Articles de revues : « Coli ST38 »

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Sugawara, Yo, Hideharu Hagiya, Yukihiro Akeda, Dan Takeuchi, Noriko Sakamoto, Yuki Matsumoto, Daisuke Motooka, Isao Nishi, Kazunori Tomono et Shigeyuki Hamada. « Community spread and acquisition of clinically relevant Escherichia coli harbouring blaNDM among healthy Japanese residents of Yangon, Myanmar ». Journal of Antimicrobial Chemotherapy 76, n^o 6 (24 mars 2021) : 1448–54. http://dx.doi.org/10.1093/jac/dkab070.

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Abstract Background Carbapenemase-producing Enterobacterales (CPE) are spreading in hospitals, environment and retail foods in Yangon, Myanmar. Objectives To investigate whether CPE colonize healthy individuals living in Yangon and whether clinical-related strains are spreading in the community. Methods CPE was isolated from faecal samples obtained from healthy Japanese residents of Yangon with no history of hospitalization. Isolates were subjected to WGS using short- and long-read sequencers and compared with those previously isolated in Yangon. Results Six Escherichia coli strains harbouring blaNDM-1 or blaNDM-5 belonging to five different STs—ST10, ST38, ST48, ST410 and ST8453—were isolated from 69 volunteers. The ST38 isolates were related to those previously isolated from retail food in Yangon. The ST410 and ST8453 isolates were highly related to previous Yangon isolates including those of clinical and food origins. Conclusions The analysis suggested the acquisition of blaNDM-positive E. coli, which are disseminating in a clinical setting and through retail foods, by healthy residents in Yangon.

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Fonseca, Erica L., Sergio M. Morgado, Raquel V. Caldart et Ana Carolina Vicente. « Global Genomic Epidemiology of Escherichia coli (ExPEC) ST38 Lineage Revealed a Virulome Associated with Human Infections ». Microorganisms 10, n^o 12 (15 décembre 2022) : 2482. http://dx.doi.org/10.3390/microorganisms10122482.

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Background: Most of the extraintestinal human infections worldwide are caused by specific extraintestinal pathogenic Escherichia coli (ExPEC) lineages, which also present a zoonotic character. One of these lineages belongs to ST38, a high-risk globally disseminated ExPEC. To get insights on the aspects of the global ST38 epidemiology and evolution as a multidrug-resistant and pathogenic lineage concerning the three axes of the One Health concept (humans, animals, and natural environments), this study performed a global phylogenomic analysis on ST38 genomes. Methods: A phylogenetic reconstruction based on 376 ST38 genomes recovered from environments, humans, livestock, and wild and domestic animals in all continents throughout three decades was performed. The global information concerning the ST38 resistome and virulome was also approached by in silico analyses. Results: In general, the phylogenomic analyses corroborated the zoonotic character of the ExPEC ST38, since clonal strains were recovered from both animal and human sources distributed worldwide. Moreover, our findings revealed that, independent of host sources and geographic origin, the genomes were distributed in two major clades (Clades 1 and 2). However, the ST38 accessory genome was not strictly associated with clades and sub-clades, as found for the type 2 T3SS ETT2 that was evenly distributed throughout Clades 1 and 2. Of note was the presence of the Yersinia pestis-like high-pathogenicity island (HPI) exclusively in the major Clade 2, in which prevails most of the genomes from human origin recovered worldwide (2000 to 2020). Conclusions: This evidence corroborates the HPI association with successful E. coli ST38 establishment in human infections.

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Brendecke, Jana, Timo Homeier-Bachmann, Angela Schmitz Ornés, Sebastian Guenther, Stefan E. Heiden, Michael Schwabe, Elias Eger et Katharina Schaufler. « Multidrug-Resistant High-Risk Escherichia coli and Klebsiella pneumoniae Clonal Lineages Occur in Black-Headed Gulls from Two Conservation Islands in Germany ». Antibiotics 11, n^o 10 (5 octobre 2022) : 1357. http://dx.doi.org/10.3390/antibiotics11101357.

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Multidrug-resistant (MDR) Enterobacterales, including extended-spectrum β‑lactamase (ESBL)-producing Escherichia coli and Klebsiella pneumoniae, not only emerge in healthcare settings but also in other habitats, such as livestock and wildlife. The spread of these pathogens, which often combine resistance with high-level virulence, is a growing problem, as infections have become increasingly difficult to treat. Here, we investigated the occurrence of ESBL-producing E. coli and K. pneumoniae in fecal samples from two black-headed gull colonies breeding on two nature conservation islands in Western Pomerania, Germany. In addition to cloacal samples from adult birds (n = 211) and their nestlings (n = 99) during the 2021 breeding season, collective fecal samples (n = 29) were obtained. All samples were screened for ESBL producers, which were then subjected to whole-genome sequencing. We found a total of 12 ESBL-producing E. coli and K. pneumoniae consisting of 11 E. coli and 1 K. pneumoniae, and including the international high-risk E. coli sequence types (ST)131, ST38, and ST58. Eight of the investigated strains had a MDR genotype and carried a large repertoire of virulence-associated genes, including the pap operon, which is important for urinary tract infections. In addition, we identified many genes associated with adherence, biofilm formation, iron uptake, and toxin production. Finally, our analysis revealed the close phylogenetic relationship of ST38 strains with genomes originating from human sources, underlining their zoonotic and pathogenic character. This study highlights the importance of the One Health approach, and thus the interdependence between human and animal health and their surrounding environment.

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Vingino, Alexandria, Marilyn C. Roberts, Michelle Wainstein, James West, Stephanie A. Norman, Dyanna Lambourn, Jeffery Lahti et al. « Surveillance for Antibiotic-Resistant E. coli in the Salish Sea Ecosystem ». Antibiotics 10, n^o 10 (2 octobre 2021) : 1201. http://dx.doi.org/10.3390/antibiotics10101201.

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E. coli was isolated from the Salish Sea (Puget Sound) ecosystem, including samples of marine and fresh water, and wildlife dependent on this environment. E. coli isolates were assessed for phenotypic and genotypic resistance to antibiotics. A total of 305 E. coli isolates was characterized from samples collected from: marine water obtained in four quadrants of the Salish Sea; select locations near beaches; fresh water from streams near marine beaches; and fecal samples from harbor porpoises (Phocoena phocoena), harbor seals (Phoca vitulina), river otters (Lontra canadensis), and English sole (Parophrys vetulus). Isolates were evaluated using antimicrobial susceptibility typing, whole-genome sequencing, fumC, and multilocus sequence typing. Resistance and virulence genes were identified from sequence data. Of the 305 isolates from Salish Sea samples, 20 (6.6%) of the E. coli were intermediate, and 31 (10.2%) were resistant to ≥1 class of antibiotics, with 26.9% of nonsusceptible (resistant and intermediate resistant) E. coli isolates from marine mammals and 70% from river otters. The proportion of nonsusceptible isolates from animals was significantly higher than samples taken from marine water (p < 0.0001). A total of 196 unique STs was identified including 37 extraintestinal pathogenic E. coli (ExPEC)-associated STs [ST10, ST38, ST58, ST69, ST73, ST117, ST131, and ST405]. The study suggests that animals may be potential sentinels for antibiotic-resistant and ExPEC E. coli in the Salish Sea ecosystem.

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Poirel, Laurent, Sandrine Bernabeu, Nicolas Fortineau, Isabelle Podglajen, Christine Lawrence et Patrice Nordmann. « Emergence of OXA-48-Producing Escherichia coli Clone ST38 in France ». Antimicrobial Agents and Chemotherapy 55, n^o 10 (18 juillet 2011) : 4937–38. http://dx.doi.org/10.1128/aac.00413-11.

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Al Bayssari, Charbel, Abiola Olumuyiwa Olaitan, Fouad Dabboussi, Monzer Hamze et Jean-Marc Rolain. « Emergence of OXA-48-Producing Escherichia coli Clone ST38 in Fowl ». Antimicrobial Agents and Chemotherapy 59, n^o 1 (27 octobre 2014) : 745–46. http://dx.doi.org/10.1128/aac.03552-14.

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Paramita, Rafika Indah, Erni Juwita Nelwan, Fadilah Fadilah, Editha Renesteen, Nelly Puspandari et Linda Erlina. « Genome-based characterization of Escherichia coli causing bloodstream infection through next-generation sequencing ». PLOS ONE 15, n^o 12 (23 décembre 2020) : e0244358. http://dx.doi.org/10.1371/journal.pone.0244358.

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Escherichia coli are one of the commonest bacteria causing bloodstream infection (BSI). The aim of the research was to identify the serotypes, MLST (Multi Locus Sequence Type), virulence genes, and antimicrobial resistance of E. coli isolated from bloodstream infection hospitalized patients in Cipto Mangunkusumo National Hospital Jakarta. We used whole genome sequencing methods rather than the conventional one, to characterized the serotypes, MLST (Multi Locus Sequence Type), virulence genes, and antimicrobial resistance (AMR) of E. coli. The composition of E. coli sequence types (ST) was as follows: ST131 (n = 5), ST38 (n = 3), ST405 (n = 3), ST69 (n = 3), and other STs (ST1057, ST127, ST167, ST3033, ST349, ST40, ST58, ST6630). Enteroaggregative E. coli (EAEC) and Extra-intestinal pathogenic E. coli (ExPEC) groups were found dominant in our samples. Twenty isolates carried virulence genes for host cells adherence and 15 for genes that encourage E. coli immune evasion by enhancing survival in serum. ESBL-genes were present in 17 E. coli isolates. Other AMR genes also encoded resistance against aminoglycosides, quinolones, chloramphenicol, macrolides and trimethoprim. The phylogeny analysis showed that phylogroup D is dominated and followed by phylogroup B2. The E. coli isolated from 22 patients in Cipto Mangunkusumo National Hospital Jakarta showed high diversity in serotypes, sequence types, virulence genes, and AMR genes. Based on this finding, routinely screening all bacterial isolates in health care facilities can improve clinical significance. By using Whole Genome Sequencing for laboratory-based surveillance can be a valuable early warning system for emerging pathogens and resistance mechanisms.

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GERHOLD, G., M. H. SCHULZE, U. GROSS et W. BOHNE. « Multilocus sequence typing and CTX-M characterization of ESBL-producing E. coli : a prospective single-centre study in Lower Saxony, Germany ». Epidemiology and Infection 144, n^o 15 (30 juin 2016) : 3300–3304. http://dx.doi.org/10.1017/s0950268816001412.

