Oral treatment options for patients with urinary tract infections caused by extended spectrum ßeta-lactamase (ESBL) producing Enterobacteriaceae.

INTRODUCTION: Frequent use of different antibiotics to treat urinary tract infections (UTIs) exerts a variety of selective pressure on pathogens which ultimately lead to the antimicrobial resistance. Extended Spectrum ßeta-Lactamase (ESBL) producing Enterobacteriacae causing UTIs, which are usually multidrug resistant organisms, pose a great therapeutic treatment challenge. Rediscovery of forgotten antibiotics such as pivmecillinam, fosfomycin, and nitrofurantoin may be helpful in this situation until the discovery of new agents. The main aim of present study was to determine the prevalence of ESBL producing Enterobacteriacae causing UTIs and their sensitivity profile to determine alternate effective oral treatment options. METHODS: This retrospective study was conducted to determine the prevalence of ESBL producing Enterobacteriacae from urine samples and their sensitivity profile (pivmecillinam, fosfomycin, nitrofurantoin, trimethoprim and ciprofloxacin) from September 2015 to September 2017. RESULTS: A total of 986 organisms were isolated from the urine samples of 680 patients. Approximately 77% isolates were obtained from female patients (526). Of 986 organisms, Escherichia coli was the most common isolated organism (889, 90%); followed by Klebsiella species (71, 7%) and other Enterobacteriacae (26, 3%). Of 889 E. coli, approximately 98%, 96%, and 93% were found to be sensitive to fosfomycin, pivmecillinam and nitrofurantoin respectively. On the other hand pivmecillinam was most effective against Klebsiella species (83%, 59); followed by fosfomycin (62%, 44) and nitrofurantoin (42%, 30). Of 26 other Enterobacteriacae, 23 (88%), and 22 (85%) were sensitive to pivmecillinam and fosfomycin while lower sensitivity rate (15%, 4) was noted against nitrofurantoin. More than 95% of all ESBL producing Enterobacteriacae were sensitive to pivmecillinam, fosfomycin and nitrofurantoin. Trimethoprim and ciprofloxacin were least effective. CONCLUSION: The emergence of multidrug resistant ESBL producing Enterobacteriacae restricts significantly the therapeutic options. This study shows higher sensitivity rates to pivmecillinam, fosfomycin and nitrofurantoin. We recommend their use to treat uncomplicated UTIs due to ESBL producing Enterobacteriacae.

Changes in pathogen spectrum and antimicrobial resistance development in the time-course of acute necrotizing pancreatitis.

BACKGROUND AND AIM: In contrast to the first peak of multi-organ failure in acute pancreatitis, the second peak is mostly triggered by septic complications. Our aim was to analyze the spectrum of pathogens and antimicrobial resistance development in relation to the time-course of the disease and its clinical outcome. METHODS: One hundred twenty-two patients with acute necrotizing pancreatitis undergoing pancreas puncture at two tertiary academic medical centers in Germany were retrospectively analyzed. RESULTS: At species level, there was a change in spectrum from Enterococcus faecalis (∆d150 - d1 = 14.6% - 16.7% = -2.1%) to Enterococcus faecium (∆d150 - d1 = 93.1% - 16.3% = 76.8%) (P < 0.001) and from Candida albicans (∆d150 - d1 = 39.7% - 23.6% = 16.1%) to non-albicans Candida spp. (∆d150 - d1 = 43.5% - 6.4% = 37.1%) (P = 0.005). Time-to-event analysis of acquired antimicrobial resistance showed that the overall number of patients with Enterobacteriaceae presented an antimicrobial susceptibility decrease by 59.7% (∆d1 - d100 = 87.0% - 27.3% = 59.7%). The cumulative incidence of multi-resistant bacteria increased with length of hospital stay (∆d150 - d1 = 49.1% - 3.1% = 46.0%) (P = 0.004). Multivariable logistic regression analysis in relation to the pathogen spectrum and antimicrobial resistance development showed a significantly higher mortality for non-albicans Candida spp. (P = 0.039, odds ratio [OR] = 3.32 [95% confidence interval [CI]: 1.07-10.35]), E. faecium (P = 0.009, OR = 3.73 [95% CI: 1.38-10.05]), and multi-resistant bacteria (P = 0.007, OR = 5.08 [95% CI: 1.55-16.66]). CONCLUSIONS: Antimicrobial treatment of infected pancreatic necrosis becomes more challenging over time, owing to a change in spectrum favoring difficult-to-treat pathogens and an increase in multi-resistant bacteria associated with worse clinical outcomes (World Health Organization trial registration number: DRKS00014785).

