Residual risk of Pseudomonas aeruginosa waterborne contamination in intensive care unit despite the presence of filters on all water points-of-use.

OBJECTIVE: To assess the residual risk of waterborne contamination by Pseudomonas aeruginosa (PA) from water network colonized by a single genotype (Sequence Type (ST)299) despite the presence of antimicrobial filters in a medical intensive care unit (ICU). METHODS: During the first 19-month period after ICU opening, water network contamination was assessed monthly by collecting water upstream the filters. Downstream water was also sampled to assess filters efficiency. PA clinical isolates from patients were collected and compared to the waterborne ST299-PA by multiplex-rep PCR, Pulsed-Field Gel Electrophoresis (PFGE) and whole-genome sequencing. Cross-transmission events occurring independently of the genotype of PA involved were also assessed. RESULTS: From 449 samples of filtered water, 1.3% were positive for PA in inoculum varying between 1 to 104 Colony Forming Unit (CFU)/100mL according to the tap. All PA hydric isolates belonged to PA-ST299 and displayed <2 Single Nucleotide Polymorphisms (SNPs). Among 278 clinical isolates from 122 patients, 10 isolates in 5 patients showed identical profiles to the hydric PA-ST299 clone in both multiplex-rep PCR and PFGE and differed by <5 SNPs on average, confirming the water network reservoir as the source of contamination by PA for 4.09% of patients. Cross-transmission events by other genotypes of PA than PA-ST299 were responsible for the contamination of 1.75 % of patients. DISCUSSION/CONCLUSION: Antimicrobial filters are not sufficient to preserve patients from waterborne pathogens when the water network is highly contaminated. The microbiological survey of filtered water may be needed in units hosting at-risk patients for PA infections, even when all water points-of-use are protected by filters.

Highly diverse dynamics of Pseudomonas aeruginosa colonization from initial detection in cystic fibrosis patients: A 7-year longitudinal genetic diversity study.

In cystic fibrosis (CF), Pseudomonas aeruginosa (Pa) is a major pathogen that can persistently colonize patients. Genetic studies showed a high diversity of Pa, the success of widespread or 'international' clones and described epidemic clones in CF and Epidemic High-Risk (ERH) clones. Here, we characterized Pa genetic diversity over time after first colonization in CF patients, with the aim of accurately describing the dynamics of colonization in a context of scarce longitudinal studies including the first isolated Pa strain. Results represent the first genotyping data available for CF Pa in France. Forty-four CF patients with a first Pa colonization were included; 265 strains collected over 7 years in these patients were genotyped by multiplex rep-PCR, multilocus sequence typing, pulsed-field gel electrophoresis and/or whole genome sequencing. Forty-one sequence types were identified: 4 were unknown, 22 never previously reported for CF patients, and 6 corresponded to widespread clones colonizing 16 patients (36%). Unrelated strains were identified in 41 patients (93%). Twenty-six patients (59%) presented a recurrence during the study period. No specific clones were associated with transient, recurrent or persistent colonization. Our longitudinal study revealed that 9 of the 26 patients with recurrence (35%) harbored strains of different genotypes. Great genetic diversity was observed among initial Pa isolates excluding any cross-transmission. Persistent colonization may appear more complex than expected, imitating persistence, with successive colonization events by unrelated Pa.

Recurrent environmental contamination in a centralized radiopharmacy unit by Achromobacter spp: Results of a large microbiological investigation.