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SUMMARYThe increasing prevalence of extended-spectrum β-lactamase (ESBL)-producing Gram-negative bacteria is a serious threat for current healthcare settings. In this study we investigated the molecular epidemiology of ESBL-producing E. coli at the University Medical Center Göttingen in Lower Saxony, Germany. All E. coli isolates with an ESBL phenotype were collected during a 6-month period in 2014. Multilocus sequence typing and CTX-M characterization were performed on 160 isolates. Of the ESBL-producing isolates 95·6% were CTX-M positive. Compared to recent Germany-wide studies, we found CTX-M-1 to occur in higher frequency than CTX-M-15 (44·4% vs. 34·4%). CTX-M-14 and CTX-M-27 were detected at 9·4% and 5·0%, respectively. The globally dominant sequence type (ST) 131, which is often associated with CTX-M-15, occurred at a relatively low rate of 24%. Major non-ST131 sequence types were ST101 (5%), ST58 (5%), ST10 (4·4%), ST38 (4·4%), ST410 (3·8%) and ST453 (3·1%). Several of these major sequence types were previously shown to be associated with livestock farming. Together, our study indicates that E. coli lineage distribution in individual healthcare settings can significantly differ from average numbers obtained in nationwide studies.

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Huang, Lili, Hongye Hu, Chen Xu, Mi Zhou, Yuanyuan Li, Yunbing Li, Shuyan Wu et Ning Dong. « Characterization of NDM-5-Producing Escherichia coli Strains Isolated from Pediatric Patients with Bloodstream Infections in a Chinese Hospital ». Genes 14, n^o 2 (18 février 2023) : 520. http://dx.doi.org/10.3390/genes14020520.

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Escherichia coli (E. coli) bloodstream infections (BSIs) are among the most predominant causes of death in infants and children worldwide. NDM-5 (New Delhi Metallo-lactamase-5) is responsible for one of the main mechanisms of carbapenem resistance in E. coli. To analyze the phenotypic and genomic characteristics of NDM-5-producing E. coli from bloodstream infections (BSIs), a total of 114 E. coli strains was collected from a children’s hospital in Jiangsu province, China. Eight blaNDM-5-carrying E. coli strains were identified which were all carbapenem-resistant and carried diverse antimicrobial resistance genes apart from blaNDM-5. They belonged to six distinct sequence types (STs) and serotypes including one each for ST38/O7:H8, ST58/O?:H37, ST131/O25:H4, ST156/O11:H25 and ST361/O9:H30 and three strains are originating from a single clone belonging to ST410/O?:H9. Apart from blaNDM-5, the E. coli strains isolated from BSIs also carried other β-lactamase genes, including blaCMY-2 (n = 4), blaCTX-M-14 (n = 2), blaCTX-M-15 (n = 3), blaCTX-M-65 (n = 1), blaOXA-1 (n = 4) and blaTEM-1B (n = 5). The blaNDM-5 genes were located on three different types of plasmids, which were IncFII/I1 (n = 1), IncX3 (n = 4) and IncFIA/FIB/FII/Q1 (n = 3). The former two types were conjugatively transferable at frequencies of 10−3 and 10−6, respectively. The dissemination of NDM-producing strains, which exhibit resistance to the last-line antibiotics, carbapenems, may increase the muti-antimicrobial resistance burden among E. coli BSIs and further threaten public health.

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Abid, Fatma Ben, Clement K. M. Tsui, Yohei Doi, Anand Deshmukh, Christi L. McElheny, William C. Bachman, Erin L. Fowler et al. « Molecular characterization of clinical carbapenem-resistant Enterobacterales from Qatar ». European Journal of Clinical Microbiology & ; Infectious Diseases 40, n^o 8 (22 février 2021) : 1779–85. http://dx.doi.org/10.1007/s10096-021-04185-7.

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AbstractOne hundred forty-nine carbapenem-resistant Enterobacterales from clinical samples obtained between April 2014 and November 2017 were subjected to whole genome sequencing and multi-locus sequence typing. Klebsiella pneumoniae (81, 54.4%) and Escherichia coli (38, 25.5%) were the most common species. Genes encoding metallo-β-lactamases were detected in 68 (45.8%) isolates, and OXA-48-like enzymes in 60 (40.3%). blaNDM-1 (45; 30.2%) and blaOXA-48 (29; 19.5%) were the most frequent. KPC-encoding genes were identified in 5 (3.6%) isolates. Most common sequence types were E. coli ST410 (8; 21.1%) and ST38 (7; 18.4%), and K. pneumoniae ST147 (13; 16%) and ST231 (7; 8.6%).

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Guenther, Sebastian, Torsten Semmler, Annegret Stubbe, Michael Stubbe, Lothar H. Wieler et Katharina Schaufler. « Chromosomally encoded ESBL genes in Escherichia coli of ST38 from Mongolian wild birds ». Journal of Antimicrobial Chemotherapy 72, n^o 5 (3 février 2017) : 1310–13. http://dx.doi.org/10.1093/jac/dkx006.

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Markovska, Rumyana, Petya Stankova, Temenuga Stoeva, Dobrinka Ivanova, Daniela Pencheva, Radka Kaneva et Lyudmila Boyanova. « Fecal Carriage and Epidemiology of Extended-Spectrum Beta-Lactamase/Carbapenemases Producing Enterobacterales Isolates in Bulgarian Hospitals ». Antibiotics 10, n^o 6 (20 juin 2021) : 747. http://dx.doi.org/10.3390/antibiotics10060747.

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The gastrointestinal tract is an important reservoir of extended spectrum beta-lactamase (ESBL)/carbapenemase-producing Enterobacterales isolates. This study included patients from two Bulgarian hospitals. Overall, 98 ESBL producers (including 68 Escherichia coli and 20 Klebsiella pneumoniae isolates) were detected among 99 hospitalized patients, 212 patients at admission, and 92 hospital staff in 42.4%, 24.5%, and 4%, respectively. We observed blaCTX-M-15 in 47% of isolates, blaCTX-M-3 in 39% and blaCTX-M-14 in 11%. Three blaCTX-M-15 positive isolates were also blaKPC-2 positive. High transferability was detected for blaCTX-M-3 carrying plasmids (55%) with L/M and I1 replicon plasmids, followed by CTX-M-14 (36.4%) and CTX-M-15 (27.9%) with IncF plasmids. BlaKPC-2 was carried by FIIAs plasmids. Epidemiology typing revealed 8 K. pneumoniae ST types—ST15(8/20), ST17(4/20), ST37(2/20) and 9 E. coli ST types—ST131 (30.9%, 21/68), ST38 (8/68), ST95(7/68) and ST316(7/68). All ST131 isolates but one was from the highly virulent epidemic clone O25bST131. This is the first report in Bulgaria about ESBL/carbapenemase faecal carriage. We observed high ESBL/carbapenemases prevalence. A predominant number of isolates were members of highly epidemic and virulent PanEuropean clones ST15 K. pneumoniae and O25bST131 E. coli. High antibiotics usage during the COVID pandemic will worsen the situation. Routine screenings and strict infection control measures should be widely implemented.

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Yasugi, Mayo, Shingo Hatoya, Daisuke Motooka, Yuki Matsumoto, Shunsuke Shimamura, Hiroyuki Tani, Masaru Furuya et al. « Whole-genome analyses of extended-spectrum or AmpC β-lactamase-producing Escherichia coli isolates from companion dogs in Japan ». PLOS ONE 16, n^o 2 (5 février 2021) : e0246482. http://dx.doi.org/10.1371/journal.pone.0246482.

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The emergence and global spread of extended-spectrum or AmpC β-lactamase (ESBL/AmpC)-producing Enterobacteriaceae in companion animals have led to the hypothesis that companion animals might be reservoirs for cross-species transmission because of their close contact with humans. However, current knowledge in this field is limited; therefore, the role of companion animals in cross-species transmission remains to be elucidated. Herein, we studied ESBL/AmpC-producing Enterobacteriaceae, Escherichia coli in particular, isolated from extraintestinal sites and feces of companion dogs. Whole-genome sequencing analysis revealed that (i) extraintestinal E. coli isolates were most closely related to those isolated from feces from the same dog, (ii) chromosomal sequences in the ST131/C1-M27 clade isolated from companion dogs were highly similar to those in the ST131/C1-M27 clade of human origin, (iii) certain plasmids, such as IncFII/pMLST F1:A2:B20/blaCTX-M-27, IncI1/pMLST16/blaCTX-M-15, or IncI1/blaCMY-2 from dog-derived E. coli isolates, shared high homology with those from several human-derived Enterobacteriaceae, (iv) chromosomal blaCTX-M-14 was identified in the ST38 isolate from a companion dog, and (v) eight out of 14 tested ESBL/AmpC-producing E. coli isolates (i.e., ST131, ST68, ST405, and ST998) belonged to the human extraintestinal pathogenic E. coli (ExPEC) group. All of the bla-coding plasmids that were sequenced genome-wide were capable of horizontal transfer. These results suggest that companion dogs can spread ESBL/AmpC-producing ExPEC via their feces. Furthermore, at least some ESBL/AmpC-producing ExPECs and bla-coding plasmids can be transmitted between humans and companion dogs. Thus, companion dogs can act as an important reservoir for ESBL/AmpC-producing E. coli in the community.

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Turton, Jane F., Michel Doumith, Katie L. Hopkins, Claire Perry, Daniele Meunier et Neil Woodford. « Clonal expansion of Escherichia coli ST38 carrying a chromosomally integrated OXA-48 carbapenemase gene ». Journal of Medical Microbiology 65, n^o 6 (1 juin 2016) : 538–46. http://dx.doi.org/10.1099/jmm.0.000248.

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van der Bij, Akke K., Gisele Peirano, Wil H. F. Goessens, Eric R. van der Vorm, M. van Westreenen et Johann D. D. Pitout. « Clinical and Molecular Characteristics of Extended-Spectrum- β-Lactamase-Producing Escherichia coli Causing Bacteremia in the Rotterdam Area, Netherlands ». Antimicrobial Agents and Chemotherapy 55, n^o 7 (18 avril 2011) : 3576–78. http://dx.doi.org/10.1128/aac.00074-11.

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ABSTRACTWe investigated the clinical and molecular characteristics of bacteremia caused by extended-spectrum-β-lactamase (ESBL)-producingEscherichia coliover a 2-year period (2008 to 2009) in the Rotterdam region (including 1 teaching hospital and 2 community hospitals) of Netherlands. The majority of patients presented with community onset urinary and intra-abdominal infections, with an increase in prevalence during 2009. The majority ofE. coliisolates produced CTX-M-15, and 4 sequence types (ST38, ST131, ST405, and ST648) predominated. There were significant differences in clinical and molecular characteristics between the 2 community hospitals.

