Sample preparation of Gram-positive bacteria for identification by matrix assisted laser desorption/ionization time-of-flight.

A new sample preparation method was developed for fresh, whole-cell Gram-positive bacteria to be analyzed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI ToF MS). With fresh, whole-cell Gram-negative bacteria of the Enterobacteriaceae family, we had previously achieved spectra consisting of >50 peaks and mass ranges of 2-25 kDa. Because similar spectral quantity could not be achieved for Gram-positive bacteria, using this same protocol, we investigated an alternative approach that focuses on the thick peptidoglycan layer of the cell wall. Gram-positive bacteria were incubated with 0.05-0.5 mg/ml lysozyme for 30 min prior to being analyzed by MALDI ToF MS. Lysozyme is an enzymatically stable, 14-kDa protein that specifically cleaves between peptidoglycan disaccharide subunits. A significant increase in overall number of peaks (>50) in the 2-14 kDa range was observed without interference from the presence of lysozyme. We show that for four different species (Staphylococcus aureus, S. haemolyticus, Streptococcus pyogenes, and S. agalactiae) reproducible subset of peaks were found within spectra from a reference strain and two unrelated clinical isolates. The data suggests that this sample preparation may be useful for increasing the overall number of peaks within spectra for subsequent development of bacterial identification strategies.     

粪便样品中大肠杆菌多态性分子研究

以粪便样品中分离到的大肠杆菌为研究对象,比较了3种不同方法在分离鉴定大肠杆菌过程中的应用。首先,通过传统方法从粪便样品中分离,筛选和确定了一批大肠杆菌疑似菌株,再用现代分子生物学方法对待鉴定的大肠杆菌疑似菌株,已知大肠杆菌MG1655以及几种其它细菌进行ARDRA(AmplifiedRibosomalDNARestrictionAnalysis)分析,最后利用ERIC-PCR技术在个体水平上分析菌株的多样性。结果表明,所有由传统方法确定的大肠杆菌疑似菌株和MG1655都属于同一ARDRA型,并与其它细菌的ARDRA条码型不同。这说明ARDRA分析得到的结果与传统分析方法的结果吻合,利用ARDRA分析可以区分大肠杆菌和其它肠道细菌。但是在本实验中ARDRA分析不能反映大肠杆菌中不同菌株之间的多样性,ERIC-PCR则可以区分它们。     

Determination of serotypes of Shiga toxin-producing Escherichia coli isolates by intact cell matrix-assisted laser desorption ionization-time of flight mass spectrometry

Shiga toxin-producing Escherichia coli (STEC) isolates representing the serotypes O165:H25, O26:H11/H32, and O156:H25 were analyzed by matrix-assisted laser desorption/ionization (MALDI) mass spectra of whole cells, a procedure also known as intact cell mass spectrometry (ICMS or IC-MALDI MS) or MALDI-typing. We demonstrate that within the given species the three serotypes can be well discriminated by ICMS. Conditions for the construction of serotype-specific prototypic mass spectra were systematically optimized by filtering out masses that do not contribute to the discrimination of the serotypes. Binary distances between prototypic spectra and sample spectra were used to determine serotypes of unknown samples. With parameters optimized, only 0.7% of the assignments were incorrect compared to 31% when distances were calculated from alignments of unfiltered mass spectra. Within the different serotypes, clusters of genetically related E. coli most probably originating from single clones could be distinguished by restriction fragment length polymorphism analysis. Since ICMS did not reproduce these clusters, we conclude that the power of ICMS is just sufficient to discriminate E. coli serotypes under certain conditions but fails for the differentiation of E. coli below this level.     

PicU, a second serine protease autotransporter of uropathogenic Escherichia coli

Escherichia coli is the major aetiological agent of urinary tract infections (UTI). Like diarrhoeagenic strains of E. coli, uropathogenic isolates possess virulence determinants that distinguish them from commensal strains and allow them to produce the clinical manifestations associated with UTI. Several autotransporter proteins have been associated with the ability of E. coli, and other Gram-negative bacteria, to cause disease. Recently, we described the existence within uropathogenic E. coli (UPEC) strains of Sat, a toxin of the serine protease autotransporter of Enterobacteriaceae (SPATE) subfamily. Using features common to proteins secreted via the autotransporter pathway we have identified nine additional autotransporter proteins from the genomic sequence data of UPEC CFT073. Surprisingly, two additional members of the SPATE subfamily were identified. One protein, designated PicU, was homologous to the Pic protein identified in Shigella flexneri and enteroaggregative E. coli. The PicU protein was expressed and investigated for functional activity.     

