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Wang L, Chen H, Liu W, Yang L, Xu Z, Chen D. Resistome and Genome Analysis of an Extensively Drug-Resistant Klebsiella michiganensis KMIB106: Characterization of a Novel KPC Plasmid pB106-1 and a Novel Cointegrate Plasmid pB106-IMP Harboring blaIMP-4 and blaSHV-12. Antibiotics (Basel) 2023; 12:1463. [PMID: 37760759 PMCID: PMC10525660 DOI: 10.3390/antibiotics12091463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 09/07/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
Klebsiella michiganensis is a recently emerging human pathogen causing nosocomial infections. This study aimed to characterize the complete genome sequence of a clinical Klebsiella michiganensis strain KMIB106 which exhibited extensive drug-resistance. The whole genome of the strain was sequenced using PacBio RS III systems and Illumina Nextseq 500. Annotation, transposable elements and resistance gene identification were analyzed by RAST, prokka and Plasmid Finder, respectively. According to the results, KMIB106 was resistant to multiple antimicrobials, including carbapenems, but it remained susceptible to aztreonam. The genome of KMIB106 consisted of a single chromosome and three predicted plasmids. Importantly, a novel KPC plasmid pB106-1 was found to carry the array of resistance genes in a highly different order in its variable regions, including mphA, msrE, mphE, ARR-3, addA16, sul1, dfrA27, tetD and fosA3. Plasmid pB106-2 is a typical IncFII plasmid with no resistant gene. Plasmid pB106-IMP consists of the IncN and IncX3 backbones, and two resistance genes, blaIMP-4 and blaSHV-12, were identified. Our study for the first time reported an extensively drug-resistant Klebsiella michiganensis strain recovered from a child with a respiratory infection in Southern China, which carries three mega plasmids, with pB106-1 firstly identified to carry an array of resistance genes in a distinctive order, and pB106-IMP identified as a novel IncN-IncX3 cointegrate plasmid harboring two resistance genes blaIMP-4 and blaSHV-12.
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Affiliation(s)
- Linjing Wang
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China
| | - Haijun Chen
- Department of Laboratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, China
| | - Wanting Liu
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China
| | - Ling Yang
- Department of Laboratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, China
| | - Zhenbo Xu
- School of Food Science and Engineering, Research Institute for Food Nutrition and Human Health, Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety, Engineering Research Center of Starch and Vegetable Protein Processing Ministry of Education, South China University of Technology, Guangzhou 510640, China
- Department of Laboratory Medicine, The Second Affiliated Hospital of Shantou University Medical College, Shantou 515141, China
| | - Dingqiang Chen
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China
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Yang J, Shan G, Yu G, Wei J, Zhang Q, Su W, Lin Q, Zheng Z, Wu G, Li G, Chang Q, Yuan H, He Y, Chen Y, Zhang Y, Huang H, Hu W, Song R, Weng Y, Li X, Liu S. Whole genome sequencing of multidrug-resistant Proteus mirabilis strain PM1162 recovered from a urinary tract infection in China. J Glob Antimicrob Resist 2023; 33:44-50. [PMID: 36870531 DOI: 10.1016/j.jgar.2023.02.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 01/26/2023] [Accepted: 02/19/2023] [Indexed: 03/06/2023] Open
Abstract
OBJECTIVES Proteus mirabilis is an important opportunistic Gram-negative pathogen. This study reports the whole genome sequence of multidrug-resistant (MDR) P. mirabilis PM1162 and explores its antibiotic resistance genes (ARGs) and their genetic environments. METHODS P. mirabilis PM1162 was isolated from a urinary tract infection in China. Antimicrobial susceptibility was determined, and whole genome sequencing (WGS) was performed. ARGs, insertion sequence (IS) elements, and prophages were identified using ResFinder, ISfinder, and PHASTER software, respectively. Sequence comparisons and map generation were performed using BLAST and Easyfig, respectively. RESULTS On its chromosome, P. mirabilis PM1162 harboured 15 ARGs, including cat, tet(J), blaCTX-M-14 (three copies), aph(3')-Ia, qnrB4, blaDHA-1, qacE, sul1, armA, msr(E), mph(E), aadA1, and dfrA1. We focused our analysis on the four related MDR regions: (1) genetic contexts associated with blaCTX-M-14; (2) the prophage containing blaDHA-1, qnrB4, and aph(3')-Ia; (3) genetic environments associated with mph(E), msr(E), armA, sul, and qacE; and (4) the class II integron harbouring dfrA1, sat2, and aadA1. CONCLUSION This study reported the whole genome sequence of MDR P. mirabilis PM1162 and the genetic context of its ARGs. This comprehensive genomic analysis of MDR P. mirabilis PM1162 provides a deeper understanding of its MDR mechanism and elucidates the horizontal spread of its ARGs, thus providing a basis for the containment and treatment of the bacteria.