BACKGROUND: Radiopharmaceuticals preparation unit, such as every aseptic preparation units, are strictly monitored in terms of microbiological contamination. Despite all biocontamination control procedures, our radiopharmacy unit faced repeated environmental contamination by Achromobacter spp which necessitated a large environmental investigation. METHODS: Microbiological controls were carried out using Count Tact agars (Biomérieux) for flat surfaces, dry swabbing for hard to reach areas and containers were filled with a sterile water solution (then filtrated on 0.45 µm membrane and seeded). Microbiological identification was performed by mass spectrometry (MALDI-TOF-MS, Brucker) on each positive sample. RESULTS: Achromobacter spp was found in 10% of the 413 samples during the 8 months investigation period. The proportion of positive samples was stable among time but their location was unpredictable. The highest inoculum was finally found in the buckets used for biocleaning. DISCUSSION: Samples from cleaning buckets taken by dry swabbing were at first negative, but the use of a non-routinely used sampling method allowed to discover the reservoir of this persistent contamination. CONCLUSION: This investigation alerted us on the high microbiological risk associated with reusable plastic containers and the importance of a sampling method adapted to critical locations.

Phenotypic and genotypic within-host diversity of Pseudomonas aeruginosa urinary isolates.

This study aimed to assess phenotypic and molecular inter-patient and within-host diversity of Pseudomonas aeruginosa isolates responsible for urinary tract infection (UTI) or asymptomatic bacteriuria (AB). Clinical data of 120 consecutive P. aeruginosa UTI (n = 40) and AB (n = 80) were prospectively analyzed. Up to five P. aeruginosa isolates per sample were collected. Antimicrobial susceptibility testing (AST) was determined for all isolates (n = 591); a subset of 358 was characterized by multilocus sequence typing. 444 isolates (75%) were non-multidrug resistant (MDR), 113 (19%) were MDR, and 34 (6%) were extensively drug resistant. A genetically highly diverse population was observed (64 sequence types [STs]), without strict correlation between genotypes and clinical settings. 35 patients (28%; 12 UTIs and 23 ABs) presented distinct antimicrobial resistance (AMR) profiles within a given urine sample, significantly associated with previous carbapenem and fluroquinolones exposure; five of them also exhibited polyclonal UTI or AB (with isolates belonging to two STs). P. aeruginosa urinary isolates of these 120 patients were highly diverse, in terms of AMR as well as genetic background. Both within-host AMR and molecular diversity can complicate AST, treatment and control of P. aeruginosa UTI.

Persistence and Dissemination Capacities of a blaNDM-5-Harboring IncX-3 Plasmid in Escherichia coli Isolated from an Urban River in Montpellier, France.

To investigate the capacities of persistence and dissemination of blaNDM-5 within Escherichia coli and in aquatic environment, we characterized E. coli (sequence type 636) strains B26 and B28 isolated one month apart from the same urban river in Montpellier, France. The two isolates carried a pTsB26 plasmid, which sized 45,495 Kb, harbored blaNDM-5 gene and belonged to IncX-3 incompatibility group. pTsB26 was conjugative in vitro at high frequency, it was highly stable after 400 generations and it exerted no fitness cost on its host. blaNDM-5harboring plasmids are widely dispersed in E. coli all around the world, with no lineage specialization. The genomic comparison between B26 and B28 stated that the two isolates probably originated from the same clone, suggesting the persistence of pTsB26 in an E. coli host in aquatic environment.

From Copper Tolerance to Resistance in Pseudomonas aeruginosa towards Patho-Adaptation and Hospital Success.

The hospital environment constitutes a reservoir of opportunistic pathogens responsible for healthcare-associated infections (HCAI) such as Pseudomonas aeruginosa (Pa). Pa persistence within technological niches, the increasing emergence of epidemic high-risk clones in HCAI, the epidemiological link between plumbing strains and clinical strains, make it a major nosocomial pathogen. Therefore, understanding the mechanisms of Pa adaptation to hospital water systems would be useful in preventing HCAI. This review deciphers how copper resistance contributes to Pa adaptation and persistence in a hospital environment, especially within copper water systems, and ultimately to its success as a causative agent of HCAI. Numerous factors are involved in copper homeostasis in Pa, among which active efflux conferring copper tolerance, and copper-binding proteins regulating the copper compartmentalization between periplasm and cytoplasm. The functional harmony of copper homeostasis is regulated by several transcriptional regulators. The genomic island GI-7 appeared as especially responsible for the copper resistance in Pa. Mechanisms of copper and antibiotic cross-resistance and co-resistance are also identified, with potential co-regulation processes between them. Finally, copper resistance of Pa confers selective advantages in colonizing and persisting in hospital environments but also appears as an asset at the host/pathogen interface that helps in HCAI occurrence.