Genetic variability of the frameshift region in IS911 transposable elements from Escherichia coli clinical isolates

The IS911 bacterial transposable element has been analyzed for its mechanism of transposition and for the way it controls the expression of its genes by programmed -1 translational frameshifting. In the present study the prevalence of IS911 has been determined in the Enterobacteriaceae family and in other Gram-negative bacilli. Three variants, found in Escherichia coli clinical isolates and having mutations in the region implicated in frameshifting, were functionally characterized. All three were altered in their frameshifting and transposition abilities, suggesting that the frameshift region of IS911 may constitute a target for mutations reducing the transposition frequency of this mobile element in natural populations of E. coli.     

Conjugative transfer frequency of resistance genes from ESBL-producing Enterobacteriaceae strains isolated from patients hospitalized in pediatric wards

The aim of this study was to evaluate the transfer frequency of plasmids encoding extended-spectrum beta-lactamases (ESBLs) from clinical isolates of Enterobacteriaceae to E. coli K12 C600 recipient strain. Additionally, resistance patterns to antimicrobial drugs of the isolates as well as transconjugants were analyzed. Fifty-four clinical strains belonging to the Enterobacteriaceae family were isolated from children hospitalized in Medical University Hospital in Wroc?aw. All the strains studied were identified in automatic ATB system using ID32E tests. Besides, they were ESBL-positive as was confirmed by the double-disc synergy test (DDST). The minimal inhibitory concentration (MIC) was determined for twelve selected antibiotics and chemotherapeutics. The majority of the strains (87%) were able to transfer plasmid-mediated ESBL to E. coli K12 C600 recipient strain with a frequencies ranged from 10(-5) to 10(-1) per donor cell. All the isolates studied as well as their transconjugants were susceptible to imipenem, meropenem and norfloxacin (MIC <1mg/L). On the other hand, these strains displayed high level of resistance (MIC 512 - >1024 mg/L) to cefotaxime, ceftriaxone, gentamycin, amikacin and cotrimoxazole. Genetic markers conferring resistance to aminoglycosides and cotrimoxazole were often co-transferred to recipient strain in conjugation process.     

Fluorogenic assay for immediate presumptive detection of Escherichia coli in urine

A rapid and direct fluorogenic assay was used to detect Escherichia coli in urine. Most clinical isolates of E. coli produce β-glucuronidase, whereas almost all other enterobacteria lack the enzyme. Spectrofluorimetric assay of β-glucuronidase, without previous induction, was performed on growing and starved uropathogenic E. coli in artificial urine. The presence of 10³ cfu ml^-1 of E. coli in urine was detected by β-glucuronidase activity in less than 1 h. These results indicate that β-glucuronidase is a rapid, specific and sensitive indicator of the presence of E. coli in urine, and provide additional information on the biological state of the infecting bacterial population.     

The structure and antibiotic sensitivity of the causative agents of community-acquired infectious diseases of bacterial origin in children]

