Isolation and Characterization of Escherichia coli Sequence Type 131 and Other Antimicrobial-Resistant Gram-Negative Bacilli from Clinical Stool Samples from Veterans

ABSTRACTEmerging multidrug-resistant (MDR) Gram-negative bacilli (GNB), includingEscherichia colisequence type 131 (ST131) and its resistance-associatedH30 subclone, constitute an ever-growing public health threat. Their reservoirs and transmission pathways are incompletely defined. To assess diarrheal stools as a potential reservoir for ST131-H30 and other MDR GNB, we cultured 100 clinical stool samples from a Veterans Affairs Medical Center clinical laboratory (October to December 2011) for fluoroquinolone- and extended-spectrum cephalosporin (ESC)-resistantE. coliand other GNB, plus totalE. coli. We then characterized selected resistant and susceptibleE. coliisolates by clonal group, phylogenetic group, virulence genotype, and pulsotype and screened all isolates for antimicrobial resistance. Overall, 79 of 100 stool samples yielded GNB (52E. coli; 48 other GNB). Fifteen samples yielded fluoroquinolone-resistantE. coli(10 were ST131, of which 9 wereH30), 6 yielded ESC-resistantE. coli(2 were ST131, both non-H30), and 31 yielded susceptibleE. coli(1 was ST131, non-H30), for 13 total ST131-positive samples. Fourteen non-E. coliGNB were ESC resistant, and three were fluoroquinolone resistant. Regardless of species, almost half (46%) of the fluoroquinolone-resistant and/or ESC-resistant non-E. coliGNB were resistant to at least three drug classes. Fecal ST131 isolates closely resembled reference clinical ST131 isolates according to virulence genotypes and pulsed-field gel electrophoresis (PFGE) profiles. Thus, a substantial minority (30%) of veterans with diarrhea who undergo stool testing excrete antibiotic-resistant GNB, includingE. coliST131. Consequently, diarrhea may pose transmission risks for more than just diarrheal pathogens and may help disseminate clinically relevant ST131 strains and other MDR GNB within hospitals and the community.

Download Full-text

Rapid Emergence, Subsidence, and Molecular Detection of Escherichia coli Sequence Type 1193-fimH64, a New Disseminated Multidrug-Resistant Commensal and Extraintestinal Pathogen

Journal of Clinical Microbiology ◽

10.1128/jcm.01664-18 ◽

2019 ◽

Vol 57 (5) ◽

Cited By ~ 14

Author(s):

James R. Johnson ◽

Brian D. Johnston ◽

Stephen B. Porter ◽

Connie Clabots ◽

Tricia L. Bender ◽

...

Keyword(s):

Escherichia Coli ◽

Medical Center ◽

Virulence Gene ◽

The United States ◽

Multidrug Resistant ◽

Sequence Type ◽

Cross Sectional ◽

Content Type ◽

E Coli ◽

Multiplex Pcr Assay

ABSTRACT Escherichia coli sequence type 1193 (ST1193) is an emerging multidrug-resistant pathogen. We performed longitudinal and cross-sectional surveillance for ST1193 among clinical and fecal E. coli isolates from Minneapolis Veterans Affairs Medical Center (VAMC) patients and their household members, other Minnesota centers, and national VAMCs and compared these ST1193 isolates with archival human and canine ST1193 isolates from Australia (2008). We also developed and extensively validated a novel multiplex PCR assay for ST1193 and its characteristic fimH64 (type 1 fimbrial adhesin) allele. We found that ST1193-H64 (where “H64” refers to a phylogenetic subdivision within ST1193 that is characterized by the fimH64 allele), which was uniformly fluoroquinolone resistant, appeared to emerge in the United States in a geographically staggered fashion beginning around 2011. Its prevalence among clinical and fecal E. coli isolates at the Minneapolis VAMC rose rapidly beginning in 2013, peaked in early 2017, and then plateaued or declined. In comparison with other ST14 complex (STc14) isolates, ST1193-H64 isolates were more extensively multidrug resistant, whereas their virulence genotypes were less extensive but included (uniquely) K1 capsule and fimH64. Pulsed-field gel electrophoresis separated ST1193-H64 isolates from other STc14 isolates and showed genetic commonality between archival Australian versus recent U.S. isolates, fecal versus clinical isolates, and human versus canine isolates. Three main ST1193 pulsotypes differed significantly in resistance profiles and capsular types; emergent pulsotype 2123 was associated with trimethoprim-sulfamethoxazole resistance and K1 (versus K5) capsule. These findings clarify ST1193-H64’s temporal prevalence trends as a fluoroquinolone-resistant pathogen and commensal; document clonal subsets with distinctive geographic, temporal, resistance, and virulence gene associations; and establish a new laboratory tool for rapid and simple detection of ST1193-H64.