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Affiliation(s)
- Jing Yang
- Department of Pulmonary and Critical Care Medicine, Zhuhai Hospital affiliated with Jinan University (Zhuhai People's Hospital), Zhuhai, China
| | - Ge Shan
- Department of Urology, Zhuhai People's Hospital (Zhuhai Hospital affiliated with Jinan University), Zhuhai, China
| | - Guangchao Yu
- Department of Clinical Laboratory, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Jie Wei
- Department of Clinical Laboratory, Zhuhai People's Hospital (Zhuhai Hospital affiliated with Jinan University), Zhuhai, China
| | - Qinghuan Zhang
- Department of Clinical Laboratory, Zhuhai People's Hospital (Zhuhai Hospital affiliated with Jinan University), Zhuhai, China
| | - Wen Su
- Zhuhai Precision Medical Center, Zhuhai People's Hospital (Zhuhai Hospital affiliated with Jinan University), Zhuhai, China
| | - Qiuping Lin
- Zhuhai Precision Medical Center, Zhuhai People's Hospital (Zhuhai Hospital affiliated with Jinan University), Zhuhai, China
| | - Zhixiong Zheng
- Zhuhai Precision Medical Center, Zhuhai People's Hospital (Zhuhai Hospital affiliated with Jinan University), Zhuhai, China
| | - Guangliang Wu
- Department of Pharmacy, Zhuhai People's Hospital (Zhuhai Hospital affiliated with Jinan University), Zhuhai, China
| | - Guangtian Li
- Department of Anesthesiology, Zhuhai People's Hospital (Zhuhai Hospital affiliated with Jinan University), Zhuhai, China
| | - Qing Chang
- Medical Department, Hengqin Branch of Zhuhai People's Hospital, Zhuhai, China
| | - Hong Yuan
- Department of Pulmonary and Critical Care Medicine, Zhuhai Hospital affiliated with Jinan University (Zhuhai People's Hospital), Zhuhai, China
| | - Yanju He
- Department of Pulmonary and Critical Care Medicine, Zhuhai Hospital affiliated with Jinan University (Zhuhai People's Hospital), Zhuhai, China
| | - Yanling Chen
- Department of Pulmonary and Critical Care Medicine, Zhuhai Hospital affiliated with Jinan University (Zhuhai People's Hospital), Zhuhai, China
| | - Yi Zhang
- Department of Pulmonary and Critical Care Medicine, Zhuhai Hospital affiliated with Jinan University (Zhuhai People's Hospital), Zhuhai, China
| | - Haile Huang
- Department of Pulmonary and Critical Care Medicine, Zhuhai Hospital affiliated with Jinan University (Zhuhai People's Hospital), Zhuhai, China
| | - Wan Hu
- Department of Pulmonary and Critical Care Medicine, Zhuhai Hospital affiliated with Jinan University (Zhuhai People's Hospital), Zhuhai, China
| | - Rongqing Song
- Department of Pulmonary and Critical Care Medicine, Zhuhai Hospital affiliated with Jinan University (Zhuhai People's Hospital), Zhuhai, China
| | - Yuqing Weng
- Department of Pulmonary and Critical Care Medicine, Zhuhai Hospital affiliated with Jinan University (Zhuhai People's Hospital), Zhuhai, China.
| | - Xiaobin Li
- Zhuhai Precision Medical Center, Zhuhai People's Hospital (Zhuhai Hospital affiliated with Jinan University), Zhuhai, China.
| | - Shengming Liu
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Jinan University, Guangzhou, China.