Four hundred and forty pediatric patients at the age of 7 days to 15 years with various infections admitted to the Hospital within a month were examined. The biological material was inoculated to blood agar on the first days of the patient admittance to the Hospital and after the growth the organisms were isolated and identified. Antibiotic susceptibility of the isolates was assayed with the disk diffusion method. 479 strains in all were tested. The most frequent cases requiring hospitalization and antibiotic therapy were those of respiratory tract infections (54.09 per cent), urinary tract infections (26.36 per cent), cutaneous and subcutaneous fat diseases, gastrointestinal diseases and others (about 25 per cent of the cases in all). The main pathogens were Streptococcus viridans, S.aureus and S.epidermidis, as well as Enterobacteriaceae (chiefly E.coli) whose frequencies were practically equal (in 25-35 per cent of the cases). The Pneumococcus isolates amounted to 6.3 per cent. Nonfermenting bacteria (Pseudomonas aeruginosa and Acinetobacter) and some representatives of Enterobacteriaceae (Citrobacter, Serratia, Morganella) were isolated from 7 per cent of the patients. The frequency of Klebsiella and Enterobacter was about 11 per cent. The main pathogens were tested for their susceptibility to amoxycillin/clavulanic acid, ampicillin, oxacillin and gentamicin. The least active antibiotic was ampicillin. 88.8 per cent of the E.coli isolates and 100 per cent of the Klebsiella, P.mirabilis, Morganella, Citrobacter, Enterobacter and Serratia isolates were resistant to it. 53.2 per cent of the Streptococcus isolates including 64.5 per cent of the Pneumococcus isolates were as well resistant to ampicillin. 59.5 per cent of the Streptococcus isolates (mainly S.viridans and Enterococcus) was susceptible to oxacillin, 22.2 per cent of them being moderately susceptible. 62.5 per cent of the Pneumococcus isolates and 78.1 per cent of the Staphylococcus isolates were also susceptible to oxacillin. The highest susceptibility of the isolates was that to amoxycillin/clavulanic acid, i.e. 90.1 per cent of the strains, 79.9 per cent of them being highly susceptible. All the isolates of Citrobacter, Serratia and Morganella and some isolates of P.aeruginosa, Acinetobacter, Enterobacter, Klebsiella and E.coli were resistant to amoxycillin/clavulanic acid. As for the latter 5 organisms their susceptibility to amoxycillin/clavulanic acid was comparable with that to gentamicin. The susceptibility of the Streptococcus and Staphylococcus isolates to amoxycillin/clavulanic acid was significantly much higher than that to oxacillin, gentamicin and ampicillin: 93 per cent of the Streptococcus isolates (62.7 per cent of the Pneumococcus isolates) and 90.7 per cent of the Staphylococcus isolates.     

Virulence characteristics and genetic affinities of multiple drug resistant uropathogenic Escherichia coli from a semi urban locality in India

Extraintestinal pathogenic Escherichia coli (ExPEC) are of significant health concern. The emergence of drug resistant E. coli with high virulence potential is alarming. Lack of sufficient data on transmission dynamics, virulence spectrum and antimicrobial resistance of certain pathogens such as the uropathogenic E. coli (UPEC) from countries with high infection burden, such as India, hinders the infection control and management efforts. In this study, we extensively genotyped and phenotyped a collection of 150 UPEC obtained from patients belonging to a semi-urban, industrialized setting near Pune, India. The isolates representing different clinical categories were analyzed in comparison with 50 commensal E. coli isolates from India as well as 50 ExPEC strains from Germany. Virulent strains were identified based on hemolysis, haemagglutination, cell surface hydrophobicity, serum bactericidal activity as well as with the help of O serotyping. We generated antimicrobial resistance profiles for all the clinical isolates and carried out phylogenetic analysis based on repetitive extragenic palindromic (rep)-PCR. E. coli from urinary tract infection cases expressed higher percentages of type I (45%) and P fimbriae (40%) when compared to fecal isolates (25% and 8% respectively). Hemolytic group comprised of 60% of UPEC and only 2% of E. coli from feces. Additionally, we found that serum resistance and cell surface hydrophobicity were not significantly (p = 0.16/p = 0.51) associated with UPEC from clinical cases. Moreover, clinical isolates exhibited highest resistance against amoxicillin (67.3%) and least against nitrofurantoin (57.3%). We also observed that 31.3% of UPEC were extended-spectrum beta-lactamase (ESBL) producers belonging to serotype O25, of which four were also positive for O25b subgroup that is linked to B2-O25b-ST131-CTX-M-15 virulent/multiresistant type. Furthermore, isolates from India and Germany (as well as global sources) were found to be genetically distinct with no evidence to espouse expansion of E. coli from India to the west or vice-versa.     

