Prospective multicentre study of rectal carriage of multidrug-resistant Enterobacteriaceae among health-care workers in Spain

OBJECTIVES

To investigate the rectal carriage of multidrug-resistant Enterobacteriaceae (colistin-resistant, extended-spectrum β-lactamase (ESBL) -producers and/or carbapenemase-producers) among health-care workers (HCWs) from six Spanish hospitals.

METHODS

Rectal swabs from 258 HCWs, employed in intensive care units, haematology wards and clinical microbiology laboratories from six hospitals in northern Spain were studied. They were cultured in selective media for Gram-negative resistant bacteria. Detection of antimicrobial resistance genes and multilocus sequence typing were performed by PCR and further sequencing. A questionnaire including data related to risk factors of colonization/infection by resistant bacteria (age, gender, chronic diseases, immunosuppressive therapies, invasive procedures or antimicrobial treatments) was given to each participant.

RESULTS

No carbapenemase-producing Enterobacteriaceae were recovered. However, 8/258 HCWs (3.1%) were positive for ESBL-producing isolates. This rate was not higher than the colonization rate previously reported in Spain for healthy people in the community. Five isolates showed high-level resistance to colistin (MICs ranging from 8 to 128 mg/L) but all of them were negative for the mcr genes tested. No statistically significant risk factors for gut colonization by ESBL-producing or colistin-resistant Enterobacteriaceae were identified among the HCWs participating in the study.

CONCLUSIONS

Our data suggest that working in hospitals does not represent a risk for rectal carriage of multidrug-resistant Enterobacteriaceae.

Long-term endemic situation caused by a linezolid- and meticillin-resistant clone of Staphylococcus epidermidis in a tertiary hospital

BACKGROUND

Linezolid (LZD)-resistant Staphylococcus epidermidis (LRSE) are increasing, and are mainly associated with outbreaks in hospital wards with high LZD consumption.

AIM

To investigate the frequency of LRSE in a tertiary hospital in the context of LZD use.

METHODS

The frequency of LRSE and the data on LZD usage [expressed as defined daily dose (DDD) per 100 patient-days], from 2011 to 2017, were analysed retrospectively. Selected LRSE were typed by pulsed-field gel electrophoresis (PFGE) and screened for transferable LZD resistance genes. Representative isolates were typed by multi-locus sequence typing, and ribosomal mechanisms of LZD resistance were investigated.

FINDINGS

In total, 435 LRSE were detected, with frequencies ranging from 13.56% to 32.93% in the intensive care unit (ICU) where LZD consumption was high (6.34-8.10 DDDs), and from 2.48 to 6.80% in the remaining wards where LZD use was considerably lower (0.63-2.49 DDDs). The first 44 LRSE isolates recovered (June 2013-June 2014) were closely related according to PFGE patterns, and all except one were resistant to meticillin due to mecA production. Selected isolates belonged to ST2, carried SCCmec III, and had the G2576T mutation in the V domain of each of the six copies of the 23S rRNA gene. Five of the 44 isolates (11.36%) were positive for the cfr gene.

CONCLUSION

An ST2 LZD- and meticillin-resistant clone was found in the ICU and also in wards with low consumption of LZD. This highlights the need to implement and maintain infection control measures as well as antimicrobial stewardship programmes in all hospital units in order to preserve the efficacy of LZD.

Evaluation of a real-time PCR assay for rectal screening of OXA-48-producing Enterobacteriaceae in a general intensive care unit of an endemic hospital

Carbapenemase-producing Enterobacteriaceae are increasing worldwide. Rectal screening for these bacteria can inform the management of infected and colonized patients, especially those admitted to intensive care units (ICUs). A laboratory developed, qualitative duplex real-time polymerase chain reaction assay for rapid detection of OXA-48-like and VIM producing Enterobacteriaceae, performed on rectal swabs, was designed and evaluated in an intensive care unit with endemic presence of OXA-48. During analytical assay validation, no cross-reactivity was observed and 100% sensitivity and specificity were obtained for both bla_OXA-48-like and bla_VIM in all spiked clinical samples. During the clinical part of the study, the global sensitivity and specificity of the real-time PCR assay for OXA-48 detection were 95.7% and 100% (P=0.1250), respectively, in comparison with culture; no VIM-producing Enterobacteriaceae were detected. Clinical features of patients in the ICU who were colonized or infected with OXA-48 producing Enterobacteriaceae, including outcome, were analyzed. Most had severe underlying conditions, and had risk factors for colonization with carbapenemase-producing Enterobacteriaceae before or during ICU admission, such as receiving previous antimicrobial therapy, prior healthcare exposure (including long-term care), chronic disease, immunosuppression and/or the presence of an intravascular catheter and/or mechanical ventilation device. The described real-time PCR assay is fast (~2-3hours, if DNA extraction is included), simple to perform and results are easy to interpret, features which make it applicable in the routine of clinical microbiology laboratories. Implementation in endemic hospitals could contribute to early detection of patients colonized by OXA-48 producing Enterobacteriaceae and prevention of their spread.