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Dobrindt U, Wami HT, Schmidt-Wieland T, Bertsch D, Oberdorfer K, Hof H. Compared with Cotrimoxazole Nitroxoline Seems to Be a Better Option for the Treatment and Prophylaxis of Urinary Tract Infections Caused by Multidrug-Resistant Uropathogens: An In Vitro Study. Antibiotics (Basel) 2021; 10:645. [PMID: 34071539 PMCID: PMC8230139 DOI: 10.3390/antibiotics10060645] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 05/21/2021] [Accepted: 05/24/2021] [Indexed: 01/17/2023] Open
Abstract
The resistance of uropathogens to various antibiotics is increasing, but nitroxoline remains active in vitro against some relevant multidrug resistant uropathogenic bacteria. E. coli strains, which are among the most common uropathogens, are unanimously susceptible. Thus, nitroxoline is an option for the therapy of urinary tract infections caused by multiresistant bacteria. Since nitroxoline is active against bacteria in biofilms, it will also be effective in patients with indwelling catheters or foreign bodies in the urinary tract. Cotrimoxazole, on the other hand, which, in principle, can also act on bacteria in biofilms, is frequently inactive against multiresistant uropathogens. Based on phenotypic resistance data from a large number of urine isolates, structural characterisation of an MDR plasmid of a recent ST131 uropathogenic E. coli isolate, and publicly available genomic data of resistant enterobacteria, we show that nitroxoline could be used instead of cotrimoxazole for intervention against MDR uropathogens. Particularly in uropathogenic E. coli, but also in other enterobacterial uropathogens, the frequent parallel resistance to different antibiotics due to the accumulation of multiple antibiotic resistance determinants on mobile genetic elements argues for greater consideration of nitroxoline in the treatment of uncomplicated urinary tract infections.
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Affiliation(s)
- Ulrich Dobrindt
- Institut für Hygiene, Universitätsklinikum Münster, 48149 Münster, Germany;
| | - Haleluya T. Wami
- Institut für Hygiene, Universitätsklinikum Münster, 48149 Münster, Germany;
| | - Torsten Schmidt-Wieland
- MVZ Labor Limbach und Kollegen, Im Breitspiel 16, 69126 Heidelberg, Germany; (T.S.-W.); (D.B.); (K.O.); (H.H.)
| | - Daniela Bertsch
- MVZ Labor Limbach und Kollegen, Im Breitspiel 16, 69126 Heidelberg, Germany; (T.S.-W.); (D.B.); (K.O.); (H.H.)
| | - Klaus Oberdorfer
- MVZ Labor Limbach und Kollegen, Im Breitspiel 16, 69126 Heidelberg, Germany; (T.S.-W.); (D.B.); (K.O.); (H.H.)
| | - Herbert Hof
- MVZ Labor Limbach und Kollegen, Im Breitspiel 16, 69126 Heidelberg, Germany; (T.S.-W.); (D.B.); (K.O.); (H.H.)