ChromID ESBL选择性显色平板对产ESBLs肠杆菌科细菌筛选效果的评价

目的 评价ChromID ESBL选择性显色平板对产超广谱β-内酰胺酶（ESBLs）肠杆菌科细菌的筛选效果。方法 选取临床分离的371株肠杆菌科细菌进行ESBLs的检测,用ChromID ESBL选择性显色平板做筛选试验,同时用纸片确证法做确证试验,采用Kappa检验对两者结果进行一致性分析。结果 两种方法对371株肠杆菌科细菌ESBLs检测的总Kappa值为0.761。ChromID ESBL选择性显色平板法的总灵敏度为95.2%,总特异度为83.5%。对大肠埃希菌、肺炎克雷伯菌、奇异变形杆菌分别统计,其Kappa值分别为0.832、0.514、0.778;ChromID ESBL选择性显色平板法对其检测灵敏度分别为95.7%、91.3%、100.0%,特异度分别87.6%、72.9%、90.9%。另外有6株大肠埃希菌在该显色平板上显非特征色。结论 ChromID ESBL选择性显色平板对产ESBLs肠杆菌科细菌的筛选效果与纸片确证法总体一致性较好,其灵敏度和特异度较高,可应用于临床。但该显色平板对产ESBLs肺炎克雷伯菌的筛选效果与纸片确证法一致性一般,其特异度也较低;对大肠埃希菌存在一定的假阴性,对于该显色平板上生长的绿色和白色菌落需要做进一步鉴定确认。     

Frequency among Enterobacteriaceae of the DNA sequences encoding type 1 pili.

Type 1 pili, characterized by mannose-inhibitable agglutination of fowl or guinea pig erythrocytes, have been found throughout the family Enterobacteriaceae. A radiolabeled probe was prepared from a restriction endonuclease-digested fragment of the Escherichia coli pil operon and used to detect homologous DNA sequences in 236 bacteria representing 11 genera of Enterobacteriaceae. Only isolates identified as E. coli or Shigella spp. exhibited homology. In contrast, mannose-sensitive hemagglutination was observed in nine genera. Probe DNA did not hybridize to plasmid DNA, indicating a chromosomal location for the pil operon. Analysis of restriction nuclease-digested whole-cell DNA from 60 E. coli and two Shigella sp. isolates indicated that internal sequences were conserved in most strains, but that changes in flanking sequences in the chromosome were common.     

Development of a multiplex PCR approach for the identification of Shiga toxin-producing Escherichia coli strains and their major virulence factor genes

AIMS: To develop and evaluate a multiplex PCR (mPCR) system for rapid and specific identification of Shiga toxin-producing Escherichia coli (STEC) and their main virulence marker genes. METHODS AND RESULTS: A series of mPCR assays were developed using primer pairs that identify the sequences of Shiga toxins 1 and 2 (stx1 and stx2, including the stx2c, stx2d, stx2e and stx2f variants), intimin (eaeA), and enterohaemorrhagic E. coli enterohaemolysin (ehlyA). Moreover, two additional genes (rfb O157 and fliC H7), providing the genotypic identification of the O157:H7 E. coli serotype, were detected. As an internal positive control, primers designated to amplify the E. coli 16S rRNA were included in each mPCR. All the amplified genes in the E. coli reference strains were sucessfully identified by this procedure. The method was then used for the examination of 202 E. coli isolates recovered from cattle and children. Among them, 25 (12.4%) were stx positive including the strains of O157:H7 serotype (six isolates) and O157:NM serogroup (four strains). Moreover, 20 STEC strains possessed the eaeA (intimin) and ehlyA (enterohaemolysin) genes. CONCLUSIONS: The developed mPCR-based system enabled specific detection of STEC bacteria and identification of their main virulence marker genes. SIGNIFICANCE AND IMPACT OF THE STUDY: The ability to identify STEC bacteria and the majority of their virulence gene markers, including four variants of Shiga toxin, as well as the differentiation of O157:H7 from non-O157 isolates represents a considerable advancement over other PCR-based methods for rapid characterization of STEC.     

Evaluation of a commercial beta-glucuronidase test for the rapid and economical identification of Escherichia coli

A commercial beta-glucuronidase (beta-GUR) test for the rapid and economical identification of Escherichia coli was evaluated. A total of 762 clinical strains and 228 environmental isolates were studied. More than 95% of the E. coli strains were found to be beta-GUR positive. Thirty-one clinical isolates of Shigella sonnei, 10 of Enterobacter cloacae, eight of Enterobacter aerogenes, nine of Citrobacter freundii and one of Salmonella enteritidis also gave positive results. The enzyme beta-GUR was also detected in two environmental strains of E. cloacae and one C. freundii. A comparative study between the beta-GUR test and the conventional identification system was carried out in 233 consecutive isolates of lactose positive enterobacteria. Agreement was observed in 223 cases and 190 E. coli strains were correctly identified using this test. Discrepancies were found in 10 cases: nine E. coli were beta-GUR negative and one C. freundii was beta-GUR positive. Escherichia coli was the only species positive for both beta-GUR and indole tests. This procedure permits a rapid, easy, precise and inexpensive identification of E. coli. beta-GUR positive Enterobacter strains have not previously been described.     

