Comparison of PCR-based methods for typing Escherichia coli

Characterization of uropathogenic Escherichia coli phylogroups associated with antimicrobial resistance, virulence factor distribution, and virulence-related phenotypes

In this study, we compared the characteristics of different uropathogenic Escherichia coli phylogroups. A total of 844 E. coli isolated from urine were enrolled and the antimicrobial susceptibility of E. coli to 22 antibiotics was determined by disk diffusion test. The distribution of phylogroups and 20 virulence factor genes was determined by PCR. Phenotypes associated with bacterial virulence, including motility, biofilm formation, and the production of curli and siderophore, were examined. Phylogroup B2 was dominant in our isolates (64.8%), followed by phylogroups D (8.6%), B1 (7.8%), F (6.0%), C (4.5%), A (3.1%), untypable (2.8%), E (1.8%), and clade I (0.5%). The prevalence of multidrug-resistant strains was highest in phylogroup C (86.8%), followed by E (80.0%), F (75.0%), and D (71.2%). Moreover, 23.5% of the phylogroup F E. coli were extensively drug-resistant. Phylogroup B2 E. coli had an average of the highest virulence factor genes (10.1 genes/isolate). Compared to phylogroup B2 E. coli, phylogroups F and clade I E. coli had higher motility while phylogroup C E. coli had lower motility. >60% of phylogroups A and C E. coli showed very low curli production. In contrast, 14%, 10%, and 7%, of E. coli in phylogroups F, B2, and E, produced a very high amount of curli, respectively. Surprisingly, phylogroup A E. coli showed the highest virulence to larvae, followed by phylogroups B2 and C. In summary, we first characterized and revealed that the antimicrobial resistance, virulence gene distribution, motility, and curli production, were associated with in E. coli phylogroups.

Genotypic and phenotypic traits of blaCTX-M-carrying Escherichia coli strains from an UV-C-treated wastewater effluent

Wastewater treatment plants (WWTPs) are relevant sources of antibiotic resistance into aquatic environments. Disinfection of WWTPs' effluents (e.g. by UV-C irradiation) may attenuate this problem, though some clinically relevant bacteria have been shown to survive disinfection. In this study we characterized 25 CTX-M-producing Escherichia coli strains isolated from a WWTP's UV-C-irradiated effluent, aiming to identify putative human health hazards associated with such effluents. Molecular typing indicated that the strains belong to the phylogroups A, B2 and C and clustered into 9 multilocus sequence types (STs), namely B2:ST131 (n = 7), A:ST58 (n = 1), A:ST155 (n = 4), C:ST410 (n = 2), A:ST453 (n = 2), A:ST617 (n = 2), A:ST744 (n = 1), A:ST1284 (n = 3) and a putative novel ST (n = 3). PCR-screening identified 9 of the 20 antibiotic resistance genes investigated [i.e. sul1, sul2, sul3, tet(A), tet(B), bla_OXA-1-like, aacA4, aacA4-cr and qnrS1]. The more prevalent were sul1, sul2 (n = 15 isolates) and tet(A) (n = 14 isolates). Plasmid restriction analysis indicated diverse plasmid content among strains (14 distinct profiles) and mating assays yielded cefotaxime-resistant transconjugants for 8 strains. Two of the transconjugants displayed a multi-drug resistance (MDR) phenotype. All strains were classified as cytotoxic to Vero cells (9 significantly more cytotoxic than the positive control) and 10 of 21 strains were invasive towards this cell line (including all B2:ST131 strains). The 10 strains tested against G. mellonella larvae exhibited a virulent behaviour. Twenty-four and 7 of the 25 strains produced siderophores and haemolysins, respectively. Approximately 66% of the strains formed biofilms. Genome analysis of 6 selected strains identified several virulence genes encoding toxins, siderophores, and colonizing, adhesion and invasion factors. Freshwater microcosms assays showed that after 28 days of incubation 3 out of 6 strains were still detected by cultivation and 4 strains by qPCR. Resistance phenotypes of these strains remained unaltered. Overall, we confirmed WWTP's UV-C-treated outflow as a source of MDR and/or virulent E. coli strains, some probably capable of persisting in freshwater, and that carry conjugative antibiotic resistance plasmids. Hence, disinfected wastewater may still represent a risk for human health. More detailed evaluation of strains isolated from wastewater effluents is urgent, to design treatments that can mitigate the release of such bacteria.

