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https://www.readbyqxmd.com/read/29867897/the-use-of-a-combined-bioinformatics-approach-to-locate-antibiotic-resistance-genes-on-plasmids-from-whole-genome-sequences-of-salmonella-enterica-serovars-from-humans-in-ghana
#1
Egle Kudirkiene, Linda A Andoh, Shahana Ahmed, Ana Herrero-Fresno, Anders Dalsgaard, Kwasi Obiri-Danso, John E Olsen
In the current study, we identified plasmids carrying antimicrobial resistance genes in draft whole genome sequences of 16 selected Salmonella enterica isolates representing six different serovars from humans in Ghana. The plasmids and the location of resistance genes in the genomes were predicted using a combination of PlasmidFinder, ResFinder, plasmidSPAdes and BLAST genomic analysis tools. Subsequently, S1-PFGE was employed for analysis of plasmid profiles. Whole genome sequencing confirmed the presence of antimicrobial resistance genes in Salmonella isolates showing multidrug resistance phenotypically...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29778206/occurrence-and-characterisation-of-esbl-encoding-plasmids-among-escherichia-coli-isolates-from-fresh-vegetables
#2
Christin Freitag, G B Michael, Jun Li, Kristina Kadlec, Yang Wang, Melanie Hassel, Stefan Schwarz
Extended-spectrum β-lactamase (ESBL)-producing Escherichia coli isolates have been increasingly reported in different reservoirs. The aims of this study were to investigate the presence of ESBL-producing E. coli in fresh vegetables and to characterise their ESBL gene-carrying plasmids. Among the 245 samples from vegetables investigated during 2011-2013, seven putative ESBL-producing E. coli (salad n = 2, sprouts n = 5) were found. They were subjected to ESBL phenotypic confirmatory tests, detection/sequencing of ESBL genes, antimicrobial susceptibility testing (AST), phylotyping, XbaI-macrorestriction analysis, multilocus sequence typing and transformation...
June 2018: Veterinary Microbiology
https://www.readbyqxmd.com/read/29755416/complete-genomic-analysis-of-a-salmonella-enterica-serovar-typhimurium-isolate-cultured-from-ready-to-eat-pork-in-china-carrying-one-large-plasmid-containing-mcr-1
#3
Wei Wang, Zulqarnain Baloch, Mingyuan Zou, Yinping Dong, Zixin Peng, Yujie Hu, Jin Xu, Nafeesa Yasmeen, Fengqin Li, Séamus Fanning
One mcr-1 -carrying ST34-type Salmonella Typhimurium WW012 was cultured from 3,200 ready-to-eat (RTE) pork samples in 2014 in China. Broth dilution method was applied to obtain the antimicrobial susceptibility of Salmonella Typhimurium WW012. Broth matting assays were carried out to detect transferability of this phenotype and whole-genome sequencing was performed to analyze its genomic characteristic. Thirty out of 3,200 RTE samples were positive for Salmonella and the three most frequent serotypes were identified as S ...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29700006/erratum-for-fang-et-al-high-genetic-plasticity-in-multidrug-resistant-sequence-type-3-inchi2-plasmids-revealed-by-sequence-comparison-and-phylogenetic-analysis
#4
Liang-Xing Fang, Xing-Ping Li, Guo-Hui Deng, Shu-Min Li, Run-Shi Yang, Zuo-Wei Wu, Xiao-Ping Liao, Jian Sun, Ya-Hong Liu
No abstract text is available yet for this article.
May 2018: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/29609544/detection-of-ctx-m-15-harboring-escherichia-coli-isolated-from-wild-birds-in-tunisia
#5
Houssem Ben Yahia, Rym Ben Sallem, Ghassan Tayh, Naouel Klibi, Insaf Ben Amor, Haythem Gharsa, Abdellatif Boudabbous, Karim Ben Slama
BACKGROUND: The spreading of antibiotic resistant bacteria is becoming nowadays an alarming threat to human and animal health. There is increasing evidence showing that wild birds could significantly contribute to the transmission and spreading of drug-resistant bacteria. However, data for antimicrobial resistance in wild birds remain scarce, especially throughout Africa. The aims of this investigation were to analyze the prevalence of ESBL-producing E. coli in faecal samples of wild birds in Tunisia and to characterize the recovered isolates...
