Characterization of human uropathogenic ESBL-producing Escherichia coli in the Czech Republic: spread of CTX-M-27-producing strains in a university hospital

Non-antibiotic antibacterial peptides and proteins of Escherichia coli: efficacy and potency of bacteriocins

INTRODUCTION

The emergence and spread of antibiotic resistance among pathogenic bacteria drives the search for alternative antimicrobial therapies. Bacteriocins represent a potential alternative to antibiotic treatment. In contrast to antibiotics, bacteriocins are peptides or proteins that have relatively narrow spectra of antibacterial activities and are produced by a wide range of bacterial species. Bacteriocins of Escherichia coli are historically classified as microcins and colicins, and, until now, more than 30 different bacteriocin types have been identified and characterized.

AREAS COVERED

We performed bibliographical searches of online databases to review the literature regarding bacteriocins produced by E. coli with respect to their occurrence, bacteriocin role in bacterial colonization and pathogenicity, and application of their antimicrobial effect.

EXPERT OPINION

The potential use of bacteriocins for applications in human and animal medicine and the food industry includes (i) the use of bacteriocin-producing probiotic strains, (ii) recombinant production in plants and application in food, and (iii) application of purified bacteriocins.

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

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.

Extensive Genetic Commonality among Wildlife, Wastewater, Community, and Nosocomial Isolates of Escherichia coli Sequence Type 131 (H30R1 and H30Rx Subclones) That Carry blaCTX-M-27 or blaCTX-M-15

Escherichia coli sequence type 131 (ST131) is currently one of the leading causes of multidrug-resistant extraintestinal infections globally. Here, we analyzed the phenotypic and genotypic characteristics of 169 ST131 isolates from various sources (wildlife, wastewater, companion animals, community, and hospitals) to determine whether wildlife and the environment share similar strains with humans, supporting transmission of ST131 between different ecological niches. Susceptibility to 32 antimicrobials was tested by disc diffusion and broth microdilution. Antibiotic resistance genes, integrons, plasmid replicons, 52 virulence genes, and fimH-based subtypes were detected by PCR and DNA sequencing. Genomic relatedness was determined by pulsed-field gel electrophoresis (PFGE). The genetic context and plasmid versus chromosomal location of extended-spectrum beta-lactamase and AmpC beta-lactamase genes was determined by PCR and probe hybridization, respectively. The 169 ST131 study isolates segregated predominantly into bla_CTX-M-15H30Rx (60%) and bla_CTX-M-27H30R1 (25%) subclones. Within each subclone, isolates from different source groups were categorized into distinct PFGE clusters; genotypic characteristics were fairly well conserved within each major PFGE cluster. Irrespective of source, the bla_CTX-M-15H30Rx isolates typically exhibited virotype A (89%), an F2:A1:B- replicon (84%), and a 1.7-kb class 1 integron (92%) and had diverse structures upstream of the bla_CTX-M region. In contrast, the bla_CTX-M-27H30R1 isolates typically exhibited virotype C (86%), an F1:A2:B20 replicon (76%), and a conserved IS26-ΔISEcp1-bla_CTX-M-like structure. Despite considerable overall genetic diversity, our data demonstrate significant commonality between E. coli ST131 isolates from diverse environments, supporting transmission between different sources, including humans, environment, and wildlife.

Global epidemiology of CTX-M β-lactamases: temporal and geographical shifts in genotype

Globally, rates of ESBL-producing Enterobacteriaceae are rising. We undertook a literature review, and present the temporal trends in blaCTX-M epidemiology, showing that blaCTX-M-15 and blaCTX-M-14 have displaced other genotypes in many parts of the world. Explanations for these changes can be attributed to: (i) horizontal gene transfer (HGT) of plasmids; (ii) successful Escherichia coli clones; (iii) ESBLs in food animals; (iv) the natural environment; and (v) human migration and access to basic sanitation. We also provide explanations for the changing epidemiology of blaCTX-M-2 and blaCTX-M-27. Modifiable anthropogenic factors, such as poor access to basic sanitary facilities, encourage the spread of blaCTX-M and other antimicrobial resistance (AMR) genes, such as blaNDM, blaKPC and mcr-1. We provide further justification for novel preventative and interventional strategies to reduce transmission of these AMR genes.