Pseudomonas syringae pv. phaseolicola isolated from weeds in bean crop fields

Pseudomonas syringae pv. phaseolicola, the causative agent of halo blight in common bean (Phaseolus vulgaris L.), was isolated from weeds associated with bean crops in Spain. The bacterium was recovered from Fumaria sp, Mercurialis annua, Solanum nigrum and Sonchus oleraceus. Ps. s. pv. phaseolicola had previously been isolated from leguminous plants and S. nigrum, but to our knowledge, this is the first time it was recovered from the other three species. The isolates were phenotypically and genetically characterized, and they were compared with isolates recovered from common beans. Five different genotypic profiles were detected by PmeI-PFGE, two of them being of new description. Weed isolates were as pathogenic on bean plants as bean isolates, but they were not pathogenic on S. nigrum. Regarding the survival of the pathogen in weeds, Ps. s. pv. phaseolicola was isolated from So. oleraceus 11 weeks after the end of the bean crop. These results strongly support the idea of weeds as a potential source of inoculum for halo blight in bean.

SIGNIFICANCE AND IMPACT OF THE STUDY

It has traditionally been considered that the main source of inoculum of Pseudomonas syringae pv. phaseolicola causing halo blight disease in Phaseolus vulgaris are the bean seeds, and that the host range of the bacterium is almost restricted to leguminous plants. In this study, the bacterium was recovered from four nonleguminous weed species collected in bean fields, and its permanence in weeds for at least 11 weeks after the harvesting of the beans was demonstrated. We have also proved that the strains isolated from weeds were pathogenic on bean plants. Accordingly, the host range of Ps. s. pv. phaseolicola could be broader than previously thought and weeds appear to be acting as a reservoir of the pathogen until the next crop.

High heterogeneity within methicillin-resistant Staphylococcus aureus ST398 isolates, defined by Cfr9I macrorestriction-pulsed-field gel electrophoresis profiles and spa and SCCmec types

During recent years, the animal-associated methicillin-resistant Staphylococcus aureus clone ST398 has extensively been studied. The DNA of these isolates turned out to be refractory to SmaI restriction, and consequently, SmaI is unsuitable for subtyping this clone by standard pulsed-field gel electrophoresis (PFGE). Very recently, ST398 DNA was shown to be digested by Cfr9I, a neoschizomer of SmaI. In the present study, we employed Cfr9I PFGE on 100 German and 5 Dutch ST398 isolates and compared their PFGE profiles, protein A gene variable repeat regions (spa types), and types of the staphylococcal cassette chromosome mec (SCCmec). The isolates (from healthy carrier pigs, clinical samples from pigs, dust from farms, milk, and meat) were assigned to 35 profiles, which were correlated to the SCCmec type. A dendrogram with the Cfr9I patterns assigned all profiles to two clusters. Cluster A grouped nearly all isolates with SCCmec type V, and cluster B comprised all SCCmec type IVa and V* (a type V variant first identified as III) carriers plus one isolate with SCCmec type V. Both clusters also grouped methicillin-susceptible S. aureus isolates. The association of the majority of isolates with SCCmec type V in one large cluster indicated the presence of a successful subclone within the clonal complex CC398 from pigs, which has diversified. In general, the combination of Cfr9I PFGE with spa and SCCmec typing demonstrated the heterogeneity of the series analyzed and can be further used for outbreak investigations and traceability studies of the MRSA ST398 emerging clone.

Clonal complexes and diversity of exotoxin gene profiles in methicillin-resistant and methicillin-susceptible Staphylococcus aureus isolates from patients in a Spanish hospital

Molecular epidemiology studies have allowed the identification of the methicillin (meticillin)-resistant (MRSA) and methicillin-susceptible (MSSA) clonal complexes (CCs) and clones of Staphylococcus aureus circulating in a Spanish hospital recently. Of 81 isolates tested, 32.1% were MRSA. Most of them carried staphylococcal cassette chromosome mec (SCCmec) IVc (88.5%) and belonged to CC5 (88.5%; multilocus sequence typing types ST125 [mainly associated with spa type t067], ST5, and ST228). A higher diversity was found among MSSA isolates (67.9%). Eighty percent shared the genetic background of major MRSA lineages (CC5 [38.2%; ST125 and ST5], CC30 [25.5%; ST30], CC45 [14.5%; ST45 and ST47], and CC8 [1.8%; ST8]), but CC12, CC15, CC51, and CC59 were also detected. Many exotoxin genes were present in each of the 81 isolates, independent of whether they were involved in sepsis (11 to 22) or other types of infections (13 to 21), and they appeared in 73 combinations. The relevant data are that (i) all isolates were positive for hemolysin and leukotoxin genes (98.8% for lukED and 25.9% for lukPV); (ii) all contained an enterotoxin gene cluster (egc with or without seu), frequently with one or more genes encoding classical enterotoxins; (iii) about half were positive for tst and 95% were positive for exfoliatin-encoding genes (eta, etb, and/or etd); and (iv) the four agr groups were detected, with agrII (55.6%) and agrIII (23.5%) being the most frequent. Taken together, results of the present study suggest a frequent acquisition and/or loss of exotoxin genes, which may be mediated by efficient intralineage transfer of mobile genetic elements and exotoxin genes therein and by eventual breakage of interlineage barriers.