Monitoring Urban Beach Quality on a Summer Day: Determination of the Origin of Fecal Indicator Bacteria and Antimicrobial Resistance at Prophète Beach, Marseille (France).

A highly frequented beach in Marseille, France, was monitored on an hourly basis during a summer day in July 2018, to determine possible water and sand fecal pollution, in parallel with influx of beach users from 8 a.m. to 8 p.m. Fecal indicator bacteria were enumerated, together with four host-associated fecal molecular markers selected to discriminate human, dog, horse, or gull/seagull origins of the contamination. The antimicrobial resistance of bacteria in water and sand was evaluated by quantifying (i) the class 1, 2, and 3 integron integrase genes intI, and (ii) bla TEM, bla CTX-M, and bla SHV genes encoding endemic beta-lactamase enzymes. The number of beach users entering and leaving per hour during the observation period was manually counted. Photographs of the beach and the bathing area were taken every hour and used to count the number of persons in the water and on the sand, using a photo-interpretation method. The number of beach users increased from early morning to a peak by mid-afternoon, totaling more than 1,800, a very large number of users for such a small beach (less than 1 ha). An increase in fecal contamination in the water corresponded to the increase in beach attendance and number of bathers, with maximum numbers observed in the mid-afternoon. The human-specific fecal molecular marker HF183 indicated the contamination was of human origin. In the water, the load of Intl2 and 3 genes was lower than Intl1 but these genes were detected only during peak attendance and highest fecal contamination. The dynamics of the genes encoding B-lactamases involved in B-lactams resistance notably was linked to beach attendance and human fecal contamination. Fecal indicator bacteria, integron integrase genes intI, and genes encoding B-lactamases were detected in the sand. This study shows that bathers and beach users can be significant contributors to contamination of seawater and beach sand with bacteria of fecal origin and with bacteria carrying integron-integrase genes and beta lactamase encoding genes. High influx of users to beaches is a significant factor to be considered in order to reduce contamination and manage public health risk.

Peptoniphilus nemausensis sp. nov. A new Gram-positive anaerobic coccus isolated from human clinical samples, an emendated description of the genus Peptoniphilus and an evaluation of the taxonomic status of Peptoniphilus species with not validly published names.

A Gram-positive, anaerobic coccus isolated from a human surgical site infection was previously shown to belong to an unknown species of the genus Peptoniphilus initially proposed as 'Peptoniphilus nemausus' sp. nov., based on both 16S rRNA gene sequence identity of 97.9% with the most closely related species Peptoniphilus coxii and an individualized phylogenetic branching within the genus Peptoniphilus. A polyphasic characterization of the novel species is proposed herein. Whole genome sequence analysis showed an average nucleotide identity value of 84.75% and digital DNA-DNA hybridization value of 28.9% against P. coxii type strain. The strain displayed unique features among members of the genus Peptoniphilus, as it was able to hydrolyze aesculin, and produced acetate as the major metabolic end-product without associated production of butyrate. Growth was observed under microaerophilic conditions. From all these data, the isolate is confirmed as belonging to a new Peptoniphilus species, for which the name Peptoniphilus nemausensis sp. nov. is proposed. The type strain is 1804121828T (=LMG 31466T = CECT 9935T). A database survey using a highly polymorphic partial sequence of the 16S rRNA gene of P. nemausensis revealed P. nemausensis to be a particularly rare skin-associated species in humans. An emendated description of the Peptoniphilus genus is proposed based on a review of the characteristics of the 12 new species with validly published names since the genus description in 2001 and of P. nemausensis. Finally, the relationships between members of the genus Peptoniphilus were explored based on whole genome sequence analysis in order to clarify the taxonomic status of not yet validly published species showing that three pairs of species should be considered as synonyms: Peptoniphilus timonensis and 'Peptoniphilus phoceensis', Peptoniphilus lacydonensis and 'Peptoniphilus rhinitidis', Peptoniphilus tyrrelliae and Peptoniphilus senegalensis.