Global Escherichia coli Sequence Type 131 Clade with blaCTX-M-27 Gene

The Escherichia coli sequence type (ST) 131 C2/H30Rx clade with the bla_CTX-M-15 gene had been most responsible for the global dissemination of extended-spectrum β-lactamase (ESBL)-producing E. coli. ST131 C1/H30R with bla_CTX-M-27 emerged among ESBL-producing E. coli in Japan during the late 2000s. To investigate the possible expansion of a single clade_, we performed whole-genome sequencing for 43 Japan and 10 global ST131 isolates with bla_CTX-M-27 (n = 16), bla_CTX-M-14 (n = 16), bla_CTX-M-15 (n = 13), and others (n = 8). We also included 8 ST131 genomes available in public databases. Core genome-based analysis of 61 isolates showed that ST131 with bla_CTX-M-27 from 5 countries formed a distinct cluster within the C1/H30R clade, named C1-M27 clade. Accessory genome analysis identified a unique prophage-like region, supporting C1-M27 as a distinct clade. Our findings indicate that the increase of ESBL-producing E. coli in Japan is due mainly to emergence of the C1-M27 clade.

Characteristics of Quinolone Resistance in Escherichia coli Isolates from Humans, Animals, and the Environment in the Czech Republic

Escherichia coli is a common commensal bacterial species of humans and animals that may become a troublesome pathogen causing serious diseases. The aim of this study was to characterize the quinolone resistance phenotypes and genotypes in E. coli isolates of different origin from one area of the Czech Republic. E. coli isolates were obtained from hospitalized patients and outpatients, chicken farms, retailed turkeys, rooks wintering in the area, and wastewaters. Susceptibility of the isolates grown on the MacConkey agar with ciprofloxacin (0.05 mg/L) to 23 antimicrobial agents was determined. The presence of plasmid-mediated quinolone resistance (PMQR) and ESBL genes was tested by PCR and sequencing. Specific mutations in gyrA, gyrB, parC, and parE were also examined. Multilocus sequence typing and pulsed-field gel electrophoresis were performed to assess the clonal relationship. In total, 1050 E. coli isolates were obtained, including 303 isolates from humans, 156 from chickens, 105 from turkeys, 114 from the rooks, and 372 from wastewater samples. PMQR genes were detected in 262 (25%) isolates. The highest occurrence was observed in isolates from retailed turkey (49% of the isolates were positive) and inpatients (32%). The qnrS1 gene was the most common PMQR determinant identified in 146 (56%) followed by aac(6')-Ib-cr in 77 (29%), qnrB19 in 41 (16%), and qnrB1 in 9 (3%) isolates. All isolates with high level of ciprofloxacin resistance (>32 mg/L) carried double or triple mutations in gyrA combined with single or double mutations in parC. The most frequently identified substitutions were Ser(83)Leu; Asp(87)Asn in GyrA, together with Ser(80)Ile, or Glu(84)Val in ParC. Majority of these isolates showed resistance to beta-lactams and multiresistance phenotype was found in 95% isolates. Forty-eight different sequence types among 144 isolates analyzed were found, including five major clones ST131 (26), ST355 (19), ST48 (13), ST95 (10), and ST10 (5). No isolates sharing 100% relatedness and originating from different areas were identified. In conclusion, our study identified PMQR genes in E. coli isolates in all areas studied, including highly virulent multiresistant clones such as ST131 producing CTX-M-15 beta-lactamases.