Silver-resistant Enterobacteriaceae from hospital patients

The inclusion of agar medium containing 0.5 mM AgNO3 in the hospital laboratory replicating system for routine antibiotic-susceptibility determinations resulted in identification of species of Enterobacteriaceae (Escherichia coli, Enterobacter cloacae, Klebsiella pneumoniae, Proteus mirabilis, and Citrobacter freundii) with silver resistance. Since the study began in October, 1975, 11 in-hospital patients receiving silver sulfadiazine for burn wound prophylaxis have yielded silver-resistant bacteria from their infected burns. During this treatment routine burn-site cultures from these patients yielded 230 isolates of Enterobacteriaceae, including 211 which were sulfonamide-resistant, 97 of which were also silver-resistant, and 38 of which were untested for silver resistance. Seven silver-resistant but sulfonamide-sensitive isolates were incidentally recovered from respiratory specimens from four nonburn patients with silver tracheostomy tubes, one silver-resistant sulfonamide-sensitive isolate was recovered from a small infected burn on the foot of an Emergency Room patient. Previous treatment of this burn was unknown. Representative AgNO3-resistant E. coli isolates from four patients were serologically untypable. Serotyping of representative isolates of K. pneumoniae showed a diversity of types except from two patients who had been in the same ward at the same time.     

福建某基层医院CRE碳青霉烯类耐药基因分析

目的 对福建省南平市第二医院分离的碳青霉烯类耐药肠杆菌科细菌进行碳青霉烯类基因和其他β-内酰胺类耐药基因检测。方法 收集碳青霉烯类耐药肠杆菌科细菌,采用Vitek-2 Compact全自动细菌鉴定/药敏仪器进行细菌鉴定和药敏试验;采用改良Hodge试验对实验菌株进行表型检测;利用PCR及测序法对常见的碳青霉烯类和β-内酰胺类耐药基因进行检测;质粒接合试验检测碳青霉烯类耐药基因是否具有可转移性。结果 共收集到4株碳青霉烯类耐药肠杆菌科细菌,呈多重耐药性。2株改良Hodge试验阳性。试验菌株均检出碳青霉烯类耐药基因（NDM-1、IMP-8或VIM-2）,并同时携带有其他β-内酰胺类基因;4株细菌中有3株的碳青霉烯类耐药基因接合成功。结论 碳青霉烯类耐药肠杆菌科细菌已在福建基层医院出现,并具有一定传播性,应引起相关主管部门的注意,以防耐药菌的流行。     

BAMP-28 Antimicrobial Peptide Against Different MALDI Biotype of Carbapenam Resistant Enterobacteriaceae

Worldwide emergence of Carbapenam resistance in Enterobacteriaceae (CRE) are increasing globally and becoming a severe public health issue. Infections caused by CRE have limited treatment options and have been associated with high mortality rates. Due to their unique mode of action, antimicrobial peptides are novel alternatives to traditional antibiotics for tackling the issue of bacterial multidrug resistance. An easy, rapid and accurate detection of 72 clinically CRE isolates using a MALDI–TOF MS was additionally developed. The CRE isolates belonging to 33 Carbapenam-resistant Klebsiella pneumoniae, 17 Carbapenam-resistant Escherichia coli, 16 Carbapenam-resistant Enterobacter cloacae and 6 Carbapenam-resistant Citrobacter freundii carrying blaNDM-1 were definitely discriminated from reference genotype strain by MALDI–TOF MS. This rapid, accurate, and reproducible peptide signature profiling technology could have new implications in laboratory-based high-throughput differentiation of extensive libraries of Carbapenam resistant Enterobacteriaceae. Antibacterial activity of 9 short novel peptides against these CRE isolates were investigated. Although neither synthetic peptides induced significant hemolysis, or showed cytotoxic on Vero cell, only BAMP-28 peptide inhibited growth of K. pneumoniae, E. coli, C. freundii and E. cloacae with MIC₅₀ of 18–40, 20–40, 16–25 and 18–36 µM, respectively. In conclusion, MALDI–TOF MS can be used to screen for Carbapenam resistance in K. pneumoniae, E. coli, E. cloacae and C. freundii. Interestingly, BMAP-28 peptide had acceptable effect on Carbapenam resistant Enterobacteriaceae including K. pneumoniae, E. coli, C. freundii and E. Cloacae isolates with less toxicity.