April 2, 2018: BMC Microbiology
https://www.readbyqxmd.com/read/29535696/fitness-advantage-of-mcr-1-bearing-inci2-and-incx4-plasmids-in-vitro
#6
Renjie Wu, Ling-Xian Yi, Lin-Feng Yu, Jing Wang, Yiyun Liu, Xiaojie Chen, Luchao Lv, Jun Yang, Jian-Hua Liu
The objective of this study was to assess the impact of diverse plasmids bearing colistin resistance gene mcr-1 on host fitness. Forty-seven commensal E. coli isolates recovered from the pig farm where mcr-1 was first identified were screened for mcr-1. mcr-1 -bearing plasmids were characterized by sequencing. The fitness impact of mcr-1 -bearing plasmids was evaluated by in vitro competition assays. Twenty-seven (57.5%) E. coli isolates were positive for mcr-1 . The mcr-1 genes were mainly located on plasmids belonging to IncI2 ( n = 5), IncX4 ( n = 11), IncHI2/ST3 ( n = 8), IncFII ( n = 2), and IncY ( n = 2)...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29437633/high-genetic-plasticity-in-multidrug-resistant-sequence-type-3-inchi2-plasmids-revealed-by-sequence-comparison-and-phylogenetic-analysis
#7
Liang-Xing Fang, Xing-Ping Li, Guo-Hui Deng, Shu-Min Li, Run-Shi Yang, Zuo-Wei Wu, Xiao-Ping Liao, Jian Sun, Ya-Hong Liu
We report a novel fusion plasmid, pP2-3T, cointegrating sequence type 3 (ST3)-IncHI2 with an IncFII plasmid backbone mediating multidrug resistance (MDR) and virulence. Phylogenetic analysis and comparative genomics revealed that pP2-3T and other MDR ST3-IncHI2 plasmids clustered together, representing a unique IncHI2 lineage that exhibited high conservation in backbones of plasmids but possessed highly genetic plasticity in various regions by acquiring numerous antibiotic resistance genes and fusing with other plasmids...
April 2018: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/29371103/co-occurence-of-mcr-1-in-the-chromosome-and-inchi2-plasmid-persistence-of-colistin-resistance-in-escherichia-coli
#8
Jian Sun, Xing-Ping Li, Liang-Xing Fang, Ruan-Yang Sun, Yu-Zhang He, Jingxia Lin, Xiao-Ping Liao, Youjun Feng, Ya-Hong Liu
Two colistin-resistant Escherichia coli strains were characterized, which are FS13Z2S and FS3Z6C possessing chromosome encoded mcr-1 isolated from swine. Whole genome sequencing revealed that mcr-1 was in triplicate in the chromosome with another copy encoded on a pHNSHP45-2-like IncHI2 plasmid in strain FS13Z2S, whereas in strain FS3Z6C, only one copy mcr-1 was inserted in chromosome. It seems likely that the triplication of chromosome copies of mcr-1 in FS13Z2S is due to intra-molecular transposition events via a composite transposon containing a mcr-1 cassette bracketed by two copies of ISApl1, and the pap2 gene at the insertion site was truncated by an IS1294-like element...
January 22, 2018: International Journal of Antimicrobial Agents
https://www.readbyqxmd.com/read/29311089/molecular-characterization-of-imp-1-producing-enterobacter-cloacae-complex-isolates-in-tokyo
#9
Kotaro Aoki, Sohei Harada, Koji Yahara, Yoshikazu Ishii, Daisuke Motooka, Shota Nakamura, Yukihiro Akeda, Tetsuya Iida, Kazunori Tomono, Satoshi Iwata, Kyoji Moriya, Kazuhiro Tateda
Although KPC enzymes are most common among carbapenemases produced by Enterobacter cloacae complex globally, the epidemiology varies from one country to another. While previous studies have suggested that IMP enzymes are most common in Japan, detailed analysis has been scarce thus far. Here, we carried out a molecular epidemiological study and plasmid analysis of IMP-1-producing E. cloacae complex isolates collected from three hospitals in central Tokyo using whole-genome sequencing. Seventy-one isolates were classified into several sequence types (STs), and 49 isolates were identified as Enterobacter hormaechei ST78...
March 2018: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/29180279/impact-of-the-colistin-resistance-gene-mcr-1-on-bacterial-fitness
#10
Manuela Tietgen, Torsten Semmler, Sara Riedel-Christ, Volkhard A J Kempf, Antonio Molinaro, Christa Ewers, Stephan Göttig
A Klebsiella pneumoniae isolate harbouring a 217 kb IncHI2-type plasmid (pKP2442) encoding the colistin resistance gene mcr-1 was isolated from a leukaemia patient. pKP2442 was mobilised by intragenus and intergenus transconjugation from the clinical isolate to Escherichia coli J53 (transconjugation frequency 6.86 × 10-8  ± 5.57 × 10-8 ) and K. pneumoniae PRZ (transconjugation frequency 4.04 × 10-8  ± 3.03 × 10-8 ), respectively. Since acquisition of resistance determinants often results in a loss of fitness, the impact of mcr-1 on the fitness of E...