Human extraintestinal pathogenic Escherichia coli strains differ in prevalence of virulence factors, phylogroups, and bacteriocin determinants

BACKGROUND

The study used a set of 407 human extraintestinal pathogenic E. coli strains (ExPEC) isolated from (1) skin and soft tissue infections, (2) respiratory infections, (3) intra-abdominal infections, and (4) genital smears. The set was tested for bacteriocin production, for prevalence of bacteriocin and virulence determinants, and for phylogenetic typing. Results obtained from the group of ExPEC strains were compared to data from our previously published analyses of 1283 fecal commensal E. coli strains.

RESULTS

The frequency of bacteriocinogeny was significantly higher in the set of ExPEC strains (63.1 %), compared to fecal E. coli (54.2 %; p < 0.01). Microcin producers and microcin determinants dominated in ExPEC strains, while colicin producers and colicin determinants were more frequent in fecal E. coli (p < 0.01). Higher production of microcin M and lower production of microcin B17, colicin Ib, and Js was detected in the set of ExPEC strains. ExPEC strains had a significantly higher prevalence of phylogenetic group B2 (52.6 %) compared to fecal E. coli strains (38.3 %; p < 0.01).

CONCLUSIONS

Human ExPEC strains were shown to differ from human fecal strains in a number of parameters including bacteriocin production, prevalence of several bacteriocin and virulence determinants, and prevalence of phylogenetic groups. Differences in these parameters were also identified within subgroups of ExPEC strains of diverse origin. While some microcin determinants (mM, mH47) were associated with virulent strains, other bacteriocin types (mB17, Ib, and Js) were associated with fecal flora.

Colicins U and Y inhibit growth of Escherichia coli strains via recognition of conserved OmpA extracellular loop 1

Interactions of colicins U and Y with the OmpA (Outer membrane protein A) receptor molecule were studied using site-directed mutagenesis and colicin binding assay. A systematic mutagenesis of the colicin-susceptible OmpA sequence from Escherichia coli (OmpA_EC) to the colicin-resistant OmpA sequence from Serratia marcescens (OmpA_SM) was performed in regions corresponding to extracellular OmpA loops 1-4. Susceptibility to colicins U and Y was significantly affected by the OmpA mutation in loop 1. As with functional analysis, a decrease in binding capacity of His-tagged colicin U was found for recombinant OmpA with a mutated segment in loop 1 compared to control OmpA_EC. To verify the importance of the identified amino acid residues in OmpA loop 1, we introduced loop 1 from OmpA_EC into OmpA_SM, which resulted in the substantial increase of susceptibility to colicins U and Y. In addition, colicins U and Y were tested against a panel of 118 bacteriocin non-producing strains of four Escherichia species, including E. coli (39 strains), E. fergusonii (10 strains), E. hermannii (42 strains), and E. vulneris (27 strains). A majority (82%) of E. coli strains was susceptible to colicins U and Y. Interestingly, colicins U and Y also inhibited all of the 30 tested multidrug-resistant E. coli O25b-ST131 isolates. These findings, together with the fact that OmpA loop 1 is important for bacterial virulence and is evolutionary conserved, offer the potential of using colicins U and Y as specific anti-OmpA loop 1 directed antibacterial proteins.

CTX-M-27 Producing Salmonella enterica Serotypes Typhimurium and Indiana Are Prevalent among Food-Producing Animals in China

