmed,1–2,6 Guanping Chen,1,2 Min Dai,7 Fan Yang,8 Yong Xia,9 Kang Liao,10 Yingjian Liang,3 Yongqiang Yang,1,11 Siyuan Feng,1,2 Xiaobin Zheng,3,* Guo-Bao Tian1,2,*1Program in Pathobiology, The Fifth Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangdong 519000, People’s Republic of China; 2Ministry of Education, Key Laboratory of Tropical Diseases Control, Sun Yat-sen University, Guangzhou 510080, People’s Republic of China; 3Department of Respiratory Medicine, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai 519000, People’s Republic of China; 4Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, L3 5QA, UK; 5Centre for Drugs and Diagnostics, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK; 6Department of Microbiology and Immunology, Faculty of Pharmaceutical Sciences and Drug Manufacturing, Misr University for Science and Technology (MUST), Cairo, Egypt; 7School of Laboratory Medicine, Chengdu Medical College, Chengdu 610500, People’s Republic of China; 8Department of Microbiology, School of Basic Medical Science, Xinxiang Medical University, Xinxiang 453003, People’s Republic of China; 9Department of Clinical Laboratory Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou 510150, People’s Republic of China; 10Department of Clinical Laboratory, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510080, People’s Republic of China; 11School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Guangzhou 510006, People’s Republic of China*These authors contributed equally to this workPurpose: The discovery of the plasmid-mediated colistin resistance genes, mcr, revealed a mechanism of transmission of colistin resistance, which is a major, global public health concern especially among individuals infected with carbapenem-resistant Gram-negative bacteria. To monitor the spread and epidemiology of mcr genes, a convenient and reliable method to detect mcr genes in clinical isolates is needed, especially in the primary care institutions. This study aimed to establish a restriction endonuclease-based multiplex loop-mediated isothermal amplification (multi-LAMP) assay to detect mcr genes (mcr-1 to mcr-5) harbored by colistin-resistant bacteria.Methods: A triple-LAMP assay for mcr-1, mcr-3, and mcr-4 and a double-LAMP assay for mcr-2 and mcr-5 were established. The sensitivity and specificity of the LAMP reactions were determined via electrophoresis and visual detection.Results: The sensitivity of the LAMP assay was 10-fold greater than that of PCR, with high specificity among the screened primers. Specific mcr genes were distinguished in accordance with band numbers and the fragment length of the digested LAMP amplification products. Furthermore, the LAMP assay was confirmed as a rapid and reliable diagnostic technique upon application for clinical samples, and the results were consistent with those of conventional PCR assay.Conclusion: The multi-LAMP assay is a potentially promising method to detect mcr genes and will, if implemented, help prevent infections by drug-resistant bacteria in primary-care hospitals due to rapid and reliable surveillance. To our knowledge, this is the first study to report the application of LAMP to detect mcr-2 to mcr-5 genes and the first time that multi-LAMP has been applied to detect mcr genes.Keywords: mcr genes, colistin resistance, multi-LAMP, rapid detection, enzyme digestion

Fan Yang,1,* Cong Shen,2,3,* Xiaobin Zheng,4 Yan Liu,5 Mohamed Abd El-Gawad El-Sayed Ahmed,2,3,6 Zihan Zhao,2,3 Kang Liao,7 Yaling Shi,8 Xin Guo,2,3 Ruoxuan Zhong,2,3 Zhimin Xu,2,3 Guo-Bao Tian2,3 1Department of Microbiology, School of Basic Medical Science, Xinxiang Medical University, Xinxiang, China; 2Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China; 3Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China; 4Department of Respiratory Medicine, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China; 5Department of Laboratory, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China; 6Department of Microbiology and Immunology, Faculty of Pharmacy, Misr University for Science and Technology (MUST), Cairo, 6th of October City, Egypt; 7Department of Clinical Laboratory, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China; 8Department of Clinical