Improved detection of non-tuberculous mycobacteria in hospital water samples.

Non-tuberculous mycobacteria (NTM) are opportunistic pathogens commonly colonizing hospital water systems, and may be responsible for healthcare-associated infections (HAI). Investigation of HAI and outbreaks caused by NTM necessitates water analyses. However, NTM are slow-growing bacteria within the mesophilic community present in water, and are difficult to detect. Prior to culture on specific media, their recovery usually requires decontamination and concentration steps. We assessed the effectiveness of filtration as regards the recovery of 7 NTM species in hospital water samples. We also compared the use of cetylpyridinium chloride (CPC) at different concentrations and Sodium Hydroxide (NaOH) 4% in decontamination of water samples with mesophilic bacteria. Our laboratory protocol showed that membrane filtration was suitable for concentration and recovery of NTM from water. Sample decontamination with CPC was more NTM-preservative than NaOH. A combination of CPC at 0.005% and filtration allowed detection of NTM at low concentrations, ranging from 3 to 98 CFU/100mL according to the NTM species.

Achromobacter xylosoxidans and Stenotrophomonas maltophilia: Emerging Pathogens Well-Armed for Life in the Cystic Fibrosis Patients' Lung.

In patients with cystic fibrosis (CF), the lung is a remarkable ecological niche in which the microbiome is subjected to important selective pressures. An inexorable colonization by bacteria of both endogenous and environmental origin is observed in most patients, leading to a vicious cycle of infection-inflammation. In this context, long-term colonization together with competitive interactions among bacteria can lead to over-inflammation. While Pseudomonas aeruginosa and Staphylococcus aureus, the two pathogens most frequently identified in CF, have been largely studied for adaptation to the CF lung, in the last few years, there has been a growing interest in emerging pathogens of environmental origin, namely Achromobacter xylosoxidans and Stenotrophomonas maltophilia. The aim of this review is to gather all the current knowledge on the major pathophysiological traits, their supporting mechanisms, regulation and evolutionary modifications involved in colonization, virulence, and competitive interactions with other members of the lung microbiota for these emerging pathogens, with all these mechanisms being major drivers of persistence in the CF lung. Currently available research on A. xylosoxidans complex and S. maltophilia shows that these emerging pathogens share important pathophysiological features with well-known CF pathogens, making them important members of the complex bacterial community living in the CF lung.

High Occurrence of Bacterial Competition Among Clinically Documented Opportunistic Pathogens Including Achromobacter xylosoxidans in Cystic Fibrosis.