Salmonella spp. is one of the most important food-borne pathogens causing digestive tract and invasive infections in both humans and animals. Extended-spectrum β-lactamases (ESBLs) especially the CTX-M-type ESBLs are increasingly being reported worldwide and in China. These studies seldom focused on Salmonella isolates from food-producing animals. The aim of this study was to characterize the antimicrobial resistance profiles, serotypes and ESBLs and in particular, CTX-M producing Salmonella isolates from chickens and pigs in China. Salmonella isolates were identified by API20E system and polymerase chain reaction (PCR) assay; serotypes were determined using slide agglutination with hyperimmune sera; antimicrobial susceptibility was tested using the ager dilution method; the prevalence of ESBLs and PMQR genes were screened by PCR; CTX-M-producing isolates were further characterized by conjugation along with genetic relatedness and plasmid replicon type. In total, 159 Salmonella strains were identified, among which 95 strains were Salmonella enterica serovar Typhimurium, 63 strains were S. enterica serovar Indiana, and 1 strain was S. enterica serovar Enteritidis. All of these isolates presented multi-drug resistant phenotypes. Forty-five isolates carried bla_CTX-M genes, the most common subtype was CTX-M-27(34), followed by CTX-M-65(7) and CTX-M-14(4). Most bla_CTX-M genes were transmitted by non-typeable or IncN/IncFIB/IncP/IncA/C/IncHI2 plasmids with sizes ranging from 80 to 280 kb. In particular, all the 14 non-typeable plasmids were carrying bla_CTX-M-27 gene and had a similar size. PFGE profiles indicated that CTX-M-positive isolates were clonally related among the same serotype, whilst the isolates of different serotypes were genetically divergent. This suggested that both clonal spread of resistant strains and horizontal transmission of the resistance plasmids contributed to the dissemination of bla_CTX-M-9G-positive Salmonella isolates. The presence and spread of CTX-M, especially the CTX-M-27 in S. enterica serovars Typhimurium and Indiana from food-producing animals poses a potential threat for public health. Control strategies to limit the dissemination of these strains through the food chain are necessary.

Epidemic potential of Escherichia coli ST131 and Klebsiella pneumoniae ST258: a systematic review and meta-analysis

OBJECTIVES

Observational studies have suggested that Escherichia coli sequence type (ST) 131 and Klebsiella pneumoniae ST258 have hyperendemic properties. This would be obvious from continuously high incidence and/or prevalence of carriage or infection with these bacteria in specific patient populations. Hyperendemicity could result from increased transmissibility, longer duration of infectiousness, and/or higher pathogenic potential as compared with other lineages of the same species. The aim of our research is to quantitatively estimate these critical parameters for E. coli ST131 and K. pneumoniae ST258, in order to investigate whether E. coli ST131 and K. pneumoniae ST258 are truly hyperendemic clones.

PRIMARY OUTCOME MEASURES

A systematic literature search was performed to assess the evidence of transmissibility, duration of infectiousness, and pathogenicity for E. coli ST131 and K. pneumoniae ST258. Meta-regression was performed to quantify these characteristics.

RESULTS

The systematic literature search yielded 639 articles, of which 19 data sources provided information on transmissibility (E. coli ST131 n=9; K. pneumoniae ST258 n=10)), 2 on duration of infectiousness (E. coli ST131 n=2), and 324 on pathogenicity (E. coli ST131 n=285; K. pneumoniae ST258 n=39). Available data on duration of carriage and on transmissibility were insufficient for quantitative assessment. In multivariable meta-regression E. coli isolates causing infection were associated with ST131, compared to isolates only causing colonisation, suggesting that E. coli ST131 can be considered more pathogenic than non-ST131 isolates. Date of isolation, location and resistance mechanism also influenced the prevalence of ST131. E. coli ST131 was 3.2 (95% CI 2.0 to 5.0) times more pathogenic than non-ST131. For K. pneumoniae ST258 there were not enough data for meta-regression assessing the influence of colonisation versus infection on ST258 prevalence.

CONCLUSIONS

With the currently available data, it cannot be confirmed nor rejected, that E. coli ST131 or K. pneumoniae ST258 are hyperendemic clones.