Molecular Routes to Specific Identification of the Lactobacillus Casei Group at the Species, Subspecies and Strain Level

The genus Lactobacillus includes, among others, Lactobacillus casei, Lactobacillus paracasei and Lactobacillus rhamnosus, species that are collectively referred to as the Lactobacillus casei group. Many studies have shown that strains belonging to this group may decrease lactose intolerance, the effects of inflammatory bowel disease, diarrhea, constipation, food allergies and even colon cancer. Moreover, evidences exists of positive effects of these bacteria on mucosal immunity and blood cholesterol level. Because of their beneficial influence on human health, many of them are used as food additives and probiotic pharmaceuticals. It should be stressed that health-promoting properties are not attributed at the species level, but to specific strains. Therefore, procedures are necessary to allow specific identification at each phylogenetic level-genus, species and strain. In this paper we present a practical overview of molecular methods for the identification and differentiation of L. casei bacteria. The research included 30 bacterial strains belonging to three species: L.casei, L. paracasei and L. rhamnosus. Among the tested procedures were genus- and species-specific PCR, multiplex-PCR, Real-Time HRM analysis, RFLP-PCR, rep-PCR, RAPD-PCR, AFLP-PCR, and proteomic methods such as MALDI-TOF MS typing and SDS-PAGE fingerprinting. The obtained results showed that multiplex-PCR and MALDI-TOF MS turned out to be the most useful methods to identify the tested bacteria at the species level. At the strain level, the AFLP-PCR method showed the highest discriminatory power. We hope that the presented results will allow for the easy selection of an appropriate procedure, depending on the experiment conducted and the equipment capabilities of any given laboratory.

Molecular Characteristics of ST1193 Clone among Phylogenetic Group B2 Non-ST131 Fluoroquinolone-Resistant Escherichia coli

Objectives: Sequence type 1193 is emerging as a new, virulent and resistant lineage among fluoroquinolone resistant Escherichia coli (FQ^rE. coli). In this study, we investigated the prevalence and molecular characteristics of this clone isolated from a Chinese university hospital.

Methods: 73 phylogenetic group B2-FQ^r-non-ST131 isolates were collected from August 2014 and August 2015 at a Chinese university hospital. Isolates were screened for ST1193 by multilocus sequence typing. E. coli ST1193 then underwent lactose fermentation determination, susceptibility testing, virulence genotyping, PCR-based O typing, pulsed-field gel electrophoresis (PFGE) and FQ^r mechanism analysis.

Results: Of 73 B2-FQ^r-non ST131 E. coli isolates, 69.9% (n = 51) were ST1193. 90.2% (46/51) of ST1193 isolates were O75 serotype and 96.1% (49/51) of the ST1193 isolates were lactose non-fermenters. 35 clusters were identified by PFGE. ST1193 isolates exhibited a set of 3 conserved mutations defining quinolone-resistance determining region substitutions (gyrA S83L, D87N, and parC S80I). The most frequent VF genes detected in these E. coli ST1193 isolates were fyuA (yersiniabactin, 96.1%), fimH (type 1 fimbriae, 94.1%), iutA (iron uptake gene, 90.2%), kpsMT II (group II capsule, 90.2%), kpsK1 (K1 capsule, 86.3%) and PAI.

Conclusion: ST1193 lineage accounts for the majority of group B2-FQ^r-non-ST131 E. coli clinical isolates. Most of the ST1193 are serotype O75 and lactose non-fermenting. Strategic surveillance and control schemes are needed in the future for this newly emerging clone of E. coli: B2-FQ^r-ST1193.