Enterobacteriaceae dominate the core microbiome and contribute to the resistome of arugula (Eruca sativa Mill.).

BACKGROUND: Arugula is a traditional medicinal plant and popular leafy green today. It is mainly consumed raw in the Western cuisine and known to contain various bioactive secondary metabolites. However, arugula has been also associated with high-profile outbreaks causing severe food-borne human diseases. A multiphasic approach integrating data from metagenomics, amplicon sequencing, and arugula-derived bacterial cultures was employed to understand the specificity of the indigenous microbiome and resistome of the edible plant parts. RESULTS: Our results indicate that arugula is colonized by a diverse, plant habitat-specific microbiota. The indigenous phyllosphere bacterial community was shown to be dominated by Enterobacteriaceae, which are well-equipped with various antibiotic resistances. Unexpectedly, the prevalence of specific resistance mechanisms targeting therapeutic antibiotics (fluoroquinolone, chloramphenicol, phenicol, macrolide, aminocoumarin) was only surpassed by efflux pump assignments. CONCLUSIONS: Enterobacteria, being core microbiome members of arugula, have a substantial implication in the overall resistome. Detailed insights into the natural occurrence of antibiotic resistances in arugula-associated microorganisms showed that the plant is a hotspot for distinctive defense mechanisms. The specific functioning of microorganisms in this unusual ecosystem provides a unique model to study antibiotic resistances in an ecological context.

Physicochemical responses and microbiological changes of bream (Megalobrama ambycephala) to pectin based coatings enriched with clove essential oil during refrigeration.

The effectiveness of pectin coatings enriched with clove essential oil (CEO), as new edible coatings were investigated to preserve bream (Megalobrama ambycephala) fillets during refrigeration over a period of 15 days. All samples were analyzed for physicochemical (pH, PV, TBA and TVB-N), microbiological (Total viable count, Psychrophilic bacteria, Lactic acid bacteria, Enterobacteriaceae, Pseudomonas spp., H2S producing bacteria) and organoleptic attributes. The results revealed that the CEO incorporation reduced the extent of lipid oxidation, as judged by PV, TBA and TVB-N, thus extending the shelf life of bream fillets by at least 15 days. Moreover, the application of pectin coatings with CEO improved the weight loss, water holding capacity, textural and color attributes of the bream samples significantly compared to untreated sample. Pectin coating along with CEO was effective in inhibiting bacterial growth especially in gram-negative bacteria, while the growth of lactic acid bacteria remained constant for most of the storage period. The effect on the microorganisms during storage was in accordance with biochemical indexes of the quality, representing the viability of these coatings for bream preservation. Thus, the coatings developed in present study could inhibit the development of lipid oxidation during cold storage, representing an option as a seafood preservative.

Decreased antibiotic susceptibility of Enterobacteriaceae causing community-acquired urinary tract infections in French Amazonia.

OBJECTIVES: Urinary tract infections (UTIs) have rarely been studied in the Amazon region. We aimed to describe the epidemiology of bacteria causing UTIs in French Guiana. PATIENTS AND METHODS: We performed a monocenter retrospective study of adults consulting at the emergency department of Cayenne Hospital in 2014 with a diagnosis of UTI. The bacterial species and resistance profile were described. RESULTS: Two-hundred-and-eighty-nine patients presenting with UTI were included: 82 (28.4%) presented with cystitis, 166 (57.4%) with pyelonephritis, and 41 (14.2%) with male UTI. E. coli was predominant (74.1%), and had decreased susceptibility to ampicillin, amoxicillin-clavulanic acid, fluoroquinolones, co-trimoxazole, and furans compared with data from metropolitan France. Extended-spectrum beta-lactamases (ESBL) was isolated in 3.1% of E. coli and 31.6% of K. pneumoniae. CONCLUSIONS: Antibiotic susceptibility in UTI is lower than reported in metropolitan France without evidence for an excessive consumption of antibiotics.