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Park, Ji-Hyun, Kyung-Seon Bae, Jihyun Kang, Jeong-Ki Yoon et Soo-Hyung Lee. « Comprehensive Assessment of Multidrug-Resistant and Extraintestinal Pathogenic Escherichia coli in Wastewater Treatment Plant Effluents ». Microorganisms 12, n^o 6 (31 mai 2024) : 1119. http://dx.doi.org/10.3390/microorganisms12061119.

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Multidrug-resistant (MDR) Escherichia coli poses a significant threat to public health, contributing to elevated rates of morbidity, mortality, and economic burden. This study focused on investigating the antibiotic resistance profiles, resistance and virulence gene distributions, biofilm formation capabilities, and sequence types of E. coli strains resistant to six or more antibiotic classes. Among 918 strains isolated from 33 wastewater treatment plants (WWTPs), 53.6% (492/918) demonstrated resistance, 32.5% (298/918) were MDR, and over 8% (74/918) were resistant to six or more antibiotic classes, exhibiting complete resistance to ampicillin and over 90% to sulfisoxazole, nalidixic acid, and tetracycline. Key resistance genes identified included sul2, blaTEM, tetA, strA, strB, and fimH as the predominant virulence genes linked to cell adhesion but limited biofilm formation; 69% showed no biofilm formation, and approximately 3% were strong producers. Antibiotic residue analysis detected ciprofloxacin, sulfamethoxazole, and trimethoprim in all 33 WWTPs. Multilocus sequence typing analysis identified 29 genotypes, predominantly ST131, ST1193, ST38, and ST69, as high-risk clones of extraintestinal pathogenic E. coli. This study provided a comprehensive analysis of antibiotic resistance in MDR E. coli isolated from WWTPs, emphasizing the need for ongoing surveillance and research to effectively manage antibiotic resistance.

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Yamaji, Reina, Julia Rubin, Cindy Friedman, Patrick McDermott, Melody Hung-Fan et Lee Riley. « Retail Meat as a Potential Transmission Source of Community-Acquired Urinary Tract Infection ». Open Forum Infectious Diseases 4, suppl_1 (2017) : S25—S26. http://dx.doi.org/10.1093/ofid/ofx162.065.

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Abstract Background Escherichia coli causes approximately 80% of community-acquired UTI (CA-UTI), but the sources of these uropathogenic E. coli infections are not well established. Recent studies have suggested that food, especially poultry, may serve as a source of UPEC. Here we prospectively examined E. coli isolates from patients with CA-UTI and retail meat concurrently available from the same geographic region to determine the frequency of shared genotypes. Methods Between September 2016 and May 2017, we collected urine samples from patients with UTI examined at a university-affiliated healthcare center. During the same time, we recovered E.coli from retail meat products (chicken breast, ground turkey, ground beef, and pork chops) collected as part of the National Antimicrobial Resistance Monitoring System (NARMS) FDA retail meat sampling program in Northern California. Urine samples and buffered peptone water containing meat samples were cultured on MacConkey agar. Lactose-positive and indole-positive colonies were presumptively identified as E coli. Bacterial DNA was extracted by a freeze-boil method. E. coli isolates were genotyped by multilocus sequence typing (MLST). Results Of 1020 urine samples, E. coli was isolated from 210 (21%). Five pandemic MLST genotypes (ST95, ST127, ST69, ST73, and ST131) accounted for 126 (60%) isolates. Of 200 meat samples, E. coli was isolated from 76 (38%). E. coli was isolated from 29 (73%) of 40 ground turkey samples, 34 (43%) of 80 chicken breast, 7 (18%) of 40 ground beef, and 6 (15%) of 40 pork chop. ST69 and ST131 were isolated from 3 chicken samples. Other genotypes of E. coli isolates from meat samples and CA-UTI included ST10 (3), ST38 (2), ST88 (1), ST117 (5), ST906 (1), and ST1844 (1). Eleven (32%) of 34 chicken samples contained UPEC strains, compared with 4 (14%) of 29 ground turkey samples, and 1 (17%) of 6 pork chop samples; no beef samples contained UPEC strains. Conclusion Overall, we found that nearly one-quarter of retail poultry products that we tested contained UPEC strains with the same MLST genotypes found in CA-UTI patients. Foodborne transmission may account for a substantial proportion of CA-UTI. Additional studies are needed to demonstrate transmission of these genotypes from poultry to patients and to target possible prevention measures. Disclosures All authors: No reported disclosures.

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Zhang, Yanjun, Hairu Wang, Yanfang Li, Yabin Hou et Chonghua Hao. « Drug susceptibility and molecular epidemiology of Escherichia coli in bloodstream infections in Shanxi, China ». PeerJ 9 (25 octobre 2021) : e12371. http://dx.doi.org/10.7717/peerj.12371.

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Objectives We carried out a retrospective study to investigate the drug susceptibility and genetic relationship of clinical Escherichia coli isolates from patients with BSIs in Shanxi, China. Methods E. coli isolates causing BSIs were consecutively collected from June 2019 to March 2020. Antimicrobial susceptibility testing was performed by broth microdilution method. PCR was used to detect antimicrobial resistance genes coding for extended-spectrum β-lactamases (ESBLs), phylogenetic groups and seven housekeeping genes of E. coli. Results A total of 76 E. coli were collected. Antimicrobial susceptibility testing revealed that the top six E. coli resistant antibiotics were ampicillin (90.7%), ciprofloxacin (69.7%), cefazolin (65.7%), levofloxacin (63.1%), ceftriaxone and cefotaxime (56.5%). Among the 76 isolates, 43 produced ESBLs. Molecular analysis showed that CTX-M-14 was the most common ESBLs, followed by CTX-M-15 and CTX-M-55. Phylogenetic group D (42.2%) predominated, followed by group B2 (34.2%), group A (18.4%) and group B1 (5.2%). The most prevalent sequence types (STs) were ST131 (15/76), ST69 (12/76) and ST38 (6/76). Conclusions This study is the first to report the phenotypic and molecular characteristics of E. coli isolated from BSIs in Shanxi, China. Our results indicated a high prevalence of MDR in E. coli strains isolated from BSIs and a serious spread of ESBL genes in Shanxi, especially the epidemiological blaCTX-M. Phylogenetic analysis indicated genetic diversity among E. coli BSIs isolates.

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Truong, Duong Thi Quy, Yaovi Mahuton Gildas Hounmanou, Son Thi Thanh Dang, John Elmerdahl Olsen, Giang Thi Huong Truong, Nhat Thi Tran, Flemming Scheutz et Anders Dalsgaard. « Genetic Comparison of ESBL-Producing Escherichia coli from Workers and Pigs at Vietnamese Pig Farms ». Antibiotics 10, n^o 10 (25 septembre 2021) : 1165. http://dx.doi.org/10.3390/antibiotics10101165.

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We analyzed and compared genomes of Extended Spectrum Beta-Lactamase (ESBL)-producing Escherichia coli from pigs and pig farm workers at 116 farms in Vietnam. Analyses revealed the presence of blaCTX-M-55, blaCTX-M-27, blaCTX-M-15, blaCTX-M-14, blaCTX-M-3, blaCTX-M-65, blaCTX-M-24, blaDHA-1, and blaCMY2 in both hosts. Most strains from pigs contained quinolones (qnr) and colistin resistance genes (mcr-1 and mcr-3). Isolates predominantly harbored more than one plasmid replicon and some harbored plasmid replicons on the same contigs as the ESBL genes. Five strains from farm workers of ST38 (2), ST69 (1), and ST1722 (2) were classified as either uropathogenic E. coli (UPECHM)/extraintestinal pathogenic E. coli (ExPECJJ) or UPECHM, and the remaining were genetically distinct commensals. A high heterogeneity was found among the ESBL-producing E. coli from pigs and workers, with most isolates belonging to unrelated phylogroups, serogroups, and sequence types with >4046 Single-Nucleotide Polymorphisms-(SNPs). In comparing the genomes of pig isolates to those from humans, it appeared that ESBL-producing E. coli in workers did not predominantly originate from pigs but were rather host-specific. Nevertheless, the occurrence of ESBL-producing E. coli carrying plasmid-mediated colistin and quinolone resistance genes in pigs could represent a potential source for horizontal transmission to humans through food rather than direct contact.

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Sato, Toyotaka, Shin-ichi Yokota, Tooru Tachibana, Satoshi Tamai, Shigeki Maetani, Yutaka Tamura et Motohiro Horiuchi. « Isolation of Human Lineage, Fluoroquinolone-Resistant and Extended-β-Lactamase-Producing Escherichia coli Isolates from Companion Animals in Japan ». Antibiotics 10, n^o 12 (28 novembre 2021) : 1463. http://dx.doi.org/10.3390/antibiotics10121463.

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An increase in human and veterinary fluoroquinolone-resistant Escherichia coli is a global concern. In this study, we isolated fluoroquinolone-resistant E. coli isolates from companion animals and characterized them using molecular epidemiological analysis, multiplex polymerase chain reaction to detect E. coli ST131 and CTX-M type extended-spectrum β-lactamases (ESBL), and multi-locus sequence typing analysis. Using plain-CHROMagar ECC, 101 E. coli isolates were isolated from 34 rectal swabs of dogs and cats. The prevalence of resistance to fluoroquinolone and cefotaxime was 27.7% and 24.8%, respectively. The prevalence of fluoroquinolone-resistant isolates (89.3%) was higher when CHROMagar ECC with CHROMagar ESBL supplement was used for E. coli isolation. The prevalence of cefotaxime resistance was also higher (76.1%) when 1 mg/L of ciprofloxacin-containing CHROMagar ECC was used for isolation. The cefotaxime-resistant isolates possessed CTX-M type β-lactamase genes (CTX-M-14, CTX-M-15, or CTX-M-27). Seventy-five percent of fluoroquinolone-resistant isolates were sequence types ST131, ST10, ST1193, ST38, or ST648, which are associated with extensive spread in human clinical settings. In addition, we isolated three common fluoroquinolone-resistant E. coli lineages (ST131 clade C1-M-27, C1-nM27 and ST2380) from dogs and their respective owners. These observations suggest that companion animals can harbor fluoroquinolone-resistant and/or ESBL-producing E. coli, in their rectums, and that transmission of these isolates to their owners can occur.

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Kocsis, Béla, Dániel Gulyás et Dóra Szabó. « Emergence and Dissemination of Extraintestinal Pathogenic High-Risk International Clones of Escherichia coli ». Life 12, n^o 12 (10 décembre 2022) : 2077. http://dx.doi.org/10.3390/life12122077.