Experimental Evaluation of Faecal Escherichia coli and Hepatitis E Virus as Biological Indicators of Contacts Between Domestic Pigs and Eurasian Wild Boar

Domestic pigs and Eurasian wild boar (Sus scrofa) share several important viral and bacterial pathogens. Therefore, direct and indirect contacts between domestic pigs and wild boar present a risk of pathogen spillover and can lead to long-term perpetuation of infection. Biological indicators could be a powerful tool to understand and characterize contacts between wild boar and domestic pigs. Here, faecal Escherichia coli and Hepatitis E virus (HEV) were explored as potential biological indicators under experimental conditions. The data gained in our pilot study suggest that faecal E. coli can be used as biological indicator of contact between wild boar and domestic pig. For HEV, faecal transmission was also confirmed. However, molecular studies on full-genome basis did not reveal markers that would allow tracing of transmission direction. Based on these promising results, future field studies will especially target the practicability of E. coli microbiome molecular typing as surrogate of contacts at the wildlife-livestock interface.

CTX-M beta-lactamase production and virulence of Escherichia coli K1

We report a patient with neonatal meningitis caused by a CTX-M-1-producing Escherichia coli K1 strain. The influence of CTX-M production on virulence was investigated in cell culture and a newborn mouse model of meningitis. CTX-M production had no influence on virulence but was a major factor in clinical outcome.

Verocytotoxin-producing Escherichia coli O26 in raw water buffalo (Bubalus bubalis) milk products in Italy

Escherichia coli 026 is known as a verocytotoxin-producing E. coli (VTEC) organism that causes severe foodborne diseases such as hemorrhagic colitis and hemolytic uremic syndrome. Although cattle are the most important reservoir of VTEC, only a few reports on the role of water buffalo (Bubalus bubalis) as a reservoir of VTEC and on the presence of these organisms in their milk are available. However, in Southern Italy, where water buffalo are intensively reared, an outbreak of hemolytic uremic syndrome due to E. coli 026 has recently been reported, in which the consumption of typical dairy products was considered to be a common risk factor. The aims of this work were to assess the prevalence of E. coli O26 in raw water buffalo milk, to characterize the virulence gene profiles of the isolates, and to evaluate their phenotypic antimicrobial resistance pattern. Of 160 analyzed samples, 1 (0.6%) tested positive for E. coli O26, and the isolate showed the stx1+/stx2+/eae-/hlyA+ genotypic profile. The strain showed resistance against glycopeptides, macrolides, and penicillins. The presence of VTEC organisms in raw water buffalo milk could be considered to be a potential threat to consumers; however, the strict adherence to the processes used in the preparation of the most common buffalo dairy products could strongly mitigate the foodborne risk. To our knowledge, this article reports the first isolation and characterization of E. coli O26 VTEC in raw water buffalo milk.

Genodiversity of resistant Pseudomonas aeruginosa isolates in relation to antimicrobial usage density and resistance rates in intensive care units

OBJECTIVE

To evaluate the assumption that resistance rates in intensive care units (ICUs) are markedly influenced by cross-transmission events in addition to high rates of antimicrobial usage.

METHODS

This was a prospective ICU- and laboratory-based surveillance study involving 35 German ICUs from 1999 through 2004. A total of 585 ciprofloxacin- or imipenem-resistant isolates of Pseudomonas aeruginosa were investigated together with resistance rate and unit-based antimicrobial usage density. Antimicrobial use was reported in terms of defined daily doses per 1,000 patient-days. All the strains were assigned to ICU-based genotypes. Genodiversity was calculated as the numbers of indistinguishable ICU-based genotypes found per isolates tested. Reduced ICU-based genodiversity was taken as an indirect measure of frequently occurring cross-transmission events.