Catheter-associated bacterial flora in patients with benign prostatic hyperplasia: shift in antimicrobial susceptibility pattern.

BACKGROUND: Men with urinary retention secondary to benign prostatic hyperplasia (BPH) are prone to genitourinary infections. Physicians should be aware of the current antimicrobial susceptibility pattern in this population if empirical treatment is needed. The goal of this study was to evaluate variations in prevalence, composition and antimicrobial susceptibility of bacterial flora in men with indwelling catheters subjected to surgery for BPH in chosen time periods since 1994. Necessary changes in empirical therapy were also assessed. METHODS: All patients with indwelling catheters admitted to a single urological center for BPH surgery in the years 1994-1996, 2004-2006, and 2011-2015 were considered. Catheterization times and results of urine cultures from samples collected at admission were evaluated. Susceptibility for selected antimicrobials was compared separately for Gram negative and Gram positive species. For each agent and for their combinations effectiveness of empirical therapy was calculated dividing the number of patients with bacteriuria susceptible to the agents by the total number of patients with bacteriuria. RESULTS: Bacteriuria was present in 70% of 169, 72% of 132, and 69% of 156 men in the respective time periods. The incidence of Gram-positive strains increased from 10 to 37% (P < 0.001). Their susceptibility to amoxicillin/clavulanate was fluctuating (81, 61, 77%; P=NS). No vancomycin-resistant strain was present. Gram-negative flora composition was stable. Their susceptibility decreased to ciprofloxacin (70 to 53%; P = 0.01) and amoxicillin/clavulanate (56 to 37%; P < 0.01) while it increased to gentamycin (64 to 88%; P < 0.001) and co-trimoxazole (14 to 62%; P < 0.001); susceptibility to amikacin remained high (> 85%). Only two cases of resistance to carbapenems in 2004-2006 were found. In vitro effectiveness of amikacin + amoxicillin/clavulanate in empirical therapy was slowly decreasing (87 to 77%; P=NS). Imipenem was found the most effective single agent (90-95%) and its efficacy was even improved by adding vancomycin (97-98%). CONCLUSIONS: Substantial rise in the incidence of Gram-positive species and fluctuations in antimicrobial susceptibility patterns were found. Empirical therapy of genitourinary infection in catheterized men with BPH should now involve antimicrobial agents effective both to Enterococci and Enterobacteriaceae. Periodic monitoring and publishing data on antimicrobial susceptibility for this population is necessary.

Epidemiological situation of enterobacteriaceae resistant to cephalosporins third generation in the region of Mahdia, Tunisia (2002-2014).

OBJECTIVES: To determine the prevalence and to monitor the trends of resistance to broad-spectrum cephalosporins among various species of enterobacteria in the region of Mahdia (Tunisia) from 2002 to 2014. METHODS: A retrospective study was carried out in the microbiology laboratory at Tahar Sfar Teaching Hospital in Mahdia. Data concerning a thirteen-year period (2002-2014). All clinical isolates of enterobacteriaceae were identified with the API 20 E system. Antimicrobial susceptibilities were determined by disk diffusion on Mueller Hinton agar according to CA-SFM recommendations. RESULTS: During the study period, 25040 non-duplicate clinical strains of enterobacteriacae were identified. 2584 (10,3%) clinical isolates showed acquired resistance to third generation cephalosporins (3rdGC). The overall frequency of resistance increased from 8% in 2002 to 16,3% in 2014. This increase was statistically significant. High prevalence rates of 3rdGC resistance have been observed in pediatric (25,1%), in gynecologyobstetrics (21,9%) and medecine (17,4%). E. coli (21,6%), K. pneumoniae (28,6%) and E. cloacae (30,5%) showed high prevalence rates of broad-spectrum cephalosporin resistance. CONCLUSION: The resistance rates ERC3G in our region seems to be increasing. Implementation of infection control measures and identification of the mechanism responsible for third generation cephalosporins resistance are necessary to limit the spreading of these resistant enterobacteriaceae in hospitals and community settings.