April 2018: International Journal of Antimicrobial Agents
https://www.readbyqxmd.com/read/29148380/high-rate-of-mcr-1-producing-escherichia-coli-and-klebsiella-pneumoniae-among-pigs-portugal
#11
Nicolas Kieffer, Marta Aires-de-Sousa, Patrice Nordmann, Laurent Poirel
The mcr-1 (mobile colistin resistance 1) gene, which encodes phosphoethanolamine transferase, has been recently identified as a source of acquired resistance to polymyxins in Escherichia coli. Using the SuperPolymyxin selective medium, we prospectively screened 100 pigs at 2 farms in Portugal for polymyxin-resistant Enterobacteriaceae and recovered 98 plasmid-mediated MCR-1-producing isolates. Most isolates corresponded to nonclonally related E. coli belonging to many sequence types; we also found 2 Klebsiella pneumoniae sequence types...
December 2017: Emerging Infectious Diseases
https://www.readbyqxmd.com/read/29127343/global-phylogenetic-analysis-of-escherichia-coli-and-plasmids-carrying-the-mcr-1-gene-indicates-bacterial-diversity-but-plasmid-restriction
#12
Sébastien Matamoros, Jarne M van Hattem, Maris S Arcilla, Niels Willemse, Damian C Melles, John Penders, Trung Nguyen Vinh, Ngo Thi Hoa, Menno D de Jong, Constance Schultsz
To understand the dynamics behind the worldwide spread of the mcr-1 gene, we determined the population structure of Escherichia coli and of mobile genetic elements (MGEs) carrying the mcr-1 gene. After a systematic review of the literature we included 65 E. coli whole genome sequences (WGS), adding 6 recently sequenced travel related isolates, and 312 MLST profiles. We included 219 MGEs described in 7 Enterobacteriaceae species isolated from human, animal and environmental samples. Despite a high overall diversity, 2 lineages were observed in the E...
November 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29118748/remarkable-diversity-of-escherichia-coli-carrying-mcr-1-from-hospital-sewage-with-the-identification-of-two-new-mcr-1-variants
#13
Feifei Zhao, Yu Feng, Xiaoju Lü, Alan McNally, Zhiyong Zong
The plasmid-borne colistin-resistant gene mcr-1 has rapidly become a worldwide public health concern. This study aims to determine the host bacterial strains, plasmids, and genetic contexts of mcr-1 in hospital sewage. A 1-ml hospital sewage sample was cultured. Colistin-resistant bacterial colonies were selected on agar plates and were subjected to whole genome sequencing and subsequent analysis. The transfer of mcr-1 between bacterial strains was tested using conjugation. New variants of mcr-1 were cloned to test the impact of variations on the function of mcr-1 ...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29103683/complete-genetic-analysis-of-a-salmonella-enterica-serovar-indiana-isolate-accompanying-four-plasmids-carrying-mcr-1-esbl-and-other-resistance-genes-in-china
#14
Juan Wang, Xianglei Li, Juan Li, Daniel Hurley, Xue Bai, Zhongyi Yu, Yu Cao, Ellen Wall, Séamus Fanning, Li Bai
One mcr-1-carrying Salmonella enterica serovar Indiana strain D90, was identified from 1320 Salmonella enterica isolates from poultry slaughterhouse in 2012 in China. The objective of this study was to verify the transferability of the mcr-1 gene and also completely characterize the sequence of the strain at the whole-genome level. Broth matting assays were carried out to detect the transferability and whole-genome sequencing (WGS) of S. enterica serovar Indiana D90 was performed using the PacBio RS II system...
October 2017: Veterinary Microbiology
https://www.readbyqxmd.com/read/29091201/is26-mediated-formation-of-a-virulence-and-resistance-plasmid-in-salmonella-enteritidis
#15
Marcus Ho-Yin Wong, Edward Wai-Chi Chan, Sheng Chen
Objectives: To characterize a novel virulence-resistance plasmid pSE380T carried by a Salmonella enterica serotype Enteritidis clinical strain SE380. Methods: The plasmid pSE380T was conjugated to Escherichia coli strain J53 and sequenced by PacBio RSII, followed by subsequent annotation and genetic analysis. Results: Sequence analysis of this plasmid revealed that the entire Salmonella Enteritidis-specific virulence plasmid, pSEN, had been incorporated into an IncHI2 MDR plasmid, which comprises the cephalosporin and fosfomycin resistance determinants blaCTX-M-14 and fosA3...