Cystic Fibrosis (CF) airways favor abnormal microbial development. Infections are considered as polymicrobial and competition can be observed between microorganisms. The current literature on bacterial competition in CF mostly consists of studies with limited numbers of strains, mainly focused on the major pathogens Pseudomonas aeruginosa (Pa) and Staphylococcus aureus (Sa) and does not give a comprehensive overview of the overall importance of bacterial interactions or the behavior of less often encountered emerging bacteria such as Achromobacter. In this context, we screened a panel of 39 strains from six CF patients, of either clinical or domestic environmental origin, distinguished according to genotype and belonging to four opportunistic pathogens, Pa (n = 15), Sa (n = 3), Stenotrophomonas maltophilia (Sm, n = 10) and Achromobacter xylosoxidans (Ax, n = 11). We investigated their capacity to compete in terms of growth, motility, and pigment production on agar media through 203 crossing experiments. Eleven strains selected via the initial screening results were further studied for competitive growth in liquid medium and biofilm formation. Competition was noted for 33% (67/203) of the pairs of strains with 85 modifications observed between monocultures and co-cultures, impacting growth (23.6%), motility (13.8%), and/or pigment production (6.1%). Under all conditions of the study (clinical, environmental strains; intra-, inter-patients; intra-, inter-species levels), competition was significantly more frequent among pairs of strains with at least one clinical strain. While Pa mainly outcompeted other species, in one patient with chronic colonization by Ax and sporadic colonization by Pa, we showed that some Ax inhibited the growth and pigmentation of Pa whereas biofilm formation was drastically reduced. Enlarging the panel of strains tested in competition assays gave new perspectives on the complex interactions taking place among the CF airway community. Indeed, the frequent occurrence of varied, strain-dependent interactions is revealed here. We report the first results of competition assays for Ax with the ability of certain strains to outcompete Pa. Our results are linked to the patient's colonization history and question the importance of bacterial competitiveness in the colonization pattern of CF airways.

The Hydric Environment: A Hub for Clinically Relevant Carbapenemase Encoding Genes.

Carbapenems are ß-lactams antimicrobials presenting a broad activity spectrum and are considered as last-resort antibiotic. Since the 2000s, carbapenemase producing Enterobacterales (CPE) have emerged and are been quickly globally spreading. The global dissemination of carbapenemase encoding genes (CEG) within clinical relevant bacteria is attributed in part to its location onto mobile genetic elements. During the last decade, carbapenemase producing bacteria have been isolated from non-human sources including the aquatic environment. Aquatic ecosystems are particularly impacted by anthropic activities, which conduce to a bidirectional exchange between aquatic environments and human beings and therefore the aquatic environment may constitute a hub for CPE and CEG. More recently, the isolation of autochtonous aquatic bacteria carrying acquired CEG have been reported and suggest that CEG exchange by horizontal gene transfer occurred between allochtonous and autochtonous bacteria. Hence, aquatic environment plays a central role in persistence, dissemination and emergence of CEG both within environmental ecosystem and human beings, and deserves to be studied with particular attention.

Tailoring the Physicochemical Properties of Antimicrobial Peptides onto a Thiazole-Based γ-Peptide Foldamer.

Antimicrobial peptides (AMPs) are amphipathic molecules displaying broad-spectrum bactericidal activity, providing opportunities to develop a new generation of antibiotics. However, their use is limited either by poor metabolic stability or by high hemolytic activity. We herein addressed the potential of thiazole-based γ-peptide oligomers named ATCs as tunable scaffolds to design polycationic AMP mimetics. Knowing the side chain distribution along the backbone, we rationally designed facially amphiphilic sequences with bactericidal effect in the micromolar range. Since no hemolytic activity was detected up to 100 µM, this class of compounds has shown the potential for therapeutic development.

Bacterial Microbiome in Wild-Caught Anopheles Mosquitoes in Western Thailand.

Among the complex microbial community living in the mosquito midgut, some bacteria (e.g., Enterobacter spp.) can deliver effector molecules with anti-Plasmodium effects suppressing the development of malaria parasites (Plasmodium falciparum) before the öokinete can penetrate the mosquito midgut epithelium. Despite knowledge of this phenomenon, only a few studies have defined the diversity of microbiota in wild-caught adult Anopheles species. The objective of this study was to analyze and compare the bacterial microbiota in different Anopheles species, including representatives of the primary malaria vectors in western Thailand. Wild female Anopheles species were sampled from malaria-endemic areas in Tak and Mae Hong Son provinces near the Thai-Myanmar border. Midgut/abdominal bacterial diversity was assessed by examining the 16S rRNA gene, V3 hypervariable region, using PCR-Temporal Temperature Gel Electrophoresis (PCR-TTGE) profiling and sequence analysis. A total of 24 bacterial genera were identified from eight Anopheles species. Five bacterial genera were newly reported in Anopheles mosquitoes (Ferrimonas, Megasphaera, Pectobacterium, Shimwellia, and Trabulsiella). Five genera, including Megasphaera, were detected exclusively in a single-malaria (Plasmodium vivax) infected Anopheles minimus and not observed in other non-infected mosquitoes. The use of PCR-TTGE provides the first characterization of the midgut bacterial microbiome present in wild adult Anopheles in Thailand. Evidence that microbiota might impact pathogen development (suppression) in Anopheles and thereby reduce the risk of pathogen transmission deserves more studies to describe the presence and better understand the biological role of bacteria in natural mosquito populations.