     

Simple and reliable multiplex PCR assay for detection of blaTEM,bla(SHV) and blaOXA-1 genes in Enterobacteriaceae

Third-generation cephalosporin resistance is often mediated by TEM- and SHV-type beta-lactamases in Enterobacteriaceae. TEM-type and OXA-1 enzymes are the major plasmid-borne beta-lactamases implicated in amoxicillin-clavulanic acid resistance in Escherichia coli isolates. We have developed a rapid and simple multiplex polymerase chain reaction (PCR) which discriminates bla(TEM), bla(SHV) and bla(OXA-1) genes by generating fragments of 516, 392 and 619 bp respectively. Multiplex PCR analysis of 51 amoxicillin-clavulanate resistant E. coli isolates detected bla(TEM) and bla(SHV) genes in 45 and two strains, respectively, and only one strain harboured a bla(OXA-1) gene. Twenty-three of the 40 cefotaxime-resistant Enterobacteriaceae isolates produced amplicons with a size compatible with the presence of bla(TEM) (13 strains), bla(SHV) (six strains) genes or the association of both genes (four strains). These results were verified by colony hybridisation. Therefore, multiplex PCR is a suitable tool for initial rapid screening of bla genes in Enterobacteriaceae.     

Major outer membrane proteins: common antigens in enterobacteriaceae species

The major outer membrane (OM) proteins of 23 enterobacterial strains (principally clinical isolates) and five non-Enterobacteriaceae species were investigated by the sodium dodecyl sulphate-polyacrylamide gel immunoperoxidase (SGIP) technique to evaluate antigenic cross-reactivity among these proteins. All enterobacterial strains contained one or more peptidoglycan-associated major OM proteins, cross-reactive with the peptidoglycan-bound protein I of Escherichia coli, and one non-peptidoglycan-bound heat-modifiable protein, cross-reactive with protein II of E. coli. Results indicated that antigenic cross-reactivity of the major OM proteins is a general phenomenon in the family Enterobacteriaceae, independent of any molecular weight variation of the corresponding proteins in different bacterial strains. SGIP experiments carried out with OM preparations of other species showed no cross-reactivity of any of their OM proteins with enterobacterial major OM proteins. The significance of the immunological relatedness of OM proteins for the classification of some Enterobacteriaceae is discussed.     

Design and synthesis of a quintessential self-transmissible IncX1 plasmid, pX1.0

DNA exchange in bacteria via conjugative plasmids is believed to be among the most important contributing factors to the rapid evolution- and diversification rates observed in bacterial species. The IncX1 plasmids are particularly interesting in relation to enteric bacteria, and typically carry genetic loads like antibiotic resistance genes and virulence factors. So far, however, a "pure" version of these molecular parasites, without genetic loads, has yet to be isolated from the environment. Here we report the construction of pX1.0, a fully synthesized IncX1 plasmid capable of horizontal transfer between different enteric bacteria. The designed pX1.0 sequence was derived from the consensus gene content of five IncX1 plasmids and three other, more divergent, members of the same phylogenetic group. The pX1.0 plasmid was shown to replicate stably in E. coli with a plasmid DNA per total DNA ratio corresponding to approximately 3-9 plasmids per chromosome depending on the growth phase of the host. Through conjugation, pX1.0 was able to self-transfer horizontally into an isogenic strain of E. coli as well as into two additional species belonging to the family Enterobacteriaceae. Our results demonstrate the immediate applicability of recent advances made within the field of synthetic biology for designing and constructing DNA systems, previously existing only in silica.