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Multiresistant Escherichia coli has been disseminated worldwide, and it is one of the major causative agents of nosocomial infections. E. coli has a remarkable and complex genomic plasticity for taking up and accumulating genetic elements; thus, multiresistant high-risk clones can evolve. In this review, we summarise all available data about internationally disseminated extraintestinal pathogenic high-risk E. coli clones based on whole-genome sequence (WGS) data and confirmed outbreaks. Based on genetic markers, E. coli is clustered into eight phylogenetic groups. Nowadays, the E. coli ST131 clone from phylogenetic group B2 is the predominant high-risk clone worldwide. Currently, strains of the C1-M27 subclade within clade C of ST131 are circulating and becoming prominent in Canada, China, Germany, Hungary and Japan. The C1-M27 subclade is characterised by blaCTX-M-27. Recently, the ST1193 clone has been reported as an emerging high-risk clone from phylogenetic group B2. ST38 clone carrying blaOXA-244 (a blaOXA-48-like carbapenemase gene) caused several outbreaks in Germany and Switzerland. Further high-risk international E. coli clones include ST10, ST69, ST73, ST405, ST410, ST457. High-risk E. coli strains are present in different niches, in the human intestinal tract and in animals, and persist in environment. These strains can be transmitted easily within the community as well as in hospital settings. WGS analysis is a useful tool for tracking the dissemination of resistance determinants, the emergence of high-risk mulitresistant E. coli clones and to analyse changes in the E. coli population on a genomic level.

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Abril, Deisy, Ingrid Gisell Bustos Moya, Ricaurte Alejandro Marquez-Ortiz, Diego Fernando Josa Montero, Zayda Lorena Corredor Rozo, Isabel Torres Molina, Natasha Vanegas Gómez et Javier Escobar-Perez. « First Report and Comparative Genomics Analysis of a blaOXA-244-Harboring Escherichia coli Isolate Recovered in the American Continent ». Antibiotics 8, n^o 4 (13 novembre 2019) : 222. http://dx.doi.org/10.3390/antibiotics8040222.

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The carbapenemase OXA-244 is a derivate of OXA-48, and its detection is very difficult in laboratories. Here, we report the identification and genomic analysis of an Escherichia coli isolate (28Eco12) harboring the blaOXA-244 gene identified in Colombia, South America. The 28Eco12 isolate was identified during a retrospective study, and it was recovered from a patient treated in Colombia. The complete nucleotide sequence was established using the PacBio platform. A comparative genomics analysis with other blaOXA-244–harboring Escherichia coli strains was performed. The 28Eco12 isolate belonged to sequence type (ST) 38, and its genome was composed of two molecules, a chromosome of 5,343,367 bp and a plasmid of 92,027 bp, which belonged to the incompatibility group IncY and did not harbor resistance genes. The blaOXA-244 gene was chromosomally encoded and mobilized by an ISR1-related Tn6237 composite transposon. Notably, this transposon was inserted and located within a new genomic island. To our knowledge, this is the first report of a blaOXA-244–harboring Escherichia coli isolate in America. Our results suggest that the introduction of the OXA-244-producing E. coli isolate was through clonal expansion of the ST38 pandemic clone. Other isolates producing OXA-244 could be circulating silently in America.

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Schmitt, Kira, Stefan P. Kuster, Katrin Zurfluh, Rahel S. Jud, Jane E. Sykes, Roger Stephan et Barbara Willi. « Transmission Chains of Extended-Spectrum Beta-Lactamase-Producing Enterobacteriaceae at the Companion Animal Veterinary Clinic–Household Interface ». Antibiotics 10, n^o 2 (9 février 2021) : 171. http://dx.doi.org/10.3390/antibiotics10020171.

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Extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-E) among animals and humans are a public health threat. This study analyzed the occurrence of ESBL-E in a high-risk environment in a companion animal clinic and two animal patients’ households. In an intensive care unit (ICU), rectal swabs from 74 dogs and cats, 74 hand swabs from staff and 298 swabs from surfaces were analyzed for ESBL-E. Seventeen hospitalized patients (23%) and ten (3%) surfaces in the ICU tested ESBL-E positive. Transmission chains for Klebsiella pneumoniae ST307 blaCTX-M-15 and Escherichia coli ST38 blaCTX-M-14, ST88 blaCTX-M-14 and ST224 blaCTX-M-1 were observed over extended periods of time (14 to 30 days) with similar strains isolated from patients and the clinical environment. After discharge, two colonized dogs (dogs 7 and 12) and their household contacts were resampled. Dog 7 tested repeatedly positive for 77 days, dog 12 tested negative; six (24%) surfaces in the household of the persistently colonized dog tested ESBL-E positive. The owner of dog 7 and one of the owners of dog 12 were colonized. Based on whole genome sequencing, isolates from the owners, their dogs and other ICU patients belonged to the same clusters, highlighting the public health importance of ESBL-E in companion animal clinics.

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Giufrè, Maria, Giulia Errico, Monica Monaco, Maria Del Grosso, Michela Sabbatucci, Annalisa Pantosti, Marina Cerquetti et al. « Whole Genome Sequencing and Molecular Analysis of Carbapenemase-Producing Escherichia coli from Intestinal Carriage in Elderly Inpatients ». Microorganisms 10, n^o 8 (3 août 2022) : 1561. http://dx.doi.org/10.3390/microorganisms10081561.

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The spread of carbapenemase-producing (CP) Enterobacterales is currently a worldwide concern, especially in the elderly. Twelve CP-E. coli isolated from rectal swabs of colonized inpatients aged ≥65 years from four hospitals in two Italian cities (Milan and Rome) were analyzed by whole genome sequencing (WGS) to obtain multi-locus sequence typing (MLST), identification of carbapenemase-encoding genes, resistome, plasmid content, and virulence genes. MLST analysis showed the presence of 10 unrelated lineages: ST410 (three isolates from three different hospitals in two cities) and ST12, ST38, ST69, ST95, ST131, ST189, ST648, ST1288, and ST1598 (one isolate each). Most isolates (9/12, 75%) contained a serine-β-lactamase gene (5 blaKPC-3, 2 blaKPC-2, and 2 blaOXA-181), while three isolates harbored a metallo-β-lactamase gene (two blaNDM-5 and one blaVIM-1). In most CP-E. coli, the presence of more than one plasmid was observed, with the predominance of IncF. Several virulence genes were detected. All isolates contained genes enhancing the bacterial fitness, such as gad and terC, and all isolates but one, fimH, encoding type 1 fimbriae. In conclusion, CP-E. coli clones colonizing elderly patients showed heterogeneous genetic backgrounds. We recommend strict surveillance to monitor and prevent the spread of successful, high-risk clones in healthcare settings.

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Mukerji, Shewli, Marc Stegger, Alec Vincent Truswell, Tanya Laird, David Jordan, Rebecca Jane Abraham, Ali Harb, Mary Barton, Mark O’Dea et Sam Abraham. « Resistance to critically important antimicrobials in Australian silver gulls (Chroicocephalus novaehollandiae) and evidence of anthropogenic origins ». Journal of Antimicrobial Chemotherapy 74, n^o 9 (9 juillet 2019) : 2566–74. http://dx.doi.org/10.1093/jac/dkz242.

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Abstract Objectives Antimicrobial resistance (AMR) to critically important antimicrobials (CIAs) amongst Gram-negative bacteria can feasibly be transferred amongst wildlife, humans and domestic animals. This study investigated the ecology, epidemiology and origins of CIA-resistant Escherichia coli carried by Australian silver gulls (Chroicocephalus novaehollandiae), a gregarious avian wildlife species that is a common inhabitant of coastal areas with high levels of human contact. Methods Sampling locations were widely dispersed around the perimeter of the Australian continent, with sites separated by up to 3500 km. WGS was used to study the diversity and molecular characteristics of resistant isolates to ascertain their epidemiological origin. Results Investigation of 562 faecal samples revealed widespread occurrence of extended-spectrum cephalosporin-resistant (21.7%) and fluoroquinolone-resistant (23.8%) E. coli. Genome sequencing revealed that CIA-resistant E. coli isolates (n = 284) from gulls predominantly belonged to human-associated extra-intestinal pathogenic E. coli (ExPEC) clones, including ST131 (17%), ST10 (8%), ST1193 (6%), ST69 (5%) and ST38 (4%). Genomic analysis revealed that gulls carry pandemic ExPEC-ST131 clades (O25:H4 H30-R and H30-Rx) and globally emerging fluoroquinolone-resistant ST1193 identified among humans worldwide. Comparative analysis revealed that ST131 and ST1193 isolates from gulls overlapped extensively with human clinical isolates from Australia and overseas. The present study also detected single isolates of carbapenem-resistant E. coli (ST410-blaOXA-48) and colistin-resistant E. coli (ST345-mcr-1). Conclusions The carriage of diverse CIA-resistant E. coli clones that strongly resemble pathogenic clones from humans suggests that gulls can act as ecological sponges indiscriminately accumulating and disseminating CIA-resistant bacteria over vast distances.

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Cai, Jia Chang, Rong Zhang, Yan Yan Hu, Hong Wei Zhou et Gong-Xiang Chen. « Emergence of Escherichia coli Sequence Type 131 Isolates Producing KPC-2 Carbapenemase in China ». Antimicrobial Agents and Chemotherapy 58, n^o 2 (9 décembre 2013) : 1146–52. http://dx.doi.org/10.1128/aac.00912-13.

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ABSTRACTTwenty-two KPC-2-producingEscherichia coliisolates were obtained from three hospitals in Hangzhou, China, from 2007 to 2011. One isolate, with OmpC porin deficiency, exhibited high-level carbapenem resistance. Pulsed-field gel electrophoresis showed that few isolates were indistinguishable or closely related. Multilocus sequence typing indicated that sequence type 131 (ST131) was the predominant type (9 isolates, 40.9%), followed by ST648 (5 isolates), ST405 (2 isolates), ST38 (2 isolates), and 4 single STs, ST69, ST2003, ST2179, and ST744. Phylogenetic analysis indicated that 9 group B2 isolates belonged to ST131, and 5 of 11 group D isolates belonged to ST648. Only one group B1 isolate and one group A isolate were identified. A representative plasmid (pE1) was partially sequenced, and a 7,788-bp DNA fragment encoding Tn3transposase, Tn3resolvase, ISKpn8transposase, KPC-2, and ISKpn6-like transposase was obtained. TheblaKPC-2-surrounding sequence was amplified by a series of primers. The PCR results showed that 13 isolates were consistent with the genetic environment in pE1. It is the first report of rapid emergence of KPC-2-producingE. coliST131 in China. TheblaKPC-2gene of most isolates was located on a similar genetic structure.

