scholarly journals Molecular Epidemiology of NDM-1-Producing Enterobacteriaceae and Acinetobacter baumannii Isolates from Pakistan

2014 ◽  
Vol 58 (9) ◽  
pp. 5589-5593 ◽  
Author(s):  
Anna L. Sartor ◽  
Muhammad W. Raza ◽  
Shahid A. Abbasi ◽  
Kathryn M. Day ◽  
John D. Perry ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Molecular Epidemiology ◽  
Genetic Relatedness ◽  
Antibiotic Resistance Genes ◽  
Enterobacter Cloacae ◽  
Content Type ◽  
Plasmid Replicon ◽  
Genes Encoding ◽  
Clonal Spread ◽  
Encoding Genes

ABSTRACTThe molecular epidemiology of 66 NDM-producing isolates from 2 Pakistani hospitals was investigated, with their genetic relatedness determined using repetitive sequence-based PCR (Rep-PCR). PCR-based replicon typing and screening for antibiotic resistance genes encoding carbapenemases, other β-lactamases, and 16S methylases were also performed. Rep-PCR suggested a clonal spread ofEnterobacter cloacaeandEscherichia coli. A number of plasmid replicon types were identified, with the incompatibility A/C group (IncA/C) being the most common (78%). 16S methylase-encoding genes were coharbored in 81% of NDM-producingEnterobacteriaceae.

scholarly journals Systematic Nomenclature for GGDEF and EAL Domain-Containing Cyclic Di-GMP Turnover Proteins of Escherichia coli: TABLE 1

2015 ◽  
Vol 198 (1) ◽  
pp. 7-11 ◽  
Author(s):  
Regine Hengge ◽  
Michael Y. Galperin ◽  
Jean-Marc Ghigo ◽  
Mark Gomelsky ◽  
Jeffrey Green ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Molecular Mechanisms ◽  
Bacterial Species ◽  
Content Type ◽  
E Coli ◽  
Diguanylate Cyclases ◽  
Genes Encoding ◽  
Systematic Nomenclature ◽  
K 12 ◽  
Encoding Genes

In recent years,Escherichia colihas served as one of a few model bacterial species for studying cyclic di-GMP (c-di-GMP) signaling. The widely usedE. coliK-12 laboratory strains possess 29 genes encoding proteins with GGDEF and/or EAL domains, which include 12 diguanylate cyclases (DGC), 13 c-di-GMP-specific phosphodiesterases (PDE), and 4 “degenerate” enzymatically inactive proteins. In addition, six new GGDEF and EAL (GGDEF/EAL) domain-encoding genes, which encode two DGCs and four PDEs, have recently been found in genomic analyses of commensal and pathogenicE. colistrains. As a group of researchers who have been studying the molecular mechanisms and the genomic basis of c-di-GMP signaling inE. coli, we now propose a general and systematicdgcandpdenomenclature for the enzymatically active GGDEF/EAL domain-encoding genes of this model species. This nomenclature is intuitive and easy to memorize, and it can also be applied to additional genes and proteins that might be discovered in various strains ofE. coliin future studies.

scholarly journals Limited Transmission ofblaCTX-M-9-Type-Positive Escherichia coli between Humans and Poultry in Vietnam

2015 ◽  
Vol 59 (6) ◽  
pp. 3574-3577 ◽  
Author(s):  
Shuhei Ueda ◽  
Bui Thi Kim Ngan ◽  
Bui Thi Mai Huong ◽  
Itaru Hirai ◽  
Le Danh Tuyen ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antibiotic Resistance ◽  
Antibiotic Resistance Genes ◽  
Phylogenetic Group ◽  
Content Type ◽  
E Coli ◽  
Plasmid Replicon ◽  
Vietnamese Community ◽  
Group Compositions ◽  
Sequence Types

ABSTRACTWe examined whetherEscherichia coliisolates that produce CTX-M-9-type extended-spectrum β-lactamases (ESBL) are transferred between humans and chickens in a Vietnamese community. The phylogenetic group compositions, sequence types, antimicrobial resistance profiles, the prevalence of plasmid antibiotic resistance genes, and the plasmid replicon types generally differed between the human and chickenE. coliisolates. Our results suggest that transmission of theblaCTX-M-9-positiveE. colibetween humans and poultry was limited.

scholarly journals Diverse Virulence Gene Content of Shiga Toxin-Producing Escherichia coli from Finishing Swine