Distribution of virulence factors in ESBL-producing Escherichia coli isolated from the environment, livestock, food and humans

In this study, extended-spectrum ß-lactamase (ESBL)-producing Escherichia coli isolates recovered from the following sources were characterized with regard to the occurrence and distribution of uropathogenic and enteric pathogenic virulence factors: surface waters (rivers and lakes, n=60), the intestines of freshwater fish (n=33), fresh vegetables (n=26), retail poultry meat (n=13) and the fecal samples of livestock (n=28), healthy humans (n=34) and primary care patients (n=13). Among the 207 isolates, 82% tested positive by PCR for one or more of the virulence factors (VF) that predict uropathogenicity, TraT, fyuA, chuA, PAI, yfcv or vat. Uropathogenic E. coli (UPEC) were detected in each of the analyzed sources. Regarding virulence factors for intestinal pathogenic E. coli, these were found more rarely and predominantly associated with the aquatic environment, with aagR (EAEC) found in isolates from surface waters and STp (porcine heat stable enterotoxin) and LT (heat-labile enterotoxin) associated with isolates from fish. Aggregate VF scores (the number of unique virulence factors detected for each isolate) were lowest among isolates belonging to phylogenetic group B1 and highest among group B2. Clustering of the isolates by phylogenetic group, multilocus sequence type (MLST) and ESBL-types revealed clonal overlaps of A:ST10(CTX-M-1) and D:ST350(CTX-M-1) between the sources of livestock, poultry meat and healthy humans, suggesting livestock, in particular poultry, represents a potential reservoir for these particular UPEC clones. The clones A:ST10(CTX-M-55) and B2:ST131(CTX-M-27), harboring uropathogenic virulence factors were significantly associated with fresh vegetables and with fish, respectively. Further clonal complexes with source overlaps included D:ST38(CTX-M-14), D:ST69(CTX-M-15), D:ST405(CTX-M-15) and D:ST648(CTX-M-15), which were found in surface water and healthy humans. Identifying potential reservoirs of UPEC in the environment, animals, food and humans is important in order to assess routes of transmission and risk factors for acquiring UPEC.

CTX-M-27- and CTX-M-14-producing, ciprofloxacin-resistant Escherichia coli of the H30 subclonal group within ST131 drive a Japanese regional ESBL epidemic

OBJECTIVES

The global increase in ESBL-producing Escherichia coli is associated with the ST131 clonal group, especially its CTX-M-15-producing H30Rx subset. To understand the rapid spread of ESBL-producing E. coli in Japan, we investigated the molecular epidemiology and ESBL-associated genetic environments of Japanese ST131 isolates.

METHODS

Between 2001 and 2012, 1079 ESBL-producing E. coli isolates were collected at 10 Japanese acute-care hospitals. ESBL types, ST131 status, fimH allele, H30Rx-defining sequences and ESBL-associated genetic environments were defined using PCR and sequencing. Subclonal groups were defined based on fimH allele and H30Rx status.

RESULTS

Overall, 461 (43%) of the 1079 ESBL-producing E. coli isolates represented ST131. According to fimH-based subclonal typing, the ST131 isolates included 398 fimH allele 30 (H30) isolates, 49 H41 isolates, 10 H22 isolates and 4 other fimH-type isolates. The 398 H30 isolates included 396 ciprofloxacin-resistant H30R isolates, of which 64 (16%) represented the H30Rx subset. Between 2001 and 2007, the CTX-M-14-producing H30R subgroup predominated, accounting for 46% of ST131 isolates, whereas the CTX-M-27-producing H30R and CTX-M-15-producing H30Rx subgroups were rarely detected. In contrast, from 2008 onward the latter two subgroups rose to dominance, accounting for 45% and 24% of ST131 isolates, respectively, versus only 15% for the (formerly dominant) CTX-M-14-producing H30R subgroup. The emergent CTX-M-27-H30R subgroup frequently had an IS26-ΔISEcp1-blaCTX-M-27-ΔIS903D-IS26-like structure, whereas the older CTX-M-14-H30R subgroup frequently had an ISEcp1-blaCTX-M-14-IS903D-like structure.

CONCLUSIONS

This Japanese regional ESBL-producing E. coli epidemic is closely associated with newly identified CTX-M-27- and CTX-M-14-producing ST131 H30R subclonal groups and with mobile elements IS26, ISEcp1 and IS903D.