Identification of phenol- and p-cresol-producing intestinal bacteria by using media supplemented with tyrosine and its metabolites.

To identify intestinal bacteria that produce phenols (phenol and p-cresol), we screened 153 strains within 152 species in 44 genera by culture-based assay using broth media supplemented with 200 µM each of tyrosine and its predicted microbial metabolic intermediates (4-hydroxyphenylpyruvate, DL-4-hydroxyphenyllactate, 3-(p-hydroxyphenyl)propionate, 4-hydroxyphenylacetate and 4-hydroxybenzoate). Phenol-producing activity was found in 36 strains and p-cresol-producing activity in 55 strains. Sixteen strains had both types of activity. Phylogenetic analysis based on the 16S rRNA gene sequences of strains that produced 100 µM or more of phenols revealed that 16 phenol producers belonged to the Coriobacteriaceae, Enterobacteriaceae, Fusobacteriaceae and Clostridium clusters I and XIVa; four p-cresol-producing bacteria belonged to the Coriobacteriaceae and Clostridium clusters XI and XIVa; and one strain producing both belonged to the Coriobacteriaceae. A genomic search for protein homologs of enzymes involved in the metabolism of tyrosine to phenols in 10 phenol producers and four p-cresol producers, the draft genomes of which were available in public databases, predicted that phenol producers harbored tyrosine phenol-lyase or hydroxyarylic acid decarboxylase, or both, and p-cresol producers harbored p-hydroxyphenylacetate decarboxylase or tyrosine lyase, or both. These results provide important information about the bacterial strains that contribute to production of phenols in the intestine.

Raoultella sp. SM1, a novel iron-reducing and uranium-precipitating strain.

The main aim of this study was the characterisation of novel Raoutella isolate, an iron-reducing and uranium-precipitating strain, originating from microbial mats occurring in the sediments of a closed down uranium mine in Kowary (SW Poland). Characterisation was done in the context of its potential role in the functioning of these mats and the possibility to use them in uranium removal/recovery processes. In our experiment, we observed the biological precipitation of iron and uranium's secondary minerals containing oxygen, potassium, sodium and phosphor, which were identified as ningyoite-like minerals. The isolated strain, Raoultella sp. SM1, was also able to dissimilatory reduce iron (III) and uranium (VI) in the presence of citrate as an electron donor. Our studies allowed us to characterise a new strain which may be used as a model microorganism in the study of Fe and U respiratory processes and which may be useful in the bioremediation of uranium-contaminated waters and sediments. During this process, uranium may be immobilised in ningyoite-like minerals and can then be recovered in nano/micro-particle form, which may be easily transformed to uraninite.

Drastic Genome Reduction in an Herbivore's Pectinolytic Symbiont.

Pectin, an integral component of the plant cell wall, is a recalcitrant substrate against enzymatic challenges by most animals. In characterizing the source of a leaf beetle's (Cassida rubiginosa) pectin-degrading phenotype, we demonstrate its dependency on an extracellular bacterium housed in specialized organs connected to the foregut. Despite possessing the smallest genome (0.27 Mb) of any organism not subsisting within a host cell, the symbiont nonetheless retained a functional pectinolytic metabolism targeting the polysaccharide's two most abundant classes: homogalacturonan and rhamnogalacturonan I. Comparative transcriptomics revealed pectinase expression to be enriched in the symbiotic organs, consistent with enzymatic buildup in these structures following immunostaining with pectinase-targeting antibodies. Symbiont elimination results in a drastically reduced host survivorship and a diminished capacity to degrade pectin. Collectively, our findings highlight symbiosis as a strategy for an herbivore to metabolize one of nature's most complex polysaccharides and a universal component of plant tissues.

Genome analysis of crude oil degrading Franconibacter pulveris strain DJ34 revealed its genetic basis for hydrocarbon degradation and survival in oil contaminated environment.