RESULTS

The genodiversity of ciprofloxacin- and imipenem-resistant P. aeruginosa isolates was significantly lower (P <=, by Fisher exact test) in ICUs with high resistance rate and low antimicrobial usage density (genodiversity, 0.50 and 0.50, respectively) than in ICUs that featured low resistance rate in the presence of high antimicrobial usage density (genodiversity, 0.90 and 0.95, respectively). In ICUs with low genodiversity, there was a greater rise in resistance rate with increasing antimicrobial usage density, compared with that in ICUs with high diversity.

CONCLUSIONS

This study on resistant P. aeruginosa isolates supports the assumption that high resistance rate in the presence of low antimicrobial usage density results from more-frequent cross-transmission events. A greater rise in resistance rate with increasing antimicrobial usage density in ICUs with low genodiversity indicates that resistance rate in ICUs might be markedly determined by cross-transmission events other than antimicrobial usage.

Antibiotic susceptibility patterns and clones of Pseudomonas aeruginosa in Swedish ICUs

Pseudomonas aeruginosa is 1 of the bacteria most adaptive to anti-bacterial treatment. Previous studies have shown nosocomial spread and transmission of clonal strains of P. aeruginosa in European hospitals. In this study we investigated antibiotic susceptibility and clonality in 101 P. aeruginosa isolates from 88 patients admitted to 8 Swedish ICUs during 2002. We also compared phenotypes and genotypes of P. aeruginosa and carried out cluster analysis to determine if phenotypic data can be used for surveillance of clonal spread. All isolates were collected on clinical indication as part of the NPRS II study in Sweden and were subjected to AFLP analysis for genotyping. 68 isolates with unique genotypes were found. Phenotyping was performed using MIC values for 5 anti-pseudomonal agents. Almost 6% of the isolates were multi-drug resistant (MDR), and this figure rose to almost 8% when intermediate isolates were also included. We found probable clonal spread in 9 cases, but none of them was found to be an MDR strain. Phenotypical cluster analysis produced 40 clusters. Comparing partitions did not demonstrate any significant concordance between the typing methods. The conclusion of our study is that cross-transmission and clonal spread of MDR P. aeruginosa does not present a clinical problem in Swedish ICUs, but probable cross-transmission of non-MDR clones indicate a need for improved hygiene routines bedside. The phenotype clusters were not concordant with genotype clusters, and genotyping is still recommended for epidemiological tracking.

Specificity of enterobacterial repetitive intergenic consensus and repetitive extragenic palindromic polymerase chain reaction for the detection of clonality within the Enterobacter cloacae complex

An increasing number of clonal outbreaks caused by members of the E. cloacae complex is being reported. For the detection of clonality, pulsed-field gel electrophoresis (PFGE) is considered the golden standard, but PCR-based methods are cheaper, easier to perform, and provide faster results. One hundred ninety-five isolates of the E. cloacae complex isolated at the university hospital Grosshadern, Munich, Germany, were assigned to their respective genetic cluster by partial hsp60 sequencing. All study isolates belonging to genetic clusters III and VI were selected to evaluate the specificity of the enterobacterial repetitive intergenic consensus (ERIC) and repetitive extragenic palindromic (REP) polymerase chain reaction (PCR) for the identification of clonal isolates belonging to the E. cloacae complex. For these 56 isolates, PFGE was performed, yielding 3 pairs of isolates with indistinguishable patterns. ERIC PCR resulted in 7 groups with identical patterns, together encompassing 49 study isolates. Comparing the ERIC PCR with the PFGE, a specificity of 14% considering the detection of "clonal" isolates was calculated. In this respect, REP PCR performed much better, yielding a specificity of 90%. An unweighted pair-group method with arithmetic averages tree based on ERIC PCR patterns allowed an accurate classification of the isolates to the respective genovars, suggesting that the ERIC PCR differentiates between genovars rather than between strains. In contrast, REP PCR differentiates better on the strain level. A proposed diagnostic system for the detection of subsumed outbreak strains of the E. cloacae complex is presented. It is based on an initial REP PCR, which should be confirmed by PFGE in cases of identical patterns, whereas ERIC PCR does not seem to be useful for the detection of outbreak strains when dealing with isolates of the E. cloacae complex.