2014 ◽  
Vol 80 (20) ◽  
pp. 6395-6402 ◽  
Author(s):  
Marion Tseng ◽  
Pina M. Fratamico ◽  
Lori Bagi ◽  
Sabine Delannoy ◽  
Patrick Fach ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Shiga Toxin ◽  
Virulence Genes ◽  
Genetic Relatedness ◽  
Virulence Gene ◽  
Health Concern ◽  
Limited Information ◽  
Content Type ◽  
Genes Encoding ◽  
Critical Public Health

ABSTRACTShiga toxin-producingEscherichia coli(STEC) infections are a critical public health concern because they can cause severe clinical outcomes, such as hemolytic uremic syndrome, in humans. Determining the presence or absence of virulence genes is essential in assessing the potential pathogenicity of STEC strains. Currently, there is limited information about the virulence genes carried by swine STEC strains; therefore, this study was conducted to examine the presence and absence of 69 virulence genes in STEC strains recovered previously from finishing swine in a longitudinal study. A subset of STEC strains was analyzed by pulsed-field gel electrophoresis (PFGE) to examine their genetic relatedness. Swine STEC strains (n= 150) were analyzed by the use of a high-throughput real-time PCR array system, which included 69 virulence gene targets. Three major pathotypes consisted of 16 different combinations of virulence gene profiles, and serotypes were determined in the swine STEC strains. The majority of the swine STEC strains (n= 120) belonged to serotype O59:H21 and carried the same virulence gene profile, which consisted of 9 virulence genes:stx2e,iha,ecs1763,lpfAO113,estIa(STa),ehaA,paa,terE, andureD. Theeae,nleF, andnleH1-2genes were detected in one swine STEC strain (O49:H21). Other genes encoding adhesins, includingiha, were identified (n= 149). The PFGE results demonstrated that swine STEC strains from pigs raised in the same finishing barn were closely related. Our results revealed diverse virulence gene contents among the members of the swine STEC population and enhance understanding of the dynamics of transmission of STEC strains among pigs housed in the same barn.

scholarly journals Variable within- and between-Herd Diversity of CTX-M Cephalosporinase-Bearing Escherichia coli Isolates from Dairy Cattle

2012 ◽  
Vol 78 (13) ◽  
pp. 4552-4560 ◽  
Author(s):  
Dixie F. Mollenkopf ◽  
Matthew F. Weeman ◽  
Joshua B. Daniels ◽  
Melanie J. Abley ◽  
Jennifer L. Mathews ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Dairy Cattle ◽  
Coliform Bacteria ◽  
Bacterial Dna ◽  
Fecal Samples ◽  
Content Type ◽  
Beta Lactamases ◽  
E Coli ◽  
Plasmid Replicon ◽  
Encoding Genes

ABSTRACTblaCTX-Mbeta-lactamases confer resistance to critically important cephalosporin drugs. Recovered from both hospital- and community-acquired infections,blaCTX-Mwas first reported in U.S. livestock in 2010. It has been hypothesized that veterinary use of cephalosporins in livestock populations may lead to the dissemination of beta-lactamase-encoding genes. Therefore, our objectives were to estimate the frequency and distribution of coliform bacteria harboringblaCTX-Min the fecal flora of Ohio dairy cattle populations. In addition, we characterized the CTX-M alleles carried by the isolates, their plasmidic contexts, and the genetic diversity of the bacterial isolates themselves. We also evaluated the association between ceftiofur use and the likelihood of recovering cephalosporinase-producing bacteria. Thirty fresh fecal samples and owner-reported ceftiofur use data were collected from each of 25 Ohio dairy farms. Fecal samples (n= 747) yielded 70blaCTX-M-positiveEscherichia coliisolates from 5/25 herds, 715blaCMY-2E. coliisolates from 25/25 herds, and 274Salmonellaspp. from 20/25 herds. The within-herd prevalence amongblaCTX-M-positive herds ranged from 3.3 to 100% of samples. Multiple pulsed-field gel electrophoresis (PFGE) patterns, plasmid replicon types, and CTX-M genes were detected. Plasmids with CTX-M-1, -15, and -14 alleles were clonal by restriction fragment length polymorphism (RFLP) within herds, and specific plasmid incompatibility group markers were consistently associated with eachblaCTX-Mallele. PFGE of total bacterial DNA showed similar within-herd clustering, with the exception of one herd, which revealed at least 6 different PFGE signatures. We were unable to detect an association between owner-reported ceftiofur use and the probability of recoveringE. colicarryingblaCTX-MorblaCMY-2.

scholarly journals Characterization of Extended-Spectrum β-Lactamase Genes Found among Escherichia coli Isolates from Duck and Environmental Samples Obtained on a Duck Farm