Franconibacter pulveris strain DJ34, isolated from Duliajan oil fields, Assam, was characterized in terms of its taxonomic, metabolic and genomic properties. The bacterium showed utilization of diverse petroleum hydrocarbons and electron acceptors, metal resistance, and biosurfactant production. The genome (4,856,096bp) of this strain contained different genes related to the degradation of various petroleum hydrocarbons, metal transport and resistance, dissimilatory nitrate, nitrite and sulfite reduction, chemotaxy, biosurfactant synthesis, etc. Genomic comparison with other Franconibacter spp. revealed higher abundance of genes for cell motility, lipid transport and metabolism, transcription and translation in DJ34 genome. Detailed COG analysis provides deeper insights into the genomic potential of this organism for degradation and survival in oil-contaminated complex habitat. This is the first report on ecophysiology and genomic inventory of Franconibacter sp. inhabiting crude oil rich environment, which might be useful for designing the strategy for bioremediation of oil contaminated environment.

The microbial community of the gut differs between piglets fed sow milk, milk replacer or bovine colostrum.

The aim of this study was to characterise the gut microbiota composition of piglets fed bovine colostrum (BC), milk replacer (MR) or sow milk (SM) in the post-weaning period. Piglets (n 36), 23-d old, were randomly allocated to the three diets. Faecal samples were collected at 23, 25, 27 and 30 d of age. Digesta from the stomach, ileum, caecum and mid-colon was collected at 30 d of age. Bacterial DNA from all samples was subjected to amplicon sequencing of the 16S rRNA gene. Bacterial enumerations by culture and SCFA analysis were conducted as well. BC-piglets had the highest abundance of Lactococcus in the stomach (P<0·0001) and ileal (P<0·0001) digesta, whereas SM-piglets had the highest abundance of Lactobacillus in the stomach digesta (P<0·0001). MR-piglets had a high abundance of Enterobacteriaceae in the ileal digesta (P<0·0001) and a higher number of haemolytic bacteria in ileal (P=0·0002) and mid-colon (P=0·001) digesta than SM-piglets. BC-piglets showed the highest colonic concentration of iso-butyric and iso-valeric acid (P=0·02). Sequencing and culture showed that MR-piglets were colonised by a higher number of Enterobacteriaceae, whereas the gut microbiota of BC-piglets was characterised by a change in lactic acid bacteria genera when compared with SM-piglets. We conclude that especially the ileal microbiota of BC-piglets had a closer resemblance to that of SM-piglets in regard to the abundance of potential enteric pathogens than did MR-piglets. The results indicate that BC may be a useful substitute for regular milk replacers, and as a feeding supplement in the immediate post-weaning period.

Zeolite food supplementation reduces abundance of enterobacteria.

According to the World Health Organisation, antibiotics are rapidly losing potency in every country of the world. Poultry are currently perceived as a major source of pathogens and antimicrobial resistance. There is an urgent need for new and natural ways to control pathogens in poultry and humans alike. Porous, cation rich, aluminosilicate minerals, zeolites can be used as a feed additive in poultry rations, demonstrating multiple productivity benefits. Next generation sequencing of the 16S rRNA marker gene was used to phylogenetically characterize the fecal microbiota and thus investigate the ability and dose dependency of zeolite in terms of anti-pathogenic effects. A natural zeolite was used as a feed additive in laying hens at 1, 2, and 4% w/w for a 23 week period. At the end of this period cloacal swabs were collected to sample faecal microbial communities. A significant reduction in carriage of bacteria within the phylum Proteobacteria, especially in members of the pathogen-rich family Enterobacteriaceae, was noted across all three concentrations of zeolite. Zeolite supplementation of feed resulted in a reduction in the carriage of a number of poultry pathogens without disturbing beneficial bacteria. This effect was, in some phylotypes, correlated with the zeolite concentration. This result is relevant to zeolite feeding in other animal production systems, and for human pathogenesis.

Characteristics of ciprofloxacin-resistant Enterobacteriaceae isolates recovered from wastewater of an Algerian hospital.