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Shang D, Zhao H, Xu X, Arunachalam K, Chang J, Bai L, Shi C. Conjugative IncHI2 plasmid harboring novel class 1 integron mediated dissemination of multidrug resistance genes in Salmonella Typhimurium. Food Control 2021. [DOI: 10.1016/j.foodcont.2020.107810] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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5
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Harmer CJ, Pong CH, Hall RM. Structures bounded by directly-oriented members of the IS26 family are pseudo-compound transposons. Plasmid 2020; 111:102530. [DOI: 10.1016/j.plasmid.2020.102530] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 07/23/2020] [Accepted: 08/11/2020] [Indexed: 10/23/2022]
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6
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Nazir A, Zhao Y, Li M, Manzoor R, Tahir RA, Zhang X, Qing H, Tong Y. Structural Genomics of repA, repB 1-Carrying IncFIB Family pA1705- qnrS, P911021- tetA, and P1642- tetA, Multidrug-Resistant Plasmids from Klebsiella pneumoniae. Infect Drug Resist 2020; 13:1889-1903. [PMID: 32606838 PMCID: PMC7319535 DOI: 10.2147/idr.s228704] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 12/26/2019] [Indexed: 12/21/2022] Open
Abstract
Background Multidrug-resistant plasmids carrying replication genes have been widely present in various strains of Klebsiella pneumoniae. RepA and repB1 were found in plasmids belong to the IncFIB, but their detailed structural and genomic characterization was not reported yet. This is the first study that delivers structural and functional insights of repA- and repB1-carrying IncFIB plasmids. Methods Klebsiella pneumoniae strains A1705, 911021, and 1642 were isolated from the human urine samples and bronchoalveolar fluids collected from different hospitals of China. Antibacterial susceptibility and plasmid transfer ability were tested to characterize the resistant phenotypes mediated by the pA1705-qnrS, p911021-tetA, and p1642-tetA. The complete nucleotide sequences of these plasmids were determined through high-throughput sequencing technology and comparative genomic analyses of plasmids belong to the same incompatibility group were executed to extract the genomic variations and features. Results The pA1705-qnrS, p911021-tetA, and p1642-tetA are defined as non-conjugative plasmids, having two replication genes, repA and repB1 associated with IncFIB family, and unknown incompatible group, respectively. Comparative genomic analysis revealed that relatively small backbones of IncFIB plasmids integrated massive accessory module at one “hotspot” that was located between orf312 and repB1. These IncFIB plasmids exhibited the distinct profiles of accessory modules including one or two multidrug-resistant regions, many complete and remnant mobile elements comprising integrons, transposons and insertion sequences. The clusters of resistant genes were recognized in this study against different classes of antibiotics including β-lactam, phenicol, aminoglycoside, tetracycline, quinolone, trimethoprim, sulfonamide, tunicamycin, and macrolide. It has been observed that all resistant genes were located in multidrug resistance regions. Conclusion It is concluded that multidrug-resistant repA and repB1-carrying IncFIB plasmids are a key source to mediate the resistance through mobile elements among Klebsiella pneumoniae. Current findings provide a deep understanding of horizontal gene transfer among plasmids of the IncFIB family via mobile elements that will be utilized in further in vitro studies.
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Affiliation(s)
- Amina Nazir
- Key Laboratory of Molecular Medicine and Biotherapy in the Ministry of Industry and Information Technology, Department of Biology, School of Life Sciences, Beijing Institute of Technology, Beijing, People's Republic of China.,State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, People's Republic of China
| | - Yachao Zhao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, People's Republic of China
| | - Manli Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, People's Republic of China
| | - Rakia Manzoor
- State Key Laboratory of Molecular Development Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, People's Republic of China.,School of Life Science, University of Chinese Academy of Sciences, Beijing 100101, People's Republic of China
| | - Rana Adnan Tahir