Download Full-text

Heterogeneous and Flexible Transmission ofmcr-1in Hospital-AssociatedEscherichia coli

mBio ◽

10.1128/mbio.00943-18 ◽

2018 ◽

Vol 9 (4) ◽

Cited By ~ 23

Author(s):

Yingbo Shen ◽

Zuowei Wu ◽

Yang Wang ◽

Rong Zhang ◽

Hong-Wei Zhou ◽

...

Keyword(s):

Escherichia Coli ◽

Genomic Analysis ◽

Multidrug Resistant ◽

Fluoroquinolone Resistance ◽

Gram Negative Bacteria ◽

Colistin Resistance ◽

Gram Negative ◽

Content Type ◽

E Coli ◽

Genes Encoding

ABSTRACTThe recent emergence of a transferable colistin resistance mechanism, MCR-1, has gained global attention because of its threat to clinical treatment of infections caused by multidrug-resistant Gram-negative bacteria. However, the possible transmission route ofmcr-1amongEnterobacteriaceaespecies in clinical settings is largely unknown. Here, we present a comprehensive genomic analysis ofEscherichia coliisolates collected in a hospital in Hangzhou, China. We found thatmcr-1-carrying isolates from clinical infections and feces of inpatients and healthy volunteers were genetically diverse and were not closely related phylogenetically, suggesting that clonal expansion is not involved in the spread ofmcr-1. Themcr-1gene was found on either chromosomes or plasmids, but in most of theE. coliisolates,mcr-1was carried on plasmids. The genetic context of the plasmids showed considerable diversity as evidenced by the different functional insertion sequence (IS) elements, toxin-antitoxin (TA) systems, heavy metal resistance determinants, and Rep proteins of broad-host-range plasmids. Additionally, the genomic analysis revealed nosocomial transmission ofmcr-1and the coexistence ofmcr-1with other genes encoding β-lactamases and fluoroquinolone resistance in theE. coliisolates. These findings indicate thatmcr-1is heterogeneously disseminated in both commensal and pathogenic strains ofE. coli, suggest the high flexibility of this gene in its association with diverse genetic backgrounds of the hosts, and provide new insights into the genome epidemiology ofmcr-1among hospital-associatedE. colistrains.IMPORTANCEColistin represents one of the very few available drugs for treating infections caused by extensively multidrug-resistant Gram-negative bacteria. The recently emergentmcr-1colistin resistance gene threatens the clinical utility of colistin and has gained global attention. Howmcr-1spreads in hospital settings remains unknown and was investigated by whole-genome sequencing ofmcr-1-carryingEscherichia coliin this study. The findings revealed extraordinary flexibility ofmcr-1in its spread among genetically diverseE. colihosts and plasmids, nosocomial transmission ofmcr-1-carryingE. coli, and the continuous emergence of novel Inc types of plasmids carryingmcr-1and newmcr-1variants. Additionally,mcr-1was found to be frequently associated with other genes encoding β-lactams and fluoroquinolone resistance. These findings provide important information on the transmission and epidemiology ofmcr-1and are of significant public health importance as the information is expected to facilitate the control of this significant antibiotic resistance threat.

Download Full-text

Initial Assessment of the Molecular Epidemiology ofblaNDM-1in Colombia

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.03072-15 ◽

2016 ◽

Vol 60 (7) ◽

pp. 4346-4350 ◽

Cited By ~ 14

Author(s):

Laura J. Rojas ◽

Meredith S. Wright ◽

Elsa De La Cadena ◽

Gabriel Motoa ◽

Kristine M. Hujer ◽

...