INTRODUCTION: Hospital effluents are a source of environmental pollution by drugs, antibiotic-resistant bacteria, and resistance genes. Quinolones, particularly ciprofloxacin, are commonly detected in these effluents, contributing to the emergence of antimicrobial resistance. The objective of this study was to characterize ciprofloxacin-resistant Enterobacteriaceae in hospital effluents. METHODOLOGY: Isolates were selected on Tergitol-7 agar supplemented with ciprofloxacin and genotyped by ERIC-PCR. Antibiotic susceptibility testing was done using the disk diffusion method, and minimum inhibitory concentrations were determined using the agar dilution method. Resistance genes, integrons, phylogenetic groups, and sequence types were identified by PCR and sequencing. RESULTS: A total of 17 ciprofloxacin-resistant isolates were characterized: Escherichia coli, Escherichia vulneris, Klebsiella pneumoniae, Klebsiella oxytoca, Citrobacter freundii, and Citrobacter koseri/farmeri. Isolates presented concomitant resistance to nalidixic acid, ciprofloxacin, ofloxacin, and pefloxacin. A diversity in mutation patterns in gyrA and parC genes and new amino-acid substitutions in GyrA subunit were observed. Quinolone plasmidic resistance genes qnrB1, qnrB2, qnrB5/19, qnrS1, and aac(6')-Ib-cr were detected. Resistance to other antibiotic classes was observed. Class 1 integrons and resistance genes blaCTX-M-15, blaOXA-1, sul1, sul2, sul3, tetA, tetB, aadA1/2, aadA5, aph(3')-Ia, aac(3)II, dfrA1, dfrA5, dfrA7, and dfrA12 were detected. Bacterial tolerance to cadmium, zinc, and mercury was observed with the presence of the merA gene. E. coli isolates belonged to phylogenetic groups A, B1, and D and to sequence types ST405, ST443, ST101, ST10, and ST347. CONCLUSIONS: This study highlighted bacterial multidrug resistance linked to ciprofloxacin and, consequently, the risk of bacterial exposure to this antibiotic.

The coffee-machine bacteriome: biodiversity and colonisation of the wasted coffee tray leach.

Microbial communities are ubiquitous in both natural and artificial environments. However, microbial diversity is usually reduced under strong selection pressures, such as those present in habitats rich in recalcitrant or toxic compounds displaying antimicrobial properties. Caffeine is a natural alkaloid present in coffee, tea and soft drinks with well-known antibacterial properties. Here we present the first systematic analysis of coffee machine-associated bacteria. We sampled the coffee waste reservoir of ten different Nespresso machines and conducted a dynamic monitoring of the colonization process in a new machine. Our results reveal the existence of a varied bacterial community in all the machines sampled, and a rapid colonisation process of the coffee leach. The community developed from a pioneering pool of enterobacteria and other opportunistic taxa to a mature but still highly variable microbiome rich in coffee-adapted bacteria. The bacterial communities described here, for the first time, are potential drivers of biotechnologically relevant processes including decaffeination and bioremediation.

Description of Siccibacter colletis sp. nov., a novel species isolated from plant material, and emended description of Siccibacter turicensis.

A re-evaluation of the taxonomic position of two strains, 1383(T) and 2249, isolated from poppy seeds and tea leaves, which had been identified as Siccibacter turicensis (formerly Cronobacter zurichensis ), was carried out. The analysis included phenotypic characterization, 16S rRNA gene sequencing, multilocus sequence analysis (MLSA) of five housekeeping genes (atpD, fusA, glnS, gyrB and infB; 2034 bp) and ribosomal MLSA (53 loci; 22 511 bp). 16S rRNA gene sequence analysis and MLSA showed that the strains formed an independent phylogenetic lineage, with Siccibacter turicensis LMG 23730(T) as the closest neighbour. Average nucleotide identity analysis and phenotypic analysis confirmed that these strains represent a novel species, for which the name Siccibacter colletis sp. nov. is proposed. The type strain is 1383(T) ( = NCTC 14934(T) = CECT 8567(T) = LMG 28204(T)). An emended description of Siccibacter turicensis is also provided.

PHENOTYPIC AND MOLECULAR DIFFERENTIATION OF PECTOBACTERIUM AND DICKEYA SPP. CAUSING POTATO TUBER AND STEM ROT IN NORTH-WESTERN PROVINCES OF IRAN.