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REHMAN, MUHAMMAD ATTIQ, HEIDI REMPEL, CATHERINE D. CARRILLO, KIM ZIEBELL, KEVIN ALLEN, AMEE R. MANGES, EDWARD TOPP et MOUSSA S. DIARRA. « Virulence Genotype and Phenotype of Multiple Antimicrobial-Resistant Escherichia coli Isolates from Broilers Assessed from a “One-Health” Perspective ». Journal of Food Protection 85, n^o 2 (11 novembre 2021) : 336–54. http://dx.doi.org/10.4315/jfp-21-273.

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ABSTRACT Extraintestinal pathogenic Escherichia coli (ExPEC) include several serotypes that have been associated with colibacillosis in poultry and with urinary tract infections (UTIs) and newborn meningitis in humans. In this study, 57 antimicrobial-resistant E. coli from apparently healthy broiler chickens were characterized for their health and safety risks. These isolates belonged to 12 serotypes, and isolates of the same serotype were clonal based on single nucleotide variant analysis. Most of the isolates harbored plasmids; IncC and IncFIA were frequently detected. The majority of the resistant isolates harbored plasmid-mediated resistance genes, including aph(3″)-Ib, aph(6)-Id, blaCMY-2, floR, sul1, sul2, tet(A), and tet(B), in agreement with their resistant phenotypes. The class 1 integron was detected in all E. coli serotypes except O124:H25 and O7:H6. Of the 57 broiler E. coli isolates, 27 were avian pathogenic, among which 18 were also uropathogenic E. coli and the remainder were other ExPEC. The two isolates of serotype O161:H4 (ST117) were genetically related to the control avian pathogenic strains and a clinical isolate associated with UTIs. A strain of serotype O159:H45 (ST101) also was closely related to a UTI isolate. The detected virulence factors included adhesins, invasins, siderophores, type III secretion systems, and toxins in combination with other virulence determinants. A broiler isolate of serotype O7:H18 (ST38) carried the ibeA gene encoding a protein involved in invasion of brain endothelium on a 102-kbp genetic island. This isolate moderately adhered and invaded Caco-2 cells and induced mortality (42.5%) in a day-old-chick infection model. The results of this study suggest that multiple antimicrobial-resistant E. coli isolates recovered from apparent healthy broilers can be pathogenic and act as reservoirs for antimicrobial resistance genes, highlighting the necessity of their assessment in a “One-Heath” context. HIGHLIGHTS

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Bouaziz, Amira, Lotfi Loucif, Ammar Ayachi, Karima Guehaz, Esma Bendjama et Jean-Marc Rolain. « Migratory White Stork (Ciconia ciconia) : A Potential Vector of the OXA-48-Producing Escherichia coli ST38 Clone in Algeria ». Microbial Drug Resistance 24, n^o 4 (mai 2018) : 461–68. http://dx.doi.org/10.1089/mdr.2017.0174.

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Grünzweil, Olivia M., Lauren Palmer, Adriana Cabal, Michael P. Szostak, Werner Ruppitsch, Christian Kornschober, Maciej Korus et al. « Presence of β-Lactamase-producing Enterobacterales and Salmonella Isolates in Marine Mammals ». International Journal of Molecular Sciences 22, n^o 11 (31 mai 2021) : 5905. http://dx.doi.org/10.3390/ijms22115905.

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Marine mammals have been described as sentinels of the health of marine ecosystems. Therefore, the aim of this study was to investigate (i) the presence of extended-spectrum β-lactamase (ESBL)- and AmpC-producing Enterobacterales, which comprise several bacterial families important to the healthcare sector, as well as (ii) the presence of Salmonella in these coastal animals. The antimicrobial resistance pheno- and genotypes, as well as biocide susceptibility of Enterobacterales isolated from stranded marine mammals, were determined prior to their rehabilitation. All E. coli isolates (n = 27) were screened for virulence genes via DNA-based microarray, and twelve selected E. coli isolates were analyzed by whole-genome sequencing. Seventy-one percent of the Enterobacterales isolates exhibited a multidrug-resistant (MDR) pheno- and genotype. The gene blaCMY (n = 51) was the predominant β-lactamase gene. In addition, blaTEM-1 (n = 38), blaSHV-33 (n = 8), blaCTX-M-15 (n = 7), blaOXA-1 (n = 7), blaSHV-11 (n = 3), and blaDHA-1 (n = 2) were detected. The most prevalent non-β-lactamase genes were sul2 (n = 38), strA (n = 34), strB (n = 34), and tet(A) (n = 34). Escherichia coli isolates belonging to the pandemic sequence types (STs) ST38, ST167, and ST648 were identified. Among Salmonella isolates (n = 18), S. Havana was the most prevalent serotype. The present study revealed a high prevalence of MDR bacteria and the presence of pandemic high-risk clones, both of which are indicators of anthropogenic antimicrobial pollution, in marine mammals.

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Nesporova, Kristina, Adam Valcek, Costas Papagiannitsis, Iva Kutilova, Ivana Jamborova, Lenka Davidova-Gerzova, Ibrahim Bitar, Jaroslav Hrabak, Ivan Literak et Monika Dolejska. « Multi-Drug Resistant Plasmids with ESBL/AmpC and mcr-5.1 in Paraguayan Poultry Farms : The Linkage of Antibiotic Resistance and Hatcheries ». Microorganisms 9, n^o 4 (17 avril 2021) : 866. http://dx.doi.org/10.3390/microorganisms9040866.

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Poultry represents a common source of bacteria with resistance to antibiotics including the critically important ones. Selective cultivation using colistin, cefotaxime and meropenem was performed for 66 chicken samples coming from 12 farms in Paraguay while two breeding companies supplied the farms. A total of 62 Escherichia coli and 22 Klebsiella pneumoniae isolates were obtained and representative isolates were subjected to whole-genome sequencing. Relatively high prevalence of phylogenetic group D and F was observed in E. coli isolates and several zoonotic sequence types (STs) including ST457 (14 isolates), ST38 (5), ST10 (2), ST117 (2) or ST93 (4) were detected. Isolates from three farms, which purchased chicken from a Paraguayan hatchery showed higher prevalence of mcr-5.1 and blaCTX-M-8 compared to the other nine farms, which purchased chickens from a Brazilian hatchery. Moreover, none of the K. pneumoniae isolates were linked to the Paraguayan hatchery. ESBL/AmpC and mcr-5-carrying multi-drug resistant (MDR) plasmids were characterized, and complete sequences were obtained for eight plasmids. The study shed light on Paraguayan poultry farms as a reservoir of antibiotic resistance commonly conferred via MDR plasmids and showed linkage between resistance and origin of the chickens at the hatcheries level.

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Martino, Florencia, Alejandro Petroni, María Alejandra Menocal, Alejandra Corso, Roberto Melano et Diego Faccone. « New insights on mcr-1-harboring plasmids from human clinical Escherichia coli isolates ». PLOS ONE 19, n^o 2 (26 février 2024) : e0294820. http://dx.doi.org/10.1371/journal.pone.0294820.

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Mobile colistin resistance (mcr) genes were described recently in Gram-negative bacteria including carbapenem-resistant Enterobacterales. There are ten mcr genes described in different Gram-negative bacteria, however, Escherichia coli harboring mcr-1 gene is by far the most frequent combination. In Argentina, mcr-1 gene was characterized only on plasmids belonging to IncI2 group. The aim of this work was to get new insights of mcr-1-harboring plasmids from E. coli. Eight E. coli isolates from a larger collection of 192 clinical E. coli isolates carrying the mcr-1 gene were sequenced using next generation technologies. Three isolates belonged to ST131 high-risk clone, and five to single ST, ST38, ST46, ST226, ST224, and ST405. Eight diverse mcr-1-harboring plasmids were analyzed: IncI2 (1), IncX4 (3), IncHI2/2A (3) and a hybrid IncFIA/HI1A/HI1B (1) plasmid. Plasmids belonging to the IncI2 (n = 1) and IncX4 (n = 3) groups showed high similarity with previously described plasmids. Two IncHI2/HI2A plasmids, showed high identity between them, while the third, showed several differences including additional resistance genes like tet(A) and floR. One IncFIA/H1A/H1B hybrid plasmid was characterized, highly similar to pSRC27-H, a prototype plasmid lacking mcr genes. mcr-1.5 variant was found in four plasmids with three different Inc groups: IncI2, IncHI2/HI2A and the hybrid FIA/HI1A/HI1B plasmid. mcr-1.5 variant is almost exclusively described in our country and with a high frequency. In addition, six E. coli isolates carried three allelic variants codifying for CTX-M-type extended-spectrum-β-lactamases: blaCTX-M-2 (3), blaCTX-M-65 (2), and blaCTX-M-14 (1). It is the first description of mcr-1 harboring plasmids different to IncI2 group in our country. These results represents new insights about mcr-1 harboring plasmids recovered from E. coli human samples from Argentina, showing different plasmid backbones and resistance gene combinations.

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Duffy, Nadezhda, Davina Campbell, Hannah E. Reses, Elizabeth Basiliere, Chris Bower, Ghinwa Dumyati, Marion Kainer et al. « Epidemiologic Characteristics of ESBL-Producing ST131 E. coli Identified Through the Emerging Infections Program, 2017 ». Infection Control & ; Hospital Epidemiology 41, S1 (octobre 2020) : s214—s215. http://dx.doi.org/10.1017/ice.2020.758.