- Key Laboratory of Molecular Medicine and Biotherapy in the Ministry of Industry and Information Technology, Department of Biology, School of Life Sciences, Beijing Institute of Technology, Beijing, People's Republic of China
| | - Xianglilan Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, People's Republic of China
| | - Hong Qing
- Key Laboratory of Molecular Medicine and Biotherapy in the Ministry of Industry and Information Technology, Department of Biology, School of Life Sciences, Beijing Institute of Technology, Beijing, People's Republic of China
| | - Yigang Tong
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, People's Republic of China
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Whole Genome Sequencing Analysis of Porcine Faecal Commensal Escherichia coli Carrying Class 1 Integrons from Sows and Their Offspring. Microorganisms 2020; 8:microorganisms8060843. [PMID: 32512857 PMCID: PMC7355456 DOI: 10.3390/microorganisms8060843] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 06/03/2020] [Accepted: 06/03/2020] [Indexed: 12/20/2022] Open
Abstract
Intensive pig production systems often rely on the use of antimicrobials and heavy metal feed additives to maintain animal health and welfare. To gain insight into the carriage of antimicrobial resistance genes (ARGs) in the faecal flora of commercially reared healthy swine, we characterised the genome sequences of 117 porcine commensal E. coli that carried the class 1 integrase gene (intI1+). Isolates were sourced from 42 healthy sows and 126 of their offspring from a commercial breeding operation in Australia in 2017. intI1+ E. coli was detected in 28/42 (67%) sows and 90/126 (71%) piglets. Phylogroup A, particularly clonal complex 10, and phylogroup B1 featured prominently in the study collection. ST10, ST20, ST48 and ST361 were the dominant sequence types. Notably, 113/117 isolates (96%) carried three or more ARGs. Genes encoding resistance to -lactams, aminoglycosides, trimethoprim, sulphonamides, tetracyclines and heavy metals were dominant. ARGs encoding resistance to last-line agents, such as carbapenems and third generation cephalosporins, were not detected. IS26, an insertion sequence noted for its ability to capture and mobilise ARGs, was present in 108/117 (92%) intI1+ isolates, and it played a role in determining class 1 integron structure. Our data shows that healthy Australian pig faeces are an important reservoir of multidrug resistant E. coli that carry genes encoding resistance to multiple first-generation antibiotics and virulence-associated genes.
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Truncated Class 1 Integron Gene Cassette Arrays Contribute to Antimicrobial Resistance of Diarrheagenic Escherichia coli. BIOMED RESEARCH INTERNATIONAL 2020; 2020:4908189. [PMID: 32090095 PMCID: PMC7013361 DOI: 10.1155/2020/4908189] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 12/30/2019] [Indexed: 11/17/2022]
Abstract
Class 1 integrons (c1-integrons) are associated with multidrug resistance in diarrheagenic Escherichia coli (DEC). However, little is known about gene cassettes located within these c1-integrons, particularly truncated c1-integrons, in DEC strains. Therefore, the aims of the present study were to reveal the relationship between antimicrobial resistance and the presence of truncated c1-integrons in DEC isolates derived from human stool samples in Japan. A total of 162 human stool-derived DEC isolates from Japan were examined by antimicrobial susceptibility testing, PCR-based gene detection, and next-generation sequencing analyses. Results showed that 44.4% (12/27) of c1-integrons identified in the DEC isolates harbored only intI1 (an element of c1-integrons) and were truncated by IS26, Tn3, or IS1-group insertion sequences. No difference in the frequency of antimicrobial resistance was recorded between intact and truncated c1-integron-positive DEC isolates. Isolates containing intact/truncated c1-integrons, particularly enteroaggregative E. coli isolates, were resistant to a greater number of antimicrobials than isolates without c1-integrons. aadA and dfrA were the most prevalent antimicrobial resistance genes in the intact/truncated c1-integrons examined in this study. Therefore, gene cassettes located within these intact/truncated c1-integrons may only play a limited role in conferring antimicrobial resistance among DEC. However, DEC harboring truncated c1-integrons may be resistant to a greater number of antimicrobials than c1-integron-negative DEC, similar to strains harboring intact c1-integrons.