October 1, 2017: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/29081769/characterization-of-oqxab-in-escherichia-coli-isolates-from-animals-retail-meat-and-human-patients-in-guangzhou-china
#16
Jing Wang, Chan-Ping Zhi, Xiao-Jie Chen, Ze-Wen Guo, Wu-Ling Liu, Juan Luo, Xin-Yi Huang, Li Zeng, Jia-Wei Huang, Ying-Bi Xia, Meng-Ying Yi, Teng Huang, Zhen-Ling Zeng, Jian-Hua Liu
The purpose of this study was to investigate the prevalence and genetic elements of oqxAB among Escherichia coli isolates from animals, retail meat, and humans (patients with infection or colonization) in Guangzhou, China. A total of 1,354 E. coli isolates were screened for oqxAB by PCR. Fifty oqxAB -positive isolates were further characterized by pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST), S1-PFGE, genetic environment analysis, plasmid replicon typing, and plasmid sequencing...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29061750/dissemination-and-characteristics-of-a-novel-plasmid-encoded-carbapenem-hydrolyzing-class-d-%C3%AE-lactamase-oxa-436-found-in-isolates-from-four-patients-at-six-different-hospitals-in-denmark
#17
Ørjan Samuelsen, Frank Hansen, Bettina Aasnæs, Henrik Hasman, Bjarte Aarmo Lund, Hanna-Kirsti S Leiros, Berit Lilje, Jessin Janice, Lotte Jakobsen, Pia Littauer, Lillian M Søes, Barbara J Holzknecht, Leif P Andersen, Marc Stegger, Paal S Andersen, Anette M Hammerum
The diversity of OXA-48-like carbapenemases is continually expanding. In this study, we describe the dissemination and characteristics of a novel carbapenem-hydrolyzing class D β-lactamase (CHDL) named OXA-436. In total, six OXA-436-producing Enterobacteriaceae isolates, including Enterobacter asburiae ( n = 3), Citrobacter freundii ( n = 2), and Klebsiella pneumoniae ( n = 1), were identified in four patients in the period between September 2013 and April 2015. All three species of OXA-436-producing Enterobacteriaceae were found in one patient...
January 2018: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/29051246/complete-genome-sequence-of-a-colistin-resistant-escherichia-coli-strain-harboring-mcr-1-on-an-inchi2-plasmid-in-the-united-states
#18
Victoria L Gilrane, Stephen Lobo, Weihua Huang, Jian Zhuge, Changhong Yin, Donald Chen, Kimberly J Alvarez, Alexandra Budhai, Ilana Nadelman, Nevenka Dimitrova, John T Fallon, Guiqing Wang
We report here the incidental detection and complete genome sequence of a urinary Escherichia coli strain harboring mcr-1 and resistant to colistin in a New York patient returning from Portugal in 2016. This strain, with sequence type 1485 (ST1485), was a non-extended-spectrum beta-lactamase (ESBL) and non-carbapenemase producer and carried the mcr-1 gene on an IncHI2 plasmid.
October 19, 2017: Genome Announcements
https://www.readbyqxmd.com/read/29040419/high-rates-of-human-fecal-carriage-of-mcr-1-positive-multidrug-resistant-enterobacteriaceae-emerge-in-china-in-association-with-successful-plasmid-families
#19
Lan-Lan Zhong, Hang T T Phan, Cong Shen, Karina-Doris Vihta, Anna E Sheppard, Xi Huang, Kun-Jiao Zeng, Hong-Yu Li, Xue-Fei Zhang, Sandip Patil, Derrick W Crook, A Sarah Walker, Yong Xing, Jia-Lin Lin, Lian-Qiang Feng, Yohei Doi, Yong Xia, Nicole Stoesser, Guo-Bao Tian
Background: mcr-1-mediated colistin resistance in Enterobacteriaceae is concerning, as colistin is used in treating multidrug-resistant Enterobacteriaceae infections. We identified trends in human fecal mcr-1-positivity rates and colonization with mcr-1-positive, third-generation cephalosporin-resistant (3GC-R) Enterobacteriaceae in Guangzhou, China, and investigated the genetic contexts of mcr-1 in mcr-1-positive 3GC-R strains. Methods: Fecal samples were collected from in-/out-patients submitting specimens to 3 hospitals (2011-2016)...
February 10, 2018: Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America
https://www.readbyqxmd.com/read/29038441/distinct-mechanisms-of-acquisition-of-mcr-1-bearing-plasmid-by-salmonella-strains-recovered-from-animals-and-food-samples
#20
Mingquan Cui, Jinfei Zhang, Chunping Zhang, Ruichao Li, Edward Wai-Chi Chan, Chenbin Wu, Congming Wu, Sheng Chen
Since the report of its discovery in E. coli in late 2015, the plasmid-mediated colistin resistance gene, mcr-1, has been detected in various bacterial species in clinical setting and various environmental niches. However, the transmission mechanisms of this gene in Salmonella is less defined. In this study, we conducted a comprehensive study to characterize the genetic features of mcr-1-positive Salmonella strains isolated from animals and foods. Our data revealed that Salmonella recovered from animals and food specimens exhibited highly different PFGE patterns, and acquired mcr-1-encoding plasmids via different mechanism...
October 16, 2017: Scientific Reports
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