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Background: Extended-spectrum β-lactamase–producing (ESBL) Escherichia coli infection incidence is increasing in the United States. This increase may be due to the rapid expansion of ST131, which is now the predominant ESBL strain globally, often multidrug resistant, and has been shown to establish longer-term human colonization than other E. coli strains. We assessed potential risk factors that distinguish ST131 from other ESBL E. coli. Methods: From October 1 through December 31, 2017, 5 CDC Emerging Infections Program (EIP) sites pilot tested active, laboratory-based surveillance in selected counties in Colorado, Georgia, New Mexico, New York, and Tennessee. An E. coli case was defined as the first isolation from a normally sterile body site or urine in a surveillance area resident in a 30-day period resistant to 1 extended-spectrum cephalosporin antibiotic and susceptible or intermediate to all carbapenem antibiotics tested. Epidemiologic data were collected from case patients’ medical records. A convenience sample of 117 E. coli isolates from case patients was collected. All isolates underwent whole-genome sequencing to determine sequence type and the presence of ESBL genes. We compared ST131 E. coli epidemiology to other ESBL E. coli. Results: Among 117 E. coli isolates, 97 (83%) were ESBL producers. Of the 97 ESBL E. coli, 52 (54%) were ST131 (range, for 4 EIP sites submitting >10 isolates: 25%–88%; P < .001). Other common STs were ST38 (12%) and ST10 (5%). ST131 infections were more likely to be healthcare-associated than non-ST131 (56% vs 36%; P = .05) (Table 1). Among specific prior healthcare exposures, only residence in long-term care facilities (LTCFs) in the year before culture was more common among ST131 case patients (29% vs 11%; P = .03). Notably, 85% of ESBL E. coli collected from LTCF residents were ST131. ST131 E. coli were more common among patients with underlying medical conditions (81% vs 60%; P = .02). No statistically significant difference by sex, race, age, culture source, location of culture collection, and frequency of antibiotic use in the prior 30 days was observed. Conclusions:The prevalence of ST131 E. coli varies regionally. The association between ST131 and LTCFs suggests that these may be particularly important settings for ST131 acquisition. Improving infection control measures that limit ESBL transmission in these settings and preventing dissemination in facilities receiving patients from LTCFs may be necessary to contain ST131 spread.Funding: NoneDisclosures: None

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Mhaya, Amel, Rahma Trabelsi, Sabine Aillerie, Fatima M’Zali, Dominique Bégu, Slim Tounsi, Radhouane Gdoura et Corinne Arpin. « Detection of Clones B2-ST131-C2 and A-ST617 in Escherichia coli Producing Both CTX-M-15 and CTX-M-27 from Tunisian Community Patients ». Antibiotics 11, n^o 10 (29 septembre 2022) : 1329. http://dx.doi.org/10.3390/antibiotics11101329.

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During a two-month period (2017–2018), 336 urine samples positive for Escherichia coli were collected from Tunisian patients. Of the 336 samples, 266 were collected from community patients and 70 from hospital settings. In all, 15 ESBL producers were identified (8 and 7, respectively) and assigned to 13 pulsotypes, including four ESBL-producing E. coli (ESBL-E) with E1 and E2 profiles (2 isolates each) from community patients. The two strains E1 were identified as B2-ST131 subclade C2 and the two isolates E2, A-ST617. The four strains carrying both CTX-M-15 and CTX-M-27, exhibited the multireplicon IncFII/F1A/F1B with the same formula F31:A4:B1. Two isolates with patterns E3 and E4 (Dice coefficient, 78.7%) isolated from community and hospital settings of two geographic areas were assigned to the emerging ST131 C1-M27 subclade and contained the replicon F1:A-:B20. The remaining ESBL-E divided into different sequence types/associated CTX-M: 2 ST131-C2/CTX-M-15 and ST744/CTX-M-55, ST617/CTM-15, ST2973/CTX-M-55, ST6448/CTX-M-15, ST224/CTX-M-15, ST1431/CTX-M-15, and ST38/CTX-M-27, one isolate each. Our study reports for the first time the presence in the Tunisian community of two clones of E. coli, including the virulent clone ST131-C2 harboring both CTX-M-15 and CTX-M-27, and confirms the spread of the emergent clone ST131-C1-M-27, notably in community urinary tract infections.

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Byarugaba, Denis K., Bernard Erima, Godfrey Wokorach, Stephen Alafi, Hannah Kibuuka, Edison Mworozi, Ambrose K. Musinguzi, James Kiyengo, Florence Najjuka et Fred Wabwire-Mangen. « Resistome and virulome of high-risk pandemic clones of multidrug-resistant extra-intestinal pathogenic Escherichia coli (ExPEC) isolated from tertiary healthcare settings in Uganda ». PLOS ONE 18, n^o 11 (22 novembre 2023) : e0294424. http://dx.doi.org/10.1371/journal.pone.0294424.

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Multi-drug resistant (MDR) globally disseminated extraintestinal pathogenic high-risk Escherichia coli (ExPEC) clones are threatening the gains in bacterial disease management. In this study, we evaluated the genomic structure including the resistome and virulome of the E. coli isolates from extraintestinal infections using whole genome sequencing (WGS). The results highlight that isolates were highly resistant (≥ 90.0%) to commonly used antibiotics (Ampicillin, Trimethoprim-Sulfamethoxazole, Nalidixic acid, and Piperacillin) and were less (<14%) resistant to last resort antibiotics; Imipenem (10.94%) and Meropenem (10.20%). A greater proportion of the E. coli isolates belonged to phylogroup B2 (30.52%) and phylogroup A (27.37%). The sequence types ST131 of phylogroup B2 (21.05%) and ST648 of phylogroup F (9.3%) were the dominant pandemic high-risk clones identified in addition to the ST1193, ST410, ST69, ST38, ST405, and ST10. Many of the isolates were MDR and most (64.58%) carried the blaCTX-M-15 gene for extended-spectrum β-lactamases. There was a high correlation between phylogroups and the occurrence of both antimicrobial resistance and virulence genes. The cephalosporin-resistance gene blaEC-5 was only found in phylogroup B2 while blaEC-8 and blaEC-19, were only found within phylogroup D and phylogroup F respectively. Aminoglycoside gene (aadA1) was only associated with phylogroups D and C. The isolates were armed with a broad range of virulence genes including adhesins, toxins, secreted proteases, iron uptake genes, and others. The yfcv, chuA, and kpsE genes preferentially occurred among isolates of phylogroup B2. The study underlines the predominance of MDR internationally disseminated high-risk ExPEC clones with a broad range of virulence genes known to be highly transmissible in healthcare and community settings.

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Kaur, Harpreet, Inderjit Singh, Vinay Modgil, Nisha Singh, Balvinder Mohan et Neelam Taneja. « Genome sequence of pan drug-resistant enteroaggregative Escherichia coli belonging to ST38 clone from India, an emerging EAEC/UPEC hybrid pathotype ». Indian Journal of Medical Microbiology 49 (mai 2024) : 100606. http://dx.doi.org/10.1016/j.ijmmb.2024.100606.

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Sekizuka, Tsuyoshi, Mari Matsui, Kunikazu Yamane, Fumihiko Takeuchi, Makoto Ohnishi, Akira Hishinuma, Yoshichika Arakawa et Makoto Kuroda. « Complete Sequencing of the blaNDM-1-Positive IncA/C Plasmid from Escherichia coli ST38 Isolate Suggests a Possible Origin from Plant Pathogens ». PLoS ONE 6, n^o 9 (23 septembre 2011) : e25334. http://dx.doi.org/10.1371/journal.pone.0025334.

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Falgenhauer, Linda, Patrice Nordmann, Can Imirzalioglu, Yancheng Yao, Jane Falgenhauer, Anja M. Hauri, Petra Heinmüller et Trinad Chakraborty. « Cross-border emergence of clonal lineages of ST38 Escherichia coli producing the OXA-48-like carbapenemase OXA-244 in Germany and Switzerland ». International Journal of Antimicrobial Agents 56, n^o 6 (décembre 2020) : 106157. http://dx.doi.org/10.1016/j.ijantimicag.2020.106157.

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Hameed, Muhammad Fazal, Yanan Chen, Hazrat Bilal, Sabir Khan, Honghua Ge, Chen Xiaofang et Pengying Gu. « The Co-occurrence of mcr-3 and fosA3 in IncP plasmid in ST131 Escherichia coli : A novel case ». Journal of Infection in Developing Countries 16, n^o 04 (30 avril 2022) : 622–29. http://dx.doi.org/10.3855/jidc.15943.

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Introduction: Plasmid-mediated colistin resistance genes, especially mcr-3 combined with the fosfomycin resistance gene fosA3, are a grave health concern. Our study was designed to determine the epidemiological characteristics of the combination of mcr-3 and fosA3 in Anhui province, China. Methodology: A total of 127 multi-drug-resistant (MDR) E. coli strains were assessed for antibiotic resistance/sensitivity to detect mcr-3 and fosA3 using polymerase chain reaction (PCR) and sequencing. The genes of interest were conjugated using EC600, and replicon and sequence types (STs) were identified by PCR-based replicon typing (PBRT) and multilocus sequence typing (MLST). Cluster similarity and genomic relatedness among the positive isolates were confirmed by Xbal PFGE. Results: The processed E. coli isolates were highly resistant to the tested antibiotics; the prevalence of mcr-3 was 0.78% in the transferable IncP-type plasmid in ST131, whereas fosA3 prevalence was 38.58% among different transferable plasmids, including IncFIIK, IncFII and IncA/C, and in various STs including ST69, ST1193, ST12, ST46, ST57, ST1196, ST38, ST95, ST131, ST7584 and ST10184. Both were successfully transferred to EC600. The Xbal PFGE cluster exposed similarities among the STs. Conclusions: Our results show that to control the spread of colistin and fosfomycin resistance genes in human pathogens, the ban on colistin must be continued in animal feeding farms not only in China but around the world; additionally, awareness platforms on the use of colistin must be implemented and strict policies in poultry and pig farms must be maintained. Furthermore, fosfomycin misuse by patients and overuse by physicians must be strictly managed to stop the spread of fosfomycin resistance.

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Pankok, Frederik, Frieder Fuchs, Ulrike Loderstädt, Martin Kaase, Carsten Balczun, Simone Scheithauer, Hagen Frickmann et Ralf Matthias Hagen. « Molecular Epidemiology of Escherichia coli with Resistance against Third-Generation Cephalosporines Isolated from Deployed German Soldiers—A Retrospective Assessment after Deployments to the African Sahel Region and Other Sites between 2007 and 2016 ». Microorganisms 10, n^o 12 (11 décembre 2022) : 2448. http://dx.doi.org/10.3390/microorganisms10122448.

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Colonization and infection with bacteria with acquired antibiotic resistance are among the risks for soldiers on international deployments. Enterobacterales with resistance against third-generation cephalosporines are amongst the most frequently imported microorganisms. To contribute to the scarcely available epidemiological knowledge on deployment-associated resistance migration, we assessed the molecular epidemiology of third-generation cephalosporine-resistant Escherichia coli isolated between 2007 and 2016 from German soldiers after deployments, with a particular focus on the African Sahel region. A total of 51 third-generation cephalosporine-resistant E. coli isolated from 51 military returnees from deployment collected during the assessment period between 2007 and 2016 were subjected to short-read next-generation sequencing analysis. Returnees from the Sahel region (Djibouti, Mali, South Sudan, Sudan, Sudan, and Uganda) comprised a proportion of 52.9% (27/51). Repeatedly isolated sequence types according to the Warwick University scheme from returnees from the Sahel region were ST38, ST131, and ST648, confirming previous epidemiological assessments from various sub-Saharan African regions. Locally prevalent resistance genes in isolates from returnees from the Sahel region associated with third-generation resistance were blaCTX-M-15, blaCTX-M-27, blaCTX-M-1, blaTEM-169, blaCTX-M-14, blaCTX-M-99-like, blaCTX-M-125, blaSHV-12, and blaDHA-1, while virulence genes were east1, sat, and tsh in declining order of frequency of occurrence each. In line with phenotypically observed high resistance rates for aminoglycosides and trimethoprim/sulfamethoxazole, multiple associated resistance genes were observed. A similar, slightly more diverse situation was recorded for the other deployment sites. In summary, this assessment provides first next-generation sequencing-based epidemiological data on third-generation cephalosporine-resistant E. coli imported by deployed German soldiers with a particular focus on deployments to the Sahel region, thus serving as a small sentinel. The detected sequence types are well in line with the results from previous epidemiological assessments in sub-Saharan Africa.