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Spreading of extended-spectrum β-lactamase-producing Escherichia coli ST131 and Klebsiella pneumoniae ST11 in patients with pneumonia: a molecular epidemiological study. Chin Med J (Engl) 2020; 132:1894-1902. [PMID: 31408445 PMCID: PMC6708689 DOI: 10.1097/cm9.0000000000000368] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Supplemental Digital Content is available in the text Background: Extended-spectrum β-lactamase (ESBL)-producing Escherichia coli (E. coli) and Klebsiella pneumoniae (K. pneumoniae) are the important pathogens causing pneumonia. This study aimed to investigate the clinical characteristics and molecular epidemiology of ESBL-producing E. coli and K. pneumoniae causing pneumonia at a large teaching hospital in China. Methods: We collected patient's clinical data and ESBL-producing E. coli and K. pneumoniae strains causing pneumonia (from December 2015 to June 2016) at a hospital in Wuhan. The susceptibilities, multi-locus sequence typing, homologous analysis, ESBL genes by polymerase chain reaction and sequencing were determined. Results: A total of 59 ESBL-producing strains (31 E. coli and 28 K. pneumoniae) isolated from patients with pneumonia were analyzed. The majority of strains were isolated from patients were with hospital-acquired pneumonia (37/59, 62.7%), followed by community-acquired pneumonia (13/59, 22.0%), and ventilator-related pneumonia (9/59, 15.3%). The E. coli ST131 (9 isolates, 29.0%) and K. pneumoniae ST11 (5 isolates, 17.9%) were the predominant sub-types. The most prevalent ESBL gene was CTX-M-14, followed by SHV-77, CTX-M-3, SHV-11, and CTX-M-27. At least 33 (55.9%) of the ESBL-producing strains carried two or more ESBL genes. The ISEcp1 and IS26 were found upstream of all blaCTX-M (CTX-Ms) and of most blaSHV (SHVs) (57.6%), respectively. Moreover, three ESBL-producing K. pneumoniae ST11 strains which were resistant to carbapenems carried the blaNDM-1 and blaKPC-2, two of which also bearing blaOXA-48 were resistant to all antibiotics (including Tigecycline). Conclusions: Hospital-acquired pneumonia is more likely correlated with ESBL-producing E. coli and K. pneumoniae. ESBL-producing E. coli ST131 and multi-drug resistance ESBL-producing, as well as New Delhi metallo-β-lactamase-1 (NDM-1) and Klebsiella pneumoniae carbapenemases-2 (KPC-2) bearing K. pneumoniae ST11 are spreading in patients with pneumonia in hospital.
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Roy Chowdhury P, McKinnon J, Liu M, Djordjevic SP. Multidrug Resistant Uropathogenic Escherichia coli ST405 With a Novel, Composite IS 26 Transposon in a Unique Chromosomal Location. Front Microbiol 2019; 9:3212. [PMID: 30671039 PMCID: PMC6331395 DOI: 10.3389/fmicb.2018.03212] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 12/11/2018] [Indexed: 11/13/2022] Open
Abstract
Escherichia coli ST405 is an emerging urosepsis pathogen, noted for carriage of blaCTX-M, blaNDM, and a repertoire of virulence genes comparable with O25b:H4-ST131. Extraintestinal and multidrug resistant E. coli ST405 are poorly studied in Australia. Here we determined the genome sequence of a uropathogenic, multiple drug resistant E. coli ST405 (strain 2009-27) from the mid-stream urine of a hospital patient in Sydney, Australia, using a combination of Illumina and SMRT sequencing. The genome of strain 2009-27 assembled into two unitigs; a chromosome comprising 5,287,472 bp and an IncB/O plasmid, pSDJ2009-27, of 89,176 bp. In silico and phenotypic analyses showed that strain 2009-27 is a serotype O102:H6, phylogroup D ST405 resistant to ampicillin, azithromycin, kanamycin, streptomycin, trimethoprim, and sulphafurazole. The genes encoding resistance to these antibiotics reside within a novel, mobile IS26-flanked transposon, identified here as Tn6242, in the chromosomal gene yjdA. Tn6242 comprises four modules that each carries resistance genes flanked by IS26, including a class 1 integron with dfrA17 and aadA5 gene cassettes, a variant of Tn6029, and mphA. We exploited unique genetic signatures located within Tn6242 to identify strains of ST405 from Danish patients that also carry the transposon in the same chromosomal location. The acquisition of Tn6242 into yjdA in ST405 is significant because it (i) is vertically inheritable; (ii) represents a reservoir of resistance genes that can transpose onto resident/circulating plasmids; and (iii) is a site for the capture of further IS26-associated resistance gene cargo.