Keyword(s):

Hot Spot ◽

Multidrug Resistant ◽

Sequence Type ◽

Initial Assessment ◽

Genome Sequences ◽

Gram Negative ◽

Content Type ◽

E Coli ◽

Resistance Determinants ◽

Novel Complex

ABSTRACTWe report complete genome sequences of fourblaNDM-1-harboring Gram-negative multidrug-resistant (MDR) isolates from Colombia. TheblaNDM-1genes were located on 193-kb Inc FIA, 178-kb Inc A/C2, and 47-kb (unknown Inc type) plasmids. Multilocus sequence typing (MLST) revealed that these isolates belong to sequence type 10 (ST10) (Escherichia coli), ST392 (Klebsiella pneumoniae), and ST322 and ST464 (Acinetobacter baumanniiandAcinetobacter nosocomialis, respectively). Our analysis identified that the Inc A/C2 plasmid inE. colicontained a novel complex transposon (Tn125and Tn5393with three copies ofblaNDM-1) and a recombination “hot spot” for the acquisition of new resistance determinants.

Download Full-text

Activity of Eravacycline against Escherichia coli Clinical Isolates Collected from U.S. Veterans in 2011 in Relation to Coresistance Phenotype and Sequence Type 131 Genotype

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.02403-15 ◽

2015 ◽

Vol 60 (3) ◽

pp. 1888-1891 ◽

Cited By ~ 9

Author(s):

James R. Johnson ◽

Stephen B. Porter ◽

Brian D. Johnston ◽

Paul Thuras

Keyword(s):

Escherichia Coli ◽

Multidrug Resistant ◽

Veterans Affairs ◽

Sequence Type ◽

Clinical Isolates ◽

Gram Negative ◽

Content Type ◽

Medical Centers ◽

Resistant Strains ◽

Veterans Affairs Medical Centers

Eravacycline is a novel broad-spectrum fluorocycline with potent Gram-negative activity, including for multidrug-resistant strains. Among 472Escherichia coliclinical isolates from 24 Veterans Affairs medical centers (in 2011), divided equally as susceptible versus resistant to fluoroquinolones, broth microdilution eravacycline MICs were distributed unimodally, ranging from 0.03 to 1.0 μg/ml (MIC50of 0.125 μg/ml, MIC90of 0.25 μg/ml). Eravacycline MICs were ∼2-fold higher among fluoroquinolone-resistant, gentamicin-resistant, multidrug-resistant, and sequence type 131 (ST131) isolates (P< 0.01 for each comparison).

Download Full-text

Risk Factors and Prevalence of mcr-1-Positive Escherichia coli in Fecal Carriages Among Community Children in Southern Taiwan

Frontiers in Microbiology ◽

10.3389/fmicb.2021.748525 ◽

2021 ◽

Vol 12 ◽

Author(s):

Pin-Chieh Wu ◽

Ming-Fang Cheng ◽

Wan-Ling Chen ◽

Wan-Yu Hung ◽

Jiun-Ling Wang ◽

...

Keyword(s):