2012 ◽  
Vol 78 (10) ◽  
pp. 3668-3673 ◽  
Author(s):  
Junying Ma ◽  
Jian-Hua Liu ◽  
Luchao Lv ◽  
Zhiyong Zong ◽  
Yan Sun ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Water Samples ◽  
Environmental Samples ◽  
Genetic Relatedness ◽  
Antibiotic Resistance Genes ◽  
Hypothetical Protein ◽  
M Gene ◽  
Content Type ◽  
E Coli ◽  
Extended Spectrum

ABSTRACTIn this study, we focused on evaluating the occurrence of extended-spectrum β-lactamase (ESBL)-producingEscherichia coliin fecal samples of healthy ducks and environmental samples from a duck farm in South China. Duck cloacal swabs and pond water samples were cultivated on MacConkey agar plates supplemented with ceftiofur. Individual colonies were examined for ESBL production. Bacteria identified asE. coliwere screened for the presence of ESBL and plasmid-borne AmpC genes. The genetic relatedness, plasmid replicon type, and genetic background were determined. Of 245 samples analyzed, 123 hadE. coliisolates with ceftiofur MICs higher than 8 μg/ml (116 [50.4%] from 230 duck samples and 7 [46.7%] from 15 water samples).blaCTX-M,blaSHV-12,blaCMY-2, andblaDHA-1were identified in 108, 5, 9, and 1 isolates, respectively. The most commonblaCTX-Mgenes wereblaCTX-M-27(n= 34),blaCTX-M-55(n= 27),blaCTX-M-24e(n= 22), andblaCTX-M-105(n= 20), followed byblaCTX-M-14a,blaCTX-M-14b,blaCTX-M-24a, andblaCTX-M-24b. Although most of the CTX-M producers had distinct pulsotypes, clonal transmission between duck and water isolates was observed.blaCTX-Mgenes were carried by transferable IncN, IncF, and untypeable plasmids. The novel CTX-M geneblaCTX-M-105was flanked by two hypothetical protein sequences, partial ISEcp1upstream and truncated IS903D,iroN,orf1, and a Tn1721-like element downstream. It is suggested that the horizontal transfer ofblaCTX-Mgenes mediated by mobile elements and the clonal spread of CTX-M-producingE. coliisolates contributed to the dissemination ofblaCTX-Min the duck farm. Our findings highlight the importance of ducks for the dissemination of transferable antibiotic resistance genes into the environment.

scholarly journals Genome-Based Comparison of Cyclic Di-GMP Signaling in Pathogenic and Commensal Escherichia coli Strains

2015 ◽  
Vol 198 (1) ◽  
pp. 111-126 ◽  
Author(s):  
Tatyana L. Povolotsky ◽  
Regine Hengge
Keyword(s):  
Escherichia Coli ◽  
Bacterial Species ◽  
Content Type ◽  
E Coli ◽  
Large Deletions ◽  
Diguanylate Cyclases ◽  
Core Set ◽  
Genes Encoding ◽  
K 12 ◽  
Encoding Genes

ABSTRACTThe ubiquitous bacterial second messenger cyclic di-GMP (c-di-GMP) has recently become prominent as a trigger for biofilm formation in many bacteria. It is generated by diguanylate cyclases (DGCs; with GGDEF domains) and degraded by specific phosphodiesterases (PDEs; containing either EAL or HD-GYP domains). Most bacterial species contain multiples of these proteins with some having specific functions that are based on direct molecular interactions in addition to their enzymatic activities.Escherichia coliK-12 laboratory strains feature 29 genes encoding GGDEF and/or EAL domains, resulting in a set of 12 DGCs, 13 PDEs, and four enzymatically inactive “degenerate” proteins that act by direct macromolecular interactions. We present here a comparative analysis of GGDEF/EAL domain-encoding genes in 61 genomes of pathogenic, commensal, and probioticE. colistrains (including enteric pathogens such as enteroaggregative, enterohemorrhagic, enteropathogenic, enterotoxigenic, and adherent and invasiveEscherichia coliand the 2011 German outbreak O104:H4 strain, as well as extraintestinal pathogenicE. coli, such as uropathogenic and meningitis-associatedE. coli). We describe additional genes for two membrane-associated DGCs (DgcX and DgcY) and four PDEs (the membrane-associated PdeT, as well as the EAL domain-only proteins PdeW, PdeX, and PdeY), thus showing the pangenome ofE. colito contain at least 35 GGDEF/EAL domain proteins. A core set of only eight proteins is absolutely conserved in all 61 strains: DgcC (YaiC), DgcI (YliF), PdeB (YlaB), PdeH (YhjH), PdeK (YhjK), PdeN (Rtn), and the degenerate proteins CsrD and CdgI (YeaI). In all other GGDEF/EAL domain genes, diverse point and frameshift mutations, as well as small or large deletions, were discovered in various strains.IMPORTANCEOur analysis reveals interesting trends in pathogenicEscherichia colithat could reflect different host cell adherence mechanisms. These may either benefit from or be counteracted by the c-di-GMP-stimulated production of amyloid curli fibers and cellulose. Thus, EAEC, which adhere in a “stacked brick” biofilm mode, have a potential for high c-di-GMP accumulation due to DgcX, a strongly expressed additional DGC. In contrast, EHEC and UPEC, which use alternative adherence mechanisms, tend to have extra PDEs, suggesting that low cellular c-di-GMP levels are crucial for these strains under specific conditions. Overall, our study also indicates that GGDEF/EAL domain proteins evolve rapidly and thereby contribute to adaptation to host-specific and environmental niches of various types ofE. coli.