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Guiral, Elisabet, Milene Gonçalves Quiles, Laura Muñoz, Javier Moreno-Morales, Izaskun Alejo-Cancho, Pilar Salvador, Miriam J. Alvarez-Martinez, Francesc Marco et Jordi Vila. « Emergence of Resistance to Quinolones and β-Lactam Antibiotics in Enteroaggregative and Enterotoxigenic Escherichia coli Causing Traveler’s Diarrhea ». Antimicrobial Agents and Chemotherapy 63, n^o 2 (26 novembre 2018) : e01745-18. http://dx.doi.org/10.1128/aac.01745-18.

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ABSTRACT The objective of this study was to assess the antimicrobial resistance of enteroaggregative Escherichia coli (EAEC) and enterotoxigenic E. coli (ETEC) strains causing traveler’s diarrhea (TD) and to investigate the molecular characterization of antimicrobial resistance genes to third-generation cephalosporins, cephamycins, and quinolones. Overall, 39 EAEC and 43 ETEC clinical isolates were studied. The susceptibilities of EAEC and ETEC against ampicillin, amoxicillin-clavulanic acid, cefotaxime, imipenem, chloramphenicol, tetracycline, co-trimoxazole, nalidixic acid, ciprofloxacin, azithromycin, and rifaximin were determined. All genes encoding resistance determinants were detected by PCR or PCR plus DNA sequencing. The epidemiology of selected EAEC and ETEC strains was studied using multilocus sequence typing (MLST). The resistance to quinolones of EAEC and ETEC strains causing TD has significantly increased over the last decades, and high percentages have been found especially in patients traveling to India and sub-Saharan Africa. Sequence type 38 (ST38) and ST131, carrying the blaCTX-M-15 and blaCTX-M-27 genes, respectively, are highly prevalent among extended-spectrum β-lactamase (ESBL)-producing EAEC and ETEC strains. The cephamycinase ACT-20 is described in the present study for the first time in EAEC and ETEC strains causing TD in patients who had traveled to Central America. The percentages of resistance to azithromycin in EAEC and ETEC isolates from patients to Southeast Asia/India and Africa are above 25%. Meanwhile, rifaximin is still active against EAEC and ETEC, with the prevalence of resistant strains not being high. In conclusion, fluoroquinolones should no longer be considered the drugs of choice for the prevention or treatment in TD for travelers traveling to India and Africa. Azithromycin and rifaximin are still a good alternative to treat TD caused by EAEC or ETEC.

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Markovska, Rumyana, Petya Stankova, Temenuga Stoeva, Marianna Murdjeva, Yulia Marteva-Proevska, Dobrinka Ivanova, Maryia Sredkova, Atanaska Petrova, Kalina Mihova et Lyudmila Boyanova. « Dissemination of High-Risk Clones Enterobacterales among Bulgarian Fecal Carriage Isolates ». Microorganisms 10, n^o 11 (29 octobre 2022) : 2144. http://dx.doi.org/10.3390/microorganisms10112144.

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The gastrointestinal tract is an important reservoir of high-risk Enterobacteria clones and a driver of antimicrobial resistance in hospitals. In this study, patients from six hospitals in four major Bulgarian towns were included in this study. Overall, 205 cefotaxime-resistant isolates (35.3%) of Enterobacterales order were detected in fecal samples among 580 patients during the period of 2017–2019. ESBL/carbapenemase/plasmidic AmpC producer rates were 28.8%, 2.4%, and 1.2%, respectively. A wide variety of ESBLs: CTX-M-15 (41%), CTX-M-3 (24%), CTX-M-27 (11%), and CTX-M-14 (4%) was found. The carbapenemases identified in this study were New Delhi metalo-β-lactamase (NDM)-1 (5.4%) and Klebsiella carbapenemase (KPC)-2 (1.5%). Most NDM-1 isolates also produced CTX-M-15/-3 and CMY-4 β-lactamases. They belonged to ST11 Klebsiella pneumoniae clone. The epidemiology typing revealed three main high-risk K. pneumoniae clones (26%)—ST11, ST258, and ST15 and five main Escherichia coli clones—ST131 (41.7%), ST38, ST95, ST405, and ST69. Sixty-one percent of ST131 isolates were from the highly virulent epidemic clone O25b:H4-ST131. Phylotyping revealed that 69% of E. coli isolates belonged to the virulent B2 and D groups. Almost all (15/16) Enterobacter isolates were identified as E. hormaechei and the most common ST type was ST90. Among all of the isolates, a high ESBL/carbapenemases/plasmid AmpC (32.4%) prevalence was observed. A significant proportion of the isolates (37%) were members of high-risk clones including two pan-drug-resistant K. pneumoniae ST11 NDM-1 producing isolates. Due to extensive antibiotic usage during COVID-19, the situation may worsen, so routine screenings and strict infection control measures should be widely implemented.

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Hu, Yan-Yan, Jia-Chang Cai, Hong-Wei Zhou, Dan Chi, Xiao-Fei Zhang, Wei-Liang Chen, Rong Zhang et Gong-Xiang Chen. « Molecular Typing of CTX-M-Producing Escherichia coli Isolates from Environmental Water, Swine Feces, Specimens from Healthy Humans, and Human Patients ». Applied and Environmental Microbiology 79, n^o 19 (26 juillet 2013) : 5988–96. http://dx.doi.org/10.1128/aem.01740-13.

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ABSTRACTCTX-M-producingEscherichia coliis the predominant type of extended-spectrum β-lactamase (ESBL)-producingE. coliworldwide. In this study, molecular typing was conducted for 139 CTX-M-producingE. coliisolates, phenotypically positive for ESBLs, isolated from environmental water, swine, healthy humans, and hospitalized patients in Hangzhou, China. The antibiotic resistance profiles of the isolates for the cephalosporins and fluoroquinolones were determined. The isolates showed 100% resistance to cefotaxime and ceftriaxone while maintaining relatively high susceptibility to cefoxitin, cefepime, and ceftazidime. A total of 61.9% (86/139) of the isolates, regardless of origin, showed high resistance to fluoroquinolones. PCRs and DNA sequencing indicated thatblaCTX-M-14was the most prevalent CTX-M-9 group gene and thatblaCTX-M-15andblaCTX-M-55were the dominant CTX-M-1 group genes. Isolates from all sources with CTX-M types belonging to the CTX-M-1 or CTX-M-9 group were most frequently associated with epidemics. Molecular homology analysis of the isolates, conducted by phylogenetic grouping, pulsed-field gel electrophoresis (PFGE), and multilocus sequence typing (MLST), demonstrated that the dominant clones belonged to B2-ST131, D-ST648, D-ST38, or A-CC10. These four sequence types (STs) were discovered inE. coliisolates both from humans and from environmental water, suggesting frequent and continuous intercompartment transmission between humans and the aquatic environment. Seven novel sequence types were identified in the current study. In conclusion, this study is the first to report the molecular homology analysis of CTX-M-producingE. coliisolates collected from water, swine, and healthy and hospitalized humans, suggesting that pathogens in the environment might originate both from humans and from animals.

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Rafaque, Z., J. I. Dasti et S. C. Andrews. « Draft genome sequence of a uropathogenic Escherichia coli isolate (ST38 O1:H15) from Pakistan, an emerging multidrug-resistant sequence type with a high virulence profile ». New Microbes and New Infections 27 (janvier 2019) : 1–2. http://dx.doi.org/10.1016/j.nmni.2018.10.004.

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MEZIANI, Meriem, et Kaddour BENLABED. « Carbapenem resistance due to BlaOXA-48 Clone ST38 among ESBL-producing Escherichia coli isolates from patients hospitalised at the university hospital of Constantine in Algeria. » International Journal of Advanced Research 4, n^o 7 (31 juillet 2016) : 36–42. http://dx.doi.org/10.21474/ijar01/903.

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Van Vliet, Danielle, Gregory D. Wiens, Thomas P. Loch, Pierre Nicolas et Mohamed Faisal. « Genetic Diversity of Flavobacterium psychrophilum Isolates from Three Oncorhynchus spp. in the United States, as Revealed by Multilocus Sequence Typing ». Applied and Environmental Microbiology 82, n^o 11 (25 mars 2016) : 3246–55. http://dx.doi.org/10.1128/aem.00411-16.

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ABSTRACTThe use of a multilocus sequence typing (MLST) technique has identified the intraspecific genetic diversity of U.S.Flavobacterium psychrophilum, an important pathogen of salmonids worldwide. Prior to this analysis, little U.S.F. psychrophilumgenetic information was known; this is of importance when considering targeted control strategies, including vaccine development. Herein, MLST was used to investigate the genetic diversity of 96F. psychrophilumisolates recovered from rainbow trout (Oncorhynchus mykiss), coho salmon (Oncorhynchus kisutch), and Chinook salmon (Oncorhynchus tshawytscha) that originated from nine U.S. states. The isolates fell into 34 distinct sequence types (STs) that clustered in 5 clonal complexes (CCs) (n= 63) or were singletons (n= 33). The distribution of STs varied spatially, by host species, and in association with mortality events. Several STs (i.e., ST9, ST10, ST30, and ST78) were found in multiple states, whereas the remaining STs were localized to single states. With the exception of ST256, which was recovered from rainbow trout and Chinook salmon, all STs were found to infect a single host species. Isolates that were collected during bacterial cold water disease outbreaks most frequently belonged to CC-ST10 (e.g., ST10 and ST78). Collectively, the results of this study clearly demonstrate the genetic diversity ofF. psychrophilumwithin the United States and identify STs of clinical significance. Although the majority of STs described herein were novel, some (e.g., ST9, ST10, ST13, ST30, and ST31) were previously recovered on other continents, which demonstrates the transcontinental distribution ofF. psychrophilumgenotypes.IMPORTANCEFlavobacterium psychrophilumis the causative agent of bacterial cold water disease (BCWD) and rainbow trout fry syndrome (RTFS) and is an important bacterial pathogen of wild and farmed salmonids worldwide. These infections are responsible for large economic losses globally, yet the genetic diversity of this pathogen remains to be fully investigated. Previous studies have identified the genetic diversity of this pathogen in other main aquaculture regions; however, little effort has been focused on the United States. In this context, this study aims to examine the genetic diversity ofF. psychrophilumfrom the United States, as this region remains important in salmonid aquaculture.