Iran is one of the most important potato-producing countries in Asia and Oceania. Approximately 20 percent of potato cultivation in Iran occurs in the North-western provinces. Pectobacterium and Dickeya species cause important diseases in potato crop. They may incite blackleg and are responsible for tuber soft rot in storage, thereby reducing yield and quality. In order to identify and differentiate the species of soft rot bacteria, potato stems and tubers showing soft rot symptoms were collected from potato fields in North-western Iran. A total of fifty strains belonging to Pectobacterium and Dickeya species were isolated and identified from the infected tissues. Phenotypic characterization revealed a considerable variation among strains thus dividing them into five separate groups. Group 1 strains belonged to Dickeya chrysanthemi that were different from the type strain in malonate utilization. Group 2 strains were similar to Pectobacterium betavascularum but were different from the type strain in utilization of raffinose, citrate and D-sorbitol. Group 3 strains showed more resemblance to P. wasabiae but were different from the type strain with respect to acetoin production. Group 4 strains belonged to P. carotovorum subsp. carotovorum (Pcc) and group 5 strains were identified as intersubspecific of Pcc and P. carotovorum subsp. odoriferum. Polymerase chain reaction using pelY primers identified strains belonging to Pectobacterium species but not P. betavascularum.

Dickeya solani sp. nov., a pectinolytic plant-pathogenic bacterium isolated from potato (Solanum tuberosum).

Pectinolytic bacteria have been recently isolated from diseased potato plants exhibiting blackleg and slow wilt symptoms found in a number of European countries and Israel. These Gram-reaction-negative, motile, rods were identified as belonging to the genus Dickeya, previously the Pectobacterium chrysanthemi complex (Erwinia chrysanthemi), on the basis of production of a PCR product with the pelADE primers, 16S rRNA gene sequence analysis, fatty acid methyl esterase analysis, the production of phosphatases and the ability to produce indole and acids from α-methylglucoside. Differential physiological assays used previously to differentiate between strains of E. chrysanthemi, showed that these isolates belonged to biovar 3. Eight of the isolates, seven from potato and one from hyacinth, were analysed together with 21 reference strains representing all currently recognized taxa within the genus Dickeya. The novel isolates formed a distinct genetic clade in multilocus sequence analysis (MLSA) using concatenated sequences of the intergenic spacer (IGS), as well as dnaX, recA, dnaN, fusA, gapA, purA, rplB, rpoS and gyrA. Characterization by whole-cell MALDI-TOF mass spectrometry, pulsed field gel electrophoresis after digestion of whole-genome DNA with rare-cutting restriction enzymes, average nucleotide identity analysis and DNA-DNA hybridization studies, showed that although related to Dickeya dadantii, these isolates represent a novel species within the genus Dickeya, for which the name Dickeya solani sp. nov. (type strain IPO 2222(T) = LMG25993(T) = NCPPB4479(T)) is proposed.

Enterobacteriaceae Sepsis Outcome Programme annual report, 2013.

The Australian Group on Antimicrobial Resistance performs regular period-prevalence studies to monitor changes in antimicrobial resistance in selected enteric Gram-negative pathogens. The 2013 survey focussed for the first time on blood stream infections. Four thousand nine hundred and fifty-eight Enterobacteriaceae species were tested using commercial automated methods (Vitek® 2, BioMérieux; Phoenix™, BD). The results were analysed using Clinical and Laboratory Standards Institute (CLSI) and European Committee on Antimicrobial Susceptibility Testing (EUCAST) breakpoints (January 2014). Of the key resistances, non-susceptibility to the third-generation cephalosporin, ceftriaxone, was found in 7.5%/7.5% (CLSI/EUCAST criteria respectively) of Escherichia coli; 6.3%/6.3% of Klebsiella pneumoniae, and 7.4%/7.4% of K. oxytoca. Non-susceptibility rates to ciprofloxacin were 10.3%/11.3% for E. coli, 4.6%/7.5% for K. pneumoniae, 0.6%/0.6% for K. oxytoca, and 3.6%/6.1% in Enterobacter cloacae. Resistance rates to piperacillin-tazobactam were 3.1%/6.2%, 4.2%/7.0%, 11.9% /12.6%, and 17.3% /22.2% for the same 4 species respectively. Fourteen isolates were shown to harbour a carbapenemase gene, 9 blaIMP, 3 blaKPC, and 2 blaNDM.