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Affiliation(s)
- Piklu Roy Chowdhury
- The ithree Institute, University of Technology Sydney, Ultimo, NSW, Australia.,NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Macarthur, NSW, Australia
| | - Jessica McKinnon
- The ithree Institute, University of Technology Sydney, Ultimo, NSW, Australia
| | - Michael Liu
- The ithree Institute, University of Technology Sydney, Ultimo, NSW, Australia
| | - Steven P Djordjevic
- The ithree Institute, University of Technology Sydney, Ultimo, NSW, Australia
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Ku YH, Lee MF, Chuang YC, Yu WL. Detection of Plasmid-Mediated β-Lactamase Genes and Emergence of a Novel AmpC (CMH-1) in Enterobacter cloacae at a Medical Center in Southern Taiwan. J Clin Med 2018; 8:jcm8010008. [PMID: 30577544 PMCID: PMC6352282 DOI: 10.3390/jcm8010008] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 12/17/2018] [Accepted: 12/18/2018] [Indexed: 12/03/2022] Open
Abstract
The plasmid-mediated extended-spectrum β-lactamases (ESBLs) and AmpC β-lactamases in Enterobacter spp. have increasingly been reported. In this study, we investigated the prevalence of the plasmid-mediated β-lactamases in Enterobacter cloacae from bloodstream isolates at a medical center in southern Taiwan. ESBL and ampC genes were detected by PCRs and DNA sequencing. Conjugation experiments were conducted to confirm the transferability of the genetic resistance trait. Among 41 non-repetitive blood isolates of cefuroxime-resistant E. cloacae, eight isolates exhibited ESBL phenotype confirmed by double-disk synergistic tests. Nearly all the strains were susceptible to carbapenems. The prevalence rate of the plasmid-mediated blaampC genes was 73% (30/41), including one blaDHA-1, one blaMIR-6, two novel blaCMH-1 genes and other blaACT-like genes. Coexistence of plasmid-mediated blaACT and ESBL genes (10 with blaSHV-12 and one with blaCTX-M-3) was observed. Successful transmissions of the blaACT and blaCMH-1 were demonstrated in some transconjugants. The inducible or derepressed CMH-1 had expanded activity of isolates versus ceftazidime. Enterobacterial repetitive intergenic consensus (ERIC)-PCR analysis and pulsotype showed distinct patterns suggesting non-clonal relationship. In conclusion, plasmid-mediated blaACT-likeampC genes in E. cloacae isolates have been highly prevalent in southern Taiwan and may continue genetic evolution, contributing to the complexities in antibiotic-resistant mechanisms.
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Affiliation(s)
- Yee-Huang Ku
- Division of Infectious Disease, Department of Internal Medicine, Chi Mei Medical Center-Liouying, Tainan 710, Taiwan.
| | - Mei-Feng Lee
- Laboratory of Environmental Health, Research Center of Humanities and Technology, National University of Kaohsiung, Kaohsiung 811, Taiwan.
| | - Yin-Ching Chuang
- Department of Medical Research, Chi Mei Medical Center, Tainan 710, Taiwan.
| | - Wen-Liang Yu
- Department of Intensive Care Medicine, Chi Mei Medical Center, Tainan 710, Taiwan.
- Department of Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei 110, Taiwan.