Laboratory, Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, China *These authors contributed equally to this work Background: As a result of the growing prevalence of the plasmid-mediated mobile colistin resistance gene mcr-1 among Gram-negative bacteria, the surveillance of mcr-1 has been globally applied. In our study, we aimed to shed light on the possibility of transmission of mcr-1-resistant isolates through market retail fruits. Methods and results: Herein, 133 different fruit surface samples were collected and screened for the different MCR variants (mcr-1 to mcr-8) using PCR and confirmed with sequencing. We identify for the first time mcr-1-carrying Escherichia coli and Klebsiella pneumoniae from market retail fruits in Guangzhou, China. Minimum inhibitory concentrations were detected by the broth microdilution method. Liquid mating was performed to check the transferability of the mcr-1 gene. Pulsed field gel electrophoresis analysis of S1 nuclease-digested DNA and Southern blotting were performed to check the location of the mcr-1 gene. Then, whole-genome sequencing and in silico multilocus sequence typing analysis were performed. Conclusion: We showed that E. coli GB110 can mediate the spreading of antibiotic resistance genes through the food chain, while K. pneumoniae GB015 was considered to be the progenitor of the most successful multidrug-resistant clone. Since fruits are usually consumed fresh, this may serve as a direct source of mcr-1-producing bacteria in humans that requires prompt surveillance and intervention to limit the spread of resistance. Keywords: colistin, mcr-1, Escherichia coli, Klebsiella pneumoniae, fruit

Yingjian Liang,1,* Changli Tu,1,* Cuiyan Tan,1 Mohamed Abd El-Gawad El-Sayed Ahmed,2,3,4 Min Dai,5 Yong Xia,6 Yan Liu,7 Lan-Lan Zhong,2,3 Cong Shen,2,3 Guanping Chen,2,3 Guo-Bao Tian,2,3 Jing Liu,1 Xiaobin Zheng1 1Department of Respiratory Medicine, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China; 2Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China; 3Key Laboratory of Tropical Diseases Control, Sun Yat-sen University, Ministry of Education, Guangzhou, China; 4Department of Microbiology and Immunology, Faculty of Pharmacy, Misr University for Science and Technology (MUST), 6th of October City, Egypt; 5School of Laboratory Medicine, Chengdu Medical College, Chengdu, China; 6Department of Clinical Laboratory Medicine, Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China; 7Clinical laboratory, The Fifth Affiliated Hospital of Sun Yat-Sen University, Zhuhai, China *These authors contributed equally to this work Purpose: The main objective of this study was to decipher the prevalence, antimicrobial resistance, major virulence genes and the molecular characteristics of methicillin-resistant Staphylococcus aureus (MRSA) isolated from different clinical sources in southern China.Materials and methods: The present study was performed on 187 non-duplicate S. aureus clinical isolates collected from three tertiary hospitals in Guangdong Province, China, 2010–2016. Antimicrobial susceptibility testing was performed by the disk diffusion method and by measuring the minimum inhibitory concentration. Screening for resistance and virulence genes was performed. Clonal relatedness was determined using various molecular typing methods such as multilocus sequence typing, spa and staphylococcal chromosomal cassette mec (SCCmec) typing. Whole genome sequencing was performed for three selected isolates.Results: Out of 187 isolates, 103 (55%) were identified as MRSA. The highest prevalence rate was found among the skin and soft tissue infection (SSTI) samples (58/103), followed by sputum samples (25/103), blood stream infection samples (15/103) and others (5/103). Antimicrobial susceptibility results revealed high resistance rates for erythromycin (64.1%), clindamycin (48.5%), gentamicin (36.9%) and ciprofloxacin (33.98%). All isolates were susceptible to vancomycin. Resistance genes and mutation detected were as follows: aac(6’)-aph(2”) (24.3%), dfrG (10.7%), rpoB (21.4%), cfr (0%), fexA (1.94%), gyrA (35.92%), gyrB (0.97%), grlA (20.4%), grlB (10.68%), ermA (21.4%), ermB (18.44%), ermC (21.4%) and lnuA (18.44%). Profiling of virulence genes revealed the following: sea (11.7%), seb (21.4%), sec (0.97%), sed (0.97%), hla (86.41%), hlb (17.48%), hlg (10.68%), hld (53.4%), Tsst-1 (3.9%) and pvl (27.2%). Clonal relatedness showed that ST239-SCCmecA III-t37 clone was the most prevalent clone.Conclusion: Our study elucidated the prevalence, antibiotic resistance, pathogenicity and molecular characteristics of MRSA isolated from various clinical sources in Guangdong, China. We found that the infectious rate of MRSA was higher among SSTI than other sources. The most predominant genotype was ST239-SCCmecA III-t37 clone, indicating that ST239-t30 clone which was previously predominant had been replaced by a new clone. Keywords: MRSA, antibiotic resistance, resistance genes, virulence factors, molecular typing, whole genome sequencing

Siyuan Feng,1,2,* Cong Shen,1,2,* Hongtao Chen,3 Xiaobin Zheng,4 Yong Xia,5 Lan-Lan Zhong,1,2 Xi Huang,6 Xinwei Wu,7 Guo-Bao Tian1,2 1Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China; 2Key Laboratory of Tropical Diseases Control, Sun Yat-sen University, Ministry of Education, Guangzhou, China; 3Department of Laboratory, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China; 4Department of Respiratory Medicine, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China; 5Department of Clinical Laboratory Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China; 6Program of Pathobiology and Immunology, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China; 7Department of Microbiology, Guangzhou Center for Disease Control and Prevention, Guangzhou, China *These authors contributed equally to this work Abstract: Colistin is increasingly used as an antibiotic of last resort for treating carbapenem-resistant Enterobacteriaceae. Mobile colistin resistance gene mcr-1 has been increasingly reported in Enterobacteriaceae around the world. Of particular concern is the spread of mcr-1 into carbapenemase-producing Enterobacteriaceae, which results in highly drug-resistant strains that are potentially untreatable. Notably, such mcr-1-carrying isolates harboring carbapenemase genes have been reported in animals and patients with infection. Here, we report an Escherichia coli strain carrying co-transferable mcr-1-harboring IncX4 and blaNDM-5-harboring IncX3 plasmids, which was recovered in the context of fecal colonization. Keywords: Escherichia coli, MCR-1, NDM-5, co-production

Background: Bloodstream infection (BSI) caused by carbapenem-resistant Enterobacteriaceae are potentially life-threatening related to poorer outcomes. Colistin is considered one of the last-resort treatments against human infections caused by multidrug-resistant (MDR) Gram-negative bacteria. Therefore, emergence of strains from the blood that co-harboring mcr and carbapenem resistance genes were considered as a serious problem., Purpose: In this study, two mcr-9 -harboring MDR Enterobacter cloacae isolates BSI034 and BSI072 recovered from BSI patients were identified, one of which co-harbored mcr-9 and bla NDM-1. The genetic characteristics of the MDR plasmid needed to be clarified., Methods: S1-PFGE and Southern blotting were conducted to determine the location of mcr-9 . Whole-genome sequencing was performed to obtain the complete genome and plasmid sequences. The resistome and virulence genes of the strains, accompanied by the genetic characteristics of mcr-9 - and bla NDM-1 -harboring plasmids, were analyzed., Results: Whole-genome sequencing showed that BSI034 harbored mcr-9 -carrying IncHI2-type pBSI034-MCR9 and bla NDM-1 -carrying IncX3-type pBSI034-NDM1. The 278,517 bp pBSI034-MCR9 carried mcr-9 along with the other 19 resistance genes. mcr-9 was flanked by IS 903B (1057 bp) and IS 26 (820 bp) in the same orientation. In addition to resistance genes, strain BSI034 also carried a chromosome-located Yersinia high-pathogenicity island, which harbored genes of yersiniabactin biosynthesis operon ybtSXQPAUTE, irp1/2 , and fyuA ., Conclusion: We described the complete genome and mcr-9 / bla NDM-1 -co-harboring plasmid of E. cloacae from a BSI patient. Notable differences were observed within mosaic modules between pBSI034-MCR9 and other mcr-9 -harboring plasmids due to extensive recombination via horizontal gene transfer., Competing Interests: The authors report no conflicts of interest in this work., (© 2020 Lin et al.)