Risk Factors ◽

Escherichia Coli ◽

Bacterial Infections ◽

Medical Center ◽

Positive Association ◽

Multidrug Resistant ◽

E Coli ◽

Stool Samples ◽

Southern Taiwan ◽

Sequence Types

Colistin is the last resort antimicrobial for treating multidrug-resistant gram-negative bacterial infections. The plasmid-mediated colistin resistance gene, mcr-1, crucially influences colistin’s resistance transmission. Human fecal carriages of mcr-1-positive Escherichia coli (E. coli) were detected in many regions worldwide; however, only a few studies have focused on children. Therefore, we identified the prevalence and risk factors of mcr-1-positive E. coli in fecal carriages among community children in Southern Taiwan. In this study, 510 stool samples were collected from April 2016 to August 2019 from the pediatric department at a medical center in Southern Taiwan. These samples were collected within 3 days after admission and were all screened for the presence of the mcr-1 gene. Diet habits, travel history, pet contact, and medical history were also obtained from participants to analyze the risk factors of their fecal carriages to mcr-1-positive E. coli. Antimicrobial susceptibility testing was determined using the VITEK 2 system and the broth microdilution test. Twelve mcr-1-positive E. coli. were isolated from 2.4% of the fecal samples. Through multivariate analysis, frequent chicken consumption (at least 3 times per week) had a significantly positive association with the presence of mcr-1-positive E. coli in fecal carriages (adjust odds ratio 6.60, 95% confidence interval1.58– 27.62, p = 0.033). Additionally, multidrug resistance was more common in mcr-1-positive E. coli. (75.0% vs. 39.5%, p = 0.031) than in non-mcr-1-positive Escherichia coli. Furthermore, the percentage of extraintestinal pathogenic E. coli in mcr-1-positive isolates was 83.3%. Some multi-locus sequence types in our mcr-1-positive E. coli were also similar to those isolated from food animals in the literature. The prevalence of fecal carriages of mcr-1-positive E. coli was low among community children in Southern Taiwan. Our data shows that chicken consumption with a higher frequency increases the risk of mcr-1-positive E. coli. in fecal carriages.

Download Full-text

Draft Genomic Sequences of Three Escherichia coli Sequence Type 131 Isolates (H45, H43ii, and H43iii) from Patients in Lagos, Nigeria

Microbiology Resource Announcements ◽

10.1128/mra.00076-20 ◽

2020 ◽

Vol 9 (17) ◽

Author(s):

Yishan Yang ◽

Christopher H. Sommers ◽

Eyitayo O. Adenipekun ◽

Marina Ceruso ◽

Charlene R. Jackson ◽

...

Keyword(s):

Escherichia Coli ◽

Urinary Tract ◽

Bloodstream Infections ◽

Multidrug Resistant ◽

Sequence Type ◽

Urine Samples ◽

Genomic Sequences ◽

Content Type ◽

E Coli

Escherichia coli sequence type 131 (ST131) has recently emerged as a leading multidrug-resistant pathogen that causes urinary tract and bloodstream infections in humans. Here, we report the draft genomic sequences of three E. coli ST131 isolates, H45, H43ii, and H43iii, from urine samples of patients in Lagos, Nigeria.

Download Full-text

Draft Genome Sequence of a Multidrug-Resistant Escherichia coli Sequence Type 1193 Pandemic Clone Isolated from Wastewater in Austria

Microbiology Resource Announcements ◽

10.1128/mra.00762-21 ◽

2021 ◽

Vol 10 (37) ◽

Author(s):

Adriana Cabal ◽

Nadine Peischl ◽

Gerhard Rab ◽

Anna Stöger ◽

Burkhard Springer ◽

...

Keyword(s):

Escherichia Coli ◽

Genome Sequence ◽

Draft Genome ◽

Treatment Plant ◽

Multidrug Resistant ◽

Sequence Type ◽

Draft Genome Sequence ◽

Fluoroquinolone Resistance ◽

Content Type ◽

E Coli

Extraintestinal Escherichia coli sequence type 1193 (ST1193) is an important source of fluoroquinolone resistance, which has emerged in recent years. We report the first draft genome sequence and annotation of a multidrug-resistant E. coli ST1193 strain obtained from a wastewater treatment plant in Austria.

Download Full-text

OXA-181-Producing Extraintestinal Pathogenic Escherichia coli Sequence Type 410 Isolated from a Dog in Portugal

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.02298-19 ◽

2020 ◽

Vol 64 (4) ◽

Author(s):

Michael Brilhante ◽

Juliana Menezes ◽

Adriana Belas ◽

Claudia Feudi ◽

Stefan Schwarz ◽

...

Keyword(s):

Escherichia Coli ◽

Virulence Genes ◽

Skin Infection ◽

Multidrug Resistant ◽

Sequence Type ◽

Whole Genome ◽

Content Type ◽

E Coli ◽

Pathogenic Escherichia Coli ◽

Tract Infections

ABSTRACT Two multidrug-resistant and carbapenemase-producing Escherichia coli clones of sequence type 410 were isolated from fecal samples of a dog with skin infection on admission to an animal hospital in Portugal and 1 month after discharge. Whole-genome sequencing revealed a 126,409-bp Col156/IncFIA/IncFII multidrug resistance plasmid and a 51,479-bp IncX3 blaOXA-181-containing plasmid. The chromosome and plasmids carried virulence genes characteristic for uropathogenic E. coli, indicating that dogs may carry multidrug-resistant E. coli isolates related to those causing urinary tract infections in humans.