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Chen CY, Hsieh PH, Chang CY, Yang ST, Chen YH, Chang K, Lu PL. Molecular epidemiology of the emerging ceftriaxone resistant non-typhoidal Salmonella in southern Taiwan. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2018; 52:289-296. [PMID: 30201133 DOI: 10.1016/j.jmii.2018.08.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Revised: 08/08/2018] [Accepted: 08/15/2018] [Indexed: 11/25/2022]
Abstract
BACKGROUND/PURPOSE The increasing trend of ceftriaxone resistant non-typhoidal Salmonella (NTS) worldwide is of serious concern, however, data is lacked in southern Taiwan. METHODS Salmonella isolates were collected at a regional hospital in Kaohsiung during 2004-2013. Ceftriaxone resistant NTS isolates were further characterized for beta-lactamases, typed by pulsed field gel electrophoresis (PFGE), multilocus sequence typing (MLST) and their plasmids were analyzed by PCR replicon typing and plasmid mutilocus sequence typing. RESULTS Among 528 NTS isolates, the most common serogroup is serogroup B (44.9%), followed by serogroup D, and serogroup C. Eleven (2.1%) isolates were resistant to ceftriaxone and were distributed in three peak periods (2010, 2011, and 2013). PFGE and MLST revealed the ten serogroup B isolates were of two clones. Beta-lactamase genes were detected in 10 of the 11 isolates, including CMY-2 (5 isolates), TEM-1 (2), CTX-M-14 (1), and 2 isolates carried both TEM-1 and CMY-2. Plasmid incompatibility types were identified in 9 (81.8%) isolates; three were IncI1, three was IncHI2, one was IncFIB and two had both replicons of IncI1 and IncHI2. The only ESBL gene blaCTM-X-14 was found in an isolate with plasmid belonged to IncHI2, which has not been reported in NTS in Taiwan before. Most MLST types and plasmid MLST types of NTS isolates in this study are different from those in northern Taiwan. CONCLUSION Though clonal spread of ceftriaxone resistant NTS was suggested by PFGE and MLST, plasmid characterization and beta-lactamase detection revealed their plasmid types and beta-lactamase types were different.
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Affiliation(s)
- Chi-Yu Chen
- Division of Infectious Diseases, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan; Department of Internal Medicine, Kaohsiung Municipal Hsiao-Kang Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan; Department of Emergency Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Ping-Hsuan Hsieh
- Department of Laboratory Medicine, E-DA Hospital, Kaohsiung, Taiwan; Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Chung-Yu Chang
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Department of Microbiology and Immunology, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Shan-Tzu Yang
- Department of Internal Medicine, Kaohsiung Municipal Hsiao-Kang Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Yen-Hsu Chen
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Department of Internal Medicine, Kaohsiung Municipal Ta-Tung Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Ko Chang
- Division of Infectious Diseases, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan; Department of Internal Medicine, Kaohsiung Municipal Hsiao-Kang Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan.
| | - Po-Liang Lu
- Division of Infectious Diseases, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan; School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Division of Clinical Microbiology, Department of Laboratory Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
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Liakopoulos A, Mevius D, Ceccarelli D. A Review of SHV Extended-Spectrum β-Lactamases: Neglected Yet Ubiquitous. Front Microbiol 2016; 7:1374. [PMID: 27656166 PMCID: PMC5011133 DOI: 10.3389/fmicb.2016.01374] [Citation(s) in RCA: 119] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 08/19/2016] [Indexed: 12/29/2022] Open
Abstract
β-lactamases are the primary cause of resistance to β-lactams among members of the family Enterobacteriaceae. SHV enzymes have emerged in Enterobacteriaceae causing infections in health care in the last decades of the Twentieth century, and they are now observed in isolates in different epidemiological settings both in human, animal and the environment. Likely originated from a chromosomal penicillinase of Klebsiella pneumoniae, SHV β-lactamases currently encompass a large number of allelic variants including extended-spectrum β-lactamases (ESBL), non-ESBL and several not classified variants. SHV enzymes have evolved from a narrow- to an extended-spectrum of hydrolyzing activity, including monobactams and carbapenems, as a result of amino acid changes that altered the configuration around the active site of the β -lactamases. SHV-ESBLs are usually encoded by self-transmissible plasmids that frequently carry resistance genes to other drug classes and have become widespread throughout the world in several Enterobacteriaceae, emphasizing their clinical significance.
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Affiliation(s)
- Apostolos Liakopoulos
- Department of Bacteriology and Epidemiology, Central Veterinary Institute of Wageningen UR Lelystad, Netherlands
| | - Dik Mevius
- Department of Bacteriology and Epidemiology, Central Veterinary Institute of Wageningen URLelystad, Netherlands; Faculty of Veterinary Medicine, Utrecht UniversityUtrecht, Netherlands
| | - Daniela Ceccarelli
- Department of Bacteriology and Epidemiology, Central Veterinary Institute of Wageningen UR Lelystad, Netherlands
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