Comparative and Evolutionary Genomics of Isolates Provide Insight into the Pathoadaptation of Aeromonas.

Aeromonads are ubiquitous aquatic bacteria that cause opportunistic infections in humans, but their pathogenesis remains poorly understood. A pathogenomic approach was undertaken to provide insights into the emergence and evolution of pathogenic traits in aeromonads. The genomes of 64 Aeromonas strains representative of the whole genus were analyzed to study the distribution, phylogeny, and synteny of the flanking sequences of 13 virulence-associated genes. The reconstructed evolutionary histories varied markedly depending on the gene analyzed and ranged from vertical evolution, which followed the core genome evolution (alt and colAh), to complex evolution, involving gene loss by insertion sequence-driven gene disruption, horizontal gene transfer, and paraphyly with some virulence genes associated with a phylogroup (aer, ser, and type 3 secretion system components) or no phylogroup (type 3 secretion system effectors, Ast, ExoA, and RtxA toxins). The general pathogenomic overview of aeromonads showed great complexity with diverse evolution modes and gene organization and uneven distribution of virulence genes in the genus; the results provided insights into aeromonad pathoadaptation or the ability of members of this group to emerge as pathogens. Finally, these findings suggest that aeromonad virulence-associated genes should be examined at the population level and that studies performed on type or model strains at the species level cannot be generalized to the whole species.

Comparative Whole-Genome Phylogeny of Animal, Environmental, and Human Strains Confirms the Genogroup Organization and Diversity of the Stenotrophomonas maltophilia Complex.

The Stenotrophomonas maltophilia complex (Smc) comprises opportunistic environmental Gram-negative bacilli responsible for a variety of infections in both humans and animals. Beyond its large genetic diversity, its genetic organization in genogroups was recently confirmed through the whole-genome sequencing of human and environmental strains. As they are poorly represented in these analyses, we sequenced the whole genomes of 93 animal strains to determine their genetic background and characteristics. Combining these data with 81 newly sequenced human strains and the genomes available from RefSeq, we performed a genomic analysis that included 375 nonduplicated genomes with various origins (animal, 104; human, 226; environment, 30; unknown, 15). Phylogenetic analysis and clustering based on genome-wide average nucleotide identity confirmed and specified the genetic organization of Smc in at least 20 genogroups. Two new genogroups were identified, and two previously described groups were further divided into two subgroups each. Comparing the strains isolated from different host types and their genogroup affiliation, we observed a clear disequilibrium in certain groups. Surprisingly, some antimicrobial resistance genes, integrons, and/or clusters of attC sites lacking integron-integrase (CALIN) sequences targeting antimicrobial compounds extensively used in animals were mainly identified in animal strains. We also identified genes commonly found in animal strains coding for efflux systems. The result of a large whole-genome analysis performed by us supports the hypothesis of the putative contribution of animals as a reservoir of Stenotrophomonas maltophilia complex strains and/or resistance genes for strains in humans.IMPORTANCE Given its naturally large antimicrobial resistance profile, the Stenotrophomonas maltophilia complex (Smc) is a set of emerging pathogens of immunosuppressed and cystic fibrosis patients. As it is group of environmental microorganisms, this adaptation to humans is an opportunity to understand the genetic and metabolic selective mechanisms involved in this process. The previously reported genomic organization was incomplete, as data from animal strains were underrepresented. We added the missing piece of the puzzle with whole-genome sequencing of 93 strains of animal origin. Beyond describing the phylogenetic organization, we confirmed the genetic diversity of the Smc, which could not be estimated through routine phenotype- or matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF)-based laboratory tests. Animals strains seem to play a key role in the diversity of Smc and could act as a reservoir for mobile resistance genes. Some genogroups seem to be associated with particular hosts; the genetic support of this association and the role of the determinants/corresponding genes need to be explored.