Download Full-text

Independent Host Factors and Bacterial Genetic Determinants of the Emergence and Dominance of Escherichia coli Sequence Type 131 CTX-M-27 in a Community Pediatric Cohort Study

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00382-19 ◽

2019 ◽

Vol 63 (7) ◽

Cited By ~ 7

Author(s):

André Birgy ◽

Corinne Levy ◽

Marie-Hélène Nicolas-Chanoine ◽

Aurélie Cointe ◽

Claire A. Hobson ◽

...

Keyword(s):

Escherichia Coli ◽

Day Care ◽

Care Center ◽

Multidrug Resistant ◽

Sequence Type ◽

Content Type ◽

Extended Spectrum Beta Lactamase ◽

E Coli ◽

Fecal Carriage ◽

Recent Emergence

ABSTRACT The recent emergence and diffusion in the community of Escherichia coli isolates belonging to the multidrug-resistant and CTX-M-27-producing sequence type 131 (ST131) C1-M27 cluster makes this cluster potentially as epidemic as the worldwide E. coli ST131 subclade C2 composed of multidrug-resistant isolates producing CTX-M-15. Thirty-five extended-spectrum beta-lactamase (ESBL)-producing ST131 isolates were identified in a cohort of 1,885 French children over a 5-year period. They were sequenced to characterize the ST131 E. coli isolates producing CTX-M-27 recently emerging in France. ST131 isolates producing CTX-M-27 (n = 17), and particularly those belonging to the C1-M27 cluster (n = 14), carried many resistance-encoding genes and predominantly an F1:A2:B20 plasmid type. In multivariate analysis, having been hospitalized since birth (odds ratio [OR], 10.9; 95% confidence interval [CI], 2.4 to 48.8; P = 0.002) and being cared for in a day care center (OR, 9.4; 95% CI, 1.5 to 59.0; P = 0.017) were independent risk factors for ST131 CTX-M-27 fecal carriage compared with ESBL-producing non-ST131 isolates. No independent risk factor was found when comparing CTX-M-15 (n = 11)- and CTX-M-1/14 (n = 7)-producing ST131 isolates with ESBL-producing non-ST131 isolates or with non-ESBL-producing isolates. Several factors may contribute to the increase in fecal carriage of CTX-M-27-producing E. coli isolates, namely, resistance to multiple antibiotics, capacity of the CTX-M-27 enzyme to hydrolyze both cefotaxime and ceftazidime, carriage of a peculiar F-type plasmid, and/or capacity to colonize children who have been hospitalized since birth or who attend day care centers.

Download Full-text

Specific blaCTX-M-8/IncI1 Plasmid Transfer among Genetically Diverse Escherichia coli Isolates between Humans and Chickens

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00663-17 ◽

2017 ◽

Vol 61 (6) ◽

Cited By ~ 17

Author(s):

Chihiro Norizuki ◽

Jun-ichi Wachino ◽

Masahiro Suzuki ◽

Kumiko Kawamura ◽

Noriyuki Nagano ◽

...

Keyword(s):

Escherichia Coli ◽

Plasmid Transfer ◽

Chicken Meat ◽

Sequence Type ◽

Genetic Lineage ◽

Content Type ◽

Plasmid Sequence ◽

E Coli ◽

Stool Samples ◽

Human Stool

ABSTRACT We investigated the genetic backbones of 14 bla CTX-M-8-positive Escherichia coli isolates recovered from human stool samples and chicken meat. All isolates carried IncI1 plasmids with bla CTX-M-8 (bla CTX-M-8/IncI1), and most (9/14) belonged to a specific genetic lineage, namely, plasmid sequence type 113 (pST113). The genetic contexts of the nine bla CTX-M-8/IncI1 pST113 plasmids were similar, regardless of the source. These results suggest the probable local transfer of bla CTX-M-8/IncI1 between humans and chickens with genetically diverse E. coli.

Download Full-text