How many infections are caused by patient-to-patient transmission in intensive care units?

OBJECTIVE

The proportion of intensive care unit (ICU)-acquired infections that are a consequence of nosocomial cross-transmission between patients in tertiary ICUs is unknown. Such information would be useful for the implementation of appropriate infection control measures.

DESIGN

A prospective cohort study during 18 months.

SETTING

Five ICUs from two university hospitals.

PATIENTS

All patients admitted for >/=48 hrs.

MEASUREMENT

ICU-acquired infections were ascertained during daily bedside patient and chart reviews. Episodes of potential cross-transmission were identified by highly discriminating genetic typing of all clinical and surveillance isolates of the ten bacterial species most frequently associated with nosocomial infections in ICUs. Isolation of indistinguishable isolates in two or more patients defined potential transmission episodes.

MAIN RESULTS

During 28,498 patient days, 431 ICU-acquired infections and 141 episodes of nosocomial transmissions were identified. A total of 278 infections were caused by the ten species that were genotyped, and 41 of these (14.5%) could be associated with transmissions between patients.

CONCLUSION

Infections acquired during treatment in modern tertiary ICUs are common, but a causative role of direct patient-to-patient transmission can only be ascertained for a minority of these infections on the basis of routine microbiological investigations.

[Incidence of transmission of pathogens in intensive care units. Results of the SIR 3 study]

The objective of this study was to determine the incidence of episodes of transmission of nosocomial pathogens and of those pathogens leading to nosocomial infections. Over a period of 18 months all patients from 5 intensive care units (ICUs) who stayed for more than 2 days were included in this study. Surveillance of nosocomial infections was carried out and all isolates of 10 of the most frequent pathogens in ICUs (indicator pathogens) were collected and typed. A total of 28,498 patient days and 431 nosocomial infections were observed (incidence density 15.1 per 1,000 patient days), among them 278 caused by 1 of the selected indicator pathogens. A total of 141 episodes of transmissions were identified, corresponding to an incidence of episodes of transmission of 5.0 per 1,000 patient days and 41 nosocomial infections were transmission-associated, corresponding to 14.5% of all nosocomial infections. The data of this study demonstrate that even in ICUs with average nosocomial infection rates, some nosocomial infections could be avoided.

A normalization strategy applied to HiCEP (an AFLP-based expression profiling) analysis: toward the strict alignment of valid fragments across electrophoretic patterns

Background

Gene expression analysis based on comparison of electrophoretic patterns is strongly dependent on the accuracy of DNA fragment sizing. The current normalization strategy based on molecular weight markers has limited accuracy because marker peaks are often masked by intense peaks nearby. Cumulative errors in fragment lengths cause problems in the alignment of same-length fragments across different electropherograms, especially for small fragments (< 100 bp). For accurate comparison of electrophoretic patterns, further inspection and normalization of electrophoretic data after fragment sizing by conventional strategies is needed.

Results

Here we describe a method for the normalization of a set of time-course electrophoretic data to be compared. The method uses Gaussian curves fitted to the complex peak mixtures in each electropherogram. It searches for target ranges for which patterns are dissimilar to the other patterns (called "dissimilar ranges") and for references (a kind of mean or typical pattern) in the set of resultant approximate patterns. It then constructs the optimal normalized pattern whose correlation coefficient against the reference in the range achieves the highest value among various combinations of candidates. We applied the procedure to time-course electrophoretic data produced by HiCEP, an AFLP-based expression profiling method which can detect a slight expression change in DNA fragments. We obtained dissimilar ranges whose electrophoretic patterns were obviously different from the reference and as expected, most of the fragments in the detected ranges were short (< 100 bp). The normalized electrophoretic patterns also agreed well with reference patterns.

Conclusion

The normalization strategy presented here demonstrates the importance of pre-processing before electrophoretic signal comparison, and we anticipate its usefulness especially for temporal expression analysis by the electrophoretic method.