scholarly journals Novel Cefotaximase (CTX-M-16) with Increased Catalytic Efficiency Due to Substitution Asp-240→Gly

2001 ◽  
Vol 45 (8) ◽  
pp. 2269-2275 ◽  
Author(s):  
R. Bonnet ◽  
C. Dutour ◽  
J. L. M. Sampaio ◽  
C. Chanal ◽  
D. Sirot ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
Catalytic Efficiency ◽  
Enterobacter Cloacae ◽  
E Coli ◽  
Genes Encoding ◽  
Encoding Gene ◽  
Synergy Test ◽  
Encoding Genes

ABSTRACT Three clinical strains (Escherichia coli Rio-6,E. coli Rio-7, and Enterobacter cloacae Rio-9) collected in 1996 and 1999 from hospitals in Rio de Janeiro (Brazil) were resistant to broad-spectrum cephalosporins and gave a positive double-disk synergy test. Two bla CTX-M genes encoding β-lactamases of pl 7.9 and 8.2 were implicated in this resistance: the bla CTX-M-9 gene observed inE. coli Rio-7 and E. cloacae Rio-9 and a novel CTX-M-encoding gene, designated bla CTX-M-16, observed in E. coli strain Rio-6. The deduced amino acid sequence of CTX-M-16 differed from CTX-M-9 only by the substitution Asp-240→Gly. The CTX-M-16-producing E. coli transformant exhibited the same level of resistance to cefotaxime (MIC, 16 μg/ml) but had a higher MIC of ceftazidime (MIC, 8 versus 1 μg/ml) than the CTX-M-9-producing transformant. Enzymatic studies revealed that CTX-M-16 had a 13-fold higher affinity for aztreonam and a 7.5-fold higher kcat for ceftazidime than CTX-M-9, thereby showing that the residue in position 240 can modulate the enzymatic properties of CTX-M enzymes. The two bla CTX-M-9 genes and the bla CTX-M-16 gene were located on different plasmids, suggesting the presence of mobile elements associated with CTX-M-encoding genes. CTX-M-2 and CTX-M-8 enzymes were found in Brazil in 1996, and two other CTX-M β-lactamases, CTX-M-9 and CTX-M-16, were subsequently observed. These reports are evidence of the diversity of CTX-M-type extended-spectrum β-lactamases in Brazil.

scholarly journals Molecular Epidemiology and Genetic Diversity of Fluoroquinolone-Resistant Escherichia coli Isolates from Patients with Community-Onset Infections in 30 Chinese County Hospitals

2014 ◽  
Vol 53 (3) ◽  
pp. 766-770 ◽  
Author(s):  
Lina Zhao ◽  
Jing Zhang ◽  
Beiwen Zheng ◽  
Zeqing Wei ◽  
Ping Shen ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Molecular Epidemiology ◽  
Genetic Relatedness ◽  
Quinolone Resistance ◽  
Fluoroquinolone Resistance ◽  
Genetic Characteristics ◽  
Content Type ◽  
First Report ◽  
E Coli ◽  
Community Onset