Within-Host Microevolution of Pseudomonas aeruginosa Urinary Isolates: A Seven-Patient Longitudinal Genomic and Phenotypic Study.

BACKGROUND: Pseudomonas aeruginosa is responsible for up to 10% of healthcare associated urinary tract infections (UTI), which can be difficult to treat and can lead to bacterial persistence. While numerous whole genome sequencing (WGS) analyses have explored within-host genomic adaptation and microevolution of P. aeruginosa during cystic fibrosis (CF) infections, little is known about P. aeruginosa adaptation to the urinary tract. RESULTS: Whole genome sequencing was performed on 108 P. aeruginosa urinary isolates, representing up to five isolates collected from 2 to 5 successive urine samples from seven patients hospitalized in a French hospital over 48-488 days. Clone type single nucleotide polymorphisms (ctSNPs) analysis revealed that each patient was colonized by a single clone type (<6000 SNPs between two isolates) at a given time and over time. However, 0-126 SNPs/genome/year were detected over time. Furthermore, large genomic deletions (1-5% of the genome) were identified in late isolates from three patients. For 2 of them, a convergent deletion of 70 genes was observed. Genomic adaptation (SNPs and deletion) occurred preferentially in genes encoding transcriptional regulators, two-component systems, and carbon compound catabolism. This genomic adaptation was significantly associated with a reduced fitness, particularly in artificial urine medium, but no strict correlation was identified between genomic adaptation and biofilm formation. CONCLUSION: This study provides the first insight into P. aeruginosa within-host evolution in the urinary tract. It was driven by mutational mechanisms and genomic deletions and could lead to phenotypic changes in terms of fitness and biofilm production. Further metabolomic and phenotypic analyses are needed to describe in-depth genotype-phenotype associations in this complex and dynamic host-environment.

An outbreak of Pseudomonas aeruginosa urinary tract infections following outpatient flexible cystoscopy.

The investigation of an outbreak of Pseudomonas aeruginosa urinary tract infections after ambulatory cystoscopies identified a damaged cystoscope contaminated by P aeruginosa and acting as a relay object. This outbreak urges us not to trivialize urinary tract infections occurring after an elective cystoscopy. Patients should be advised to signal the occurrence of urologic symptoms after urologic exploration.

Minimal standards for the description of new genera and species of rhizobia and agrobacteria.

Herein the members of the Subcommittee on Taxonomy of Rhizobia and Agrobacteria of the International Committee on Systematics of Prokaryotes review recent developments in rhizobial and agrobacterial taxonomy and propose updated minimal standards for the description of new species (and genera) in these groups. The essential requirements (minimal standards) for description of a new species are (1) a genome sequence of at least the proposed type strain and (2) evidence for differentiation from other species based on genome sequence comparisons. It is also recommended that (3) genetic variation within the species is documented with sequence data from several clearly different strains and (4) phenotypic features are described, and their variation documented with data from a relevant set of representative strains. Furthermore, it is encouraged that information is provided on (5) nodulation or pathogenicity phenotypes, as appropriate, with relevant gene sequences. These guidelines supplement the current rules of general bacterial taxonomy, which require (6) a name that conforms to the International Code of Nomenclature of Prokaryotes, (7) validation of the name by publication either directly in the International Journal of Systematic and Evolutionary Microbiology or in a validation list when published elsewhere, and (8) deposition of the type strain in two international culture collections in separate countries.