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Flament-Simon, Saskia-Camille, Marie-Hélène Nicolas-Chanoine, Vanesa García, Marion Duprilot, Noémie Mayer, María Pilar Alonso, Isidro García-Meniño, Jesús E. Blanco, Miguel Blanco et Jorge Blanco. « Clonal Structure, Virulence Factor-encoding Genes and Antibiotic Resistance of Escherichia coli, Causing Urinary Tract Infections and Other Extraintestinal Infections in Humans in Spain and France during 2016 ». Antibiotics 9, n^o 4 (4 avril 2020) : 161. http://dx.doi.org/10.3390/antibiotics9040161.

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Escherichia coli is the main pathogen responsible for extraintestinal infections. A total of 196 clinical E. coli consecutively isolated during 2016 in Spain (100 from Lucus Augusti hospital in Lugo) and France (96 from Beaujon hospital in Clichy) were characterized. Phylogroups, clonotypes, sequence types (STs), O:H serotypes, virulence factor (VF)-encoding genes and antibiotic resistance were determined. Approximately 10% of the infections were caused by ST131 isolates in both hospitals and approximately 60% of these infections were caused by isolates belonging to only 10 STs (ST10, ST12, ST58, ST69, ST73, ST88, ST95, ST127, ST131, ST141). ST88 isolates were frequent, especially in Spain, while ST141 isolates significantly predominated in France. The 23 ST131 isolates displayed four clonotypes: CH40-30, CH40-41, CH40-22 and CH40-298. Only 13 (6.6%) isolates were carriers of extended-spectrum beta-lactamase (ESBL) enzymes. However, 37.2% of the isolates were multidrug-resistant (MDR). Approximately 40% of the MDR isolates belonged to only four of the dominant clones (B2-CH40-30-ST131, B2-CH40-41-ST131, C-CH4-39-ST88 and D-CH35-27-ST69). Among the remaining MDR isolates, two isolates belonged to B2-CH14-64-ST1193, i.e., the new global emergent MDR clone. Moreover, a hybrid extraintestinal pathogenic E.coli (ExPEC)/enteroaggregative isolate belonging to the A-CH11-54-ST10 clone was identified.

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Deshpande, Lalitagauri M., Andrew P. Davis, F. Fredrik Dyrkell, Dimitrios Amellos et Mariana Castanheira. « 239. Epidemiologic Analysis of a Worldwide Collection of Escherichia coli ST131 Using the 1928D Core Genome (cg) Multilocus Sequence Type (MLST) Reveals Country Specific and Globally Disseminated Clades ». Open Forum Infectious Diseases 6, Supplement_2 (octobre 2019) : S136. http://dx.doi.org/10.1093/ofid/ofz360.314.

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Abstract Background Increasing antimicrobial resistance (R) among Escherichia coli (EC) isolates can be associated with the expansion of the pandemic sequence type (ST) 131 that harbors virulence factors and causes more severe infections when compared with other antimicrobial-R EC. We evaluated the core genome MLST (cgMLST) profiles and R genes using the bioinformatics tool 1928D to evaluate the epidemiology of a global ST131 EC collection and unrelated STs. Methods A total of 259 EC clinical isolates belonging to ST131 (n = 206), ST131-single loci variant (SLV; n = 25), and 28 non-ST131 isolates collected from 27 countries during 2016–2018 were selected. Whole-genome sequencing FASTQ files were uploaded to the 1928D pipeline to generate MLST, cgMLST and R gene prediction. cgMLST assignment was based on comparing >2,500 genes. Results Among 231 ST131 and SLV EC isolates, 7 clades were identified (3 major [178 isolates]; Table) applying cgMLST allele distance (ad) of ≤50 as a cutoff. A total of 21 isolates were not assigned to clades (>50 ad from ST131 and SLV). Based on >95% concordance, 11 alleles differentiated clades II and III from clade I, while 6 alleles separated clades I and III from clade II. Isolates in clades I to IV were ciprofloxacin R (MIC, ≥4 mg/L); clades I and III predominantly carried blaCTX-M-15 (39/43 and 61/66), blaOXA-1 (35/43 and 43/66), and aac(6’)-Ib-cr (39/43, 45/66) while clade II carried blaCTX-M-14-like and rarely aac(6’)Ib-cr (3/69). The most ad between the 7 ST131 clades was 216, while unrelated STs showed variable ad among isolates within that ST. Isolates bellowing to ST1193 were closely related genetically (ad of 30), but other STs had more variability among isolates (ST167, ad 552; ST38, ad 150; and ST69, ad 179). Conclusion 1928D is a robust platform for epidemiological analysis of isolates, providing additional granularity when compared with MLST. Clades II and III were closely related, but carried different blaCTX-M genes, while clades I and III were not as closely related, but both carried blaCTX-M-15, blaOXA-1, and aac(6’)Ib-cr. These findings suggest that these clades might have acquired R genes at different points in their genetic evolution. A threshold of ≤50 (cgMLST distance) was useful for classifying isolates into clades. Disclosures All authors: No reported disclosures.

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Liu, Honghui, Hany Geagea, Geneviève Rousseau, Simon Labrie, Denise Tremblay, Xinchun Liu et Sylvain Moineau. « Characterization of the Escherichia coli Virulent Myophage ST32 ». Viruses 10, n^o 11 (7 novembre 2018) : 616. http://dx.doi.org/10.3390/v10110616.

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The virulent phage ST32 that infects the Escherichia coli strain ST130 was isolated from a wastewater sample in China and analyzed. Morphological observations showed that phage ST32 belongs to the Myoviridae family, as it has an icosahedral capsid and long contractile tail. Host range analysis showed that it exhibits a broad range of hosts including non-pathogenic and pathogenic E. coli strains. Interestingly, phage ST32 had a much larger burst size when amplified at 20 °C as compared to 30 °C or 37 °C. Its double-stranded DNA genome was sequenced and found to contain 53,092 bp with a GC content of 44.14%. Seventy-nine open reading frames (ORFs) were identified and annotated as well as a tRNA-Arg. Only nineteen ORFs were assigned putative functions. A phylogenetic tree using the large terminase subunit revealed a close relatedness with four unclassified Myoviridae phages. A comparative genomic analysis of these phages showed that the Enterobacteria phage phiEcoM-GJ1 is the closest relative to ST32 and shares the same new branch in the phylogenetic tree. Still, these two phages share only 47 of 79 ORFs with more than 90% identity. Phage ST32 has unique characteristics that make it a potential biological control agent under specific conditions.

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Nüesch-Inderbinen, Magdalena, Nadine Käppeli, Marina Morach, Corinne Eicher, Sabrina Corti et Roger Stephan. « Molecular types, virulence profiles and antimicrobial resistance of Escherichia coli causing bovine mastitis ». Veterinary Record Open 6, n^o 1 (novembre 2019) : e000369. http://dx.doi.org/10.1136/vetreco-2019-000369.

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BackgroundEscherichia coli is an important aetiological agent of bovine mastitis worldwide.MethodsIn this study, 82 E. coli from bovine mastitis milk samples from 49 farms were analysed for their genetic diversity using phylogenetic grouping and multilocus sequence typing. The isolates were examined by PCR for a selection of virulence factors (VFs). Antimicrobial susceptibility profiles were assessed using the disk diffusion method.ResultsThe most prevalent phylogroups were group B1 (41.5 per cent of the isolates) and group A (30.5 per cent). A variety of 35 different sequence types (STs) were identified, including ST1125 (11 per cent), ST58 (9.8 per cent), ST10 (8.5 per cent) and ST88 (7.3 per cent). Aggregate VF scores (the number of unique VFs detected for each isolate) ranged from 1 to 3 for 63.4 per cent of the isolates and were at least 4 for 12.2 per cent. For 24.4 per cent of the isolates, the score was 0. The three most frequent VFs were traT, fyuA and iutA. The majority (72 per cent) of the isolates harboured traT. The majority (68.3 per cent) of the isolates were fully susceptible to all antimicrobials tested, with 22 per cent resistant to ampicillin and 14.6 per cent to tetracycline. Resistance rates were low for gentamicin (3.7 per cent), amoxicillin/clavulanic acid (2.4 per cent) and ceftiofur (1.2 per cent), respectively.ConclusionAmong the study’s sample population, E. coli strains were genotypically diverse, even in cows from the same farm, although some STs occurred more frequently than others. Susceptibility to clinically relevant compounds remained high.

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Eshkevari, Ladan, Susan E. Mulroney, Rupert Egan et Lixing Lao. « Effects of Acupuncture, RU-486 on the Hypothalamic-Pituitary-Adrenal Axis in Chronically Stressed Adult Male Rats ». Endocrinology 156, n^o 10 (21 juillet 2015) : 3649–60. http://dx.doi.org/10.1210/en.2015-1018.

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We have recently reported that pretreatment with electroacupuncture (EA) at stomach meridian point 36 (St36) prevents the chronic cold-stress increase in the hypothalamus-pituitary-adrenal axis (HPA), an action that may be under central control. Given that treatment for stress-related symptoms usually begins after onset of the stress responses, the objectives of the present study were to determine the efficacy of EA St36 on HPA hormones when EA St36 is given after stress was initiated, if the results are long lasting, and if blocking the glucocorticoid receptor (GR) using RU-486 had the same effects as EA St36. Adult male rats were placed in 4 groups of animals, 3 of which were exposed to cold and 1 of which was a nontreatment control group. After exposure to the cold stress, 2 groups were treated with either EA St36 or sham-EA, repeated over 10 days. The increase in ACTH and corticosterone observed in stress-only rats was prevented in EA St36 animals, and the effects remained intact 4 days after withdrawal of EA but continuation of cold stress. When the GR was blocked with RU-486, the efficacy of EA St36 remained unchanged. GR blockade did significantly elevate ACTH, which is not seen with EA St36, suggesting that EA St36 does act centrally. The elevated HPA hormones in stress-only rats were associated with a significant increase in depressive and anxious behavior; this was not observed in the stressed EA St36 animals. The results indicate that EA specifically at St36 vs sham-EA is effective in treating chronic poststress exposure.

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