The high frequency of fluoroquinolone resistance inEscherichia coliis a feature of clinical bacteriology in China, where the molecular epidemiology and genetic characteristics of this resistance in county hospitals remain unclear. A total of 590 nonduplicateE. coliisolates from 30 county hospitals located across seven Chinese regions were examined for plasmid-mediated quinolone resistance (PMQR) genes and mutations in quinolone resistance-determining regions (QRDRs). Multilocus sequence typing (MLST) and phylogenetic analysis of fluoroquinolone-resistant isolates were used to determine their genetic relatedness. The ciprofloxacin resistance rate of community-onsetE. coliwas 51.2%, and at least one PMQR gene was carried by 220 (37.3%) isolates. These includedqnr(3.7%),aac(6′)-Ib-cr(19.7%),qepA(14.4%), andoqxAB(3.8%). Two noveloqxBmutants were identified and namedoqxB20andoqxB29. From 60 sequence types (STs) isolated, 5 novel STs (ST4499 to ST4503) were identified. ST1193 (7.9%) was the second most abundant ST among fluoroquinolone-resistant isolates (ST131 was the most common, with 14.6%), and this is the first report of it in China. This is also the first report of ST2115 and ST3014 isolates from human samples. Ciprofloxacin-resistantE. coliisolates fell mainly into phylogroups B2 and D. The rates of fluoroquinolone resistance and the prevalence of PMQR genes in community-onsetE. coliisolates from Chinese county hospitals were high. The wide-ranging molecular epidemiology ofE. coliisolates from scattered locations across China indicates that fluoroquinolone resistance evolved from different sources.

scholarly journals Molecular Epidemiology of Dairy Cattle-AssociatedEscherichia coliCarryingblaCTX-MGenes in Washington State

2018 ◽  
Vol 84 (6) ◽  
Author(s):  
Josephine A. Afema ◽  
Sara Ahmed ◽  
Thomas E. Besser ◽  
Lisa P. Jones ◽  
William M. Sischo ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Dairy Cattle ◽  
Molecular Epidemiology ◽  
Washington State ◽  
M Gene ◽  
Antimicrobial Drugs ◽  
Content Type ◽  
E Coli ◽  
Plasmid Replicon ◽  
Sequence Types

ABSTRACTAn increase in the prevalence of commensalEscherichia colicarryingblaCTX-Mgenes among dairy cattle was observed between 2008 and 2012 in Washington State. To study the molecular epidemiology of this change, we selected 126blaCTX-M-positive and 126blaCTX-M-negative isolates for determinations of the multilocus sequence types (MLSTs) and antibiotic resistance phenotypes fromE. coliobtained during a previous study. For 99 isolates, we also determined theblaCTX-Malleles using PCR and sequencing and identified the replicon types ofblaCTX-M-carrying plasmids. TheblaCTX-M-negativeE. coliisolates comprised 76 sequence types (STs) compared with 32 STs inblaCTX-M-positiveE. coliisolates. TheblaCTX-M-positiveE. coliisolates formed three MLST clonal complexes, accounting for 83% of these isolates; 52% ofblaCTX-M-negativeE. coliisolates clustered into 10 clonal complexes, and the remainder were singletons. Overall,blaCTX-M-negativeE. coliisolates had more diverse genotypes that were distinct to farms, whereasblaCTX-M-positiveE. coliisolates had a clonal population structure and were widely disseminated on farms in both regions included in the study. Plasmid replicon types included IncI1 which predominated, followed by IncFIB and IncFIA/FIB.blaCTX-M-15was the predominant CTX-M gene allele, followed byblaCTX-M-27andblaCTX-M-14. There was no significant association between plasmid replicon types and bacterial STs, and neither clonal complexes nor major plasmid groups were associated with two discrete dairy-farming regions of Washington State.IMPORTANCEInfections caused by extended-spectrum β-lactamase (ESBL)-producingEscherichia colioccur globally and present treatment challenges because of their resistance to multiple antimicrobial drugs. Cattle are potential reservoirs of ESBL-producingEnterobacteriaceae, and so understanding the causes of successful dissemination ofblaCTX-Mgenes in commensal bacteria will inform future approaches for the prevention of antibiotic-resistant pathogen emergence.

scholarly journals Autotransporter Protein-Encoding Genes of Diarrheagenic Escherichia coli Are Found in both Typical and Atypical Enteropathogenic E. coli Strains

2012 ◽  
Vol 79 (1) ◽  
pp. 411-414 ◽  
Author(s):  
Afonso G. Abreu ◽  
Vanessa Bueris ◽  
Tatiane M. Porangaba ◽  
Marcelo P. Sircili ◽  
Fernando Navarro-Garcia ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Content Type ◽  
E Coli ◽  
Diarrheagenic Escherichia Coli ◽  
Virulence Markers ◽  
Protein Encoding ◽  
Encoding Genes ◽  
Specific Virulence

ABSTRACTAutotransporter (AT) protein-encoding genes of diarrheagenicEscherichia coli(DEC) pathotypes (cah,eatA,ehaABCDJ,espC,espI,espP,pet,pic,sat, andtibA) were detected in typical and atypical enteropathogenicE. coli(EPEC) in frequencies between 0.8% and 39.3%. Although these ATs have been described in particular DEC pathotypes, their presence in EPEC indicates that they should not be considered specific virulence markers.

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