Erwinia persicina Causing Chlorosis and Necrotic Spots in Leaves and Tendrils of Pisum sativum in Southeastern Spain

In 2003, symptoms of generalized chlorosis as well as necrosis in leaves and tendrils were observed in Pisum sativum L. cv Tirabeque grown in green fields in southeastern Spain (Granada Province), and by 2004, the disease affected approximately 12 ha. Bacteria isolated from symptomatic samples were gram negative, rod shaped, motile, oxidase negative, facultatively anaerobic, and fermentative, which coincided with the general characteristics of the family Enterobacteriaceae. The gene encoding the 16S rRNA from two isolates (LPPA 406 and LPPA 408) was sequenced after PCR amplification (1). The two sequences were identical (EMBL Accession No. AM294946 for LPPA 408) and showed 99% similarity with several strains of Erwinia persicina (including the type strain ATCC 35998, LPPA 373, LMG 11254, GS04, and LMG 2691). Additional biochemical tests were performed using E. persicina ATCC 49742 as a control. The three strains were negative for arginine dihydrolase activity, indol production, hydrolysis of casein, and hydrolysis of gelatin. In contrast, they were positive for assimilation of adonitol, l-lactate, mannitol, m-inositol, erythritol, sorbitol, sucrose, nitrate reduction, hydrolysis of aesculin, and growth in 5% NaCl at 36°C. Nevertheless, E. persicina ATTC 49742, but not the isolates from P. sativum, produced a pink pigment. The latter isolates were also tested for pathogenicity. Bacterial suspensions (10⁸ CFU/ml) were spray inoculated on 10 pea seedlings of cv. Tirabeque. Seedlings were covered with transparent plastic bags for 2 days and held in an incubation chamber at 22°C and 80% relative humidity with a 12-h photoperiod. Assays were conducted twice. Symptoms that developed were similar to those originally observed in the field, whereas symptoms did not occur on control seedlings sprayed with sterile distilled water. Bacteria sharing the characteristics of the inoculated isolates were recovered from symptomatic plants, hence fulfilling Koch's postulates. E. persicina has been isolated previously from bean in the United States (3) and southeastern Spain (1) and from tomato, banana, and cucumber in Japan (2). To our knowledge, this is the first report of the bacterium on P. sativum. References: (1) A. J. González et al. Plant Dis. 89:109, 2005. (2) M. V. Hao et al. Int. J. Syst. Bacteriol. 40:379, 1990. (3) M. L. Schuster et al. Fitopatol. Bras. 6:345, 1990.

Pseudomonas viridiflava Causing Necrotic Leaf Spots and Defoliation on Hebe spp. in Northern Spain

Hebe spp. is gaining interest as an ornamental crop in Spain. In October of 2003, plants of Hebe spp. (cv. Pink Paradise, Recurva, and Topiaria) grown in a nursery located in a northern region of Spain (Principality of Asturias) developed dark reddish spots in leaves. The spots (favored by high-humidity conditions) appeared initially in internal and lower leaves, but eventually progressed to the rest of the plant causing extensive defoliation. Samples from symptomatic leaves were processed for microbiological analysis. From the samples, Stemphylium sp. and fluorescent Pseudomonas sp., identified by conventional microbiological methods (1,3), were consistently recovered. Two isolates of the fungi and two of the bacterium (LPPA 365 and LPPA 366) were used in artificial inoculations of healthy plants (cv. New Zeeland) and all were performed in duplicate. A Stemphylium sp. was inoculated by irrigation of four seedlings with a suspension obtained by homogenization of the mycelium collected from two plates of potato dextrose agar in 100 ml of sterile distilled water. An equal number of seedlings were sprayed with a bacterial suspension (10⁸ CFU/ml) in yeast extract peptone glucose broth. The same methods were used to inoculate all four combinations of fungi and bacteria. The seedlings were maintained at 22°C during 1 month with a 16/8-h photo-period, but in inoculations with bacteria they were initially kept under transparent plastic bags for 48 h to facilitate entry. Seedlings treated with sterile distilled water were included as controls. Although a powdery film of sooty mold was observed in some of the leaves irrigated with one of the two Stemphylium sp. strains, rusty lesions and defoliation did not occur on plants inoculated with the fungal isolates alone. In contrast, symptoms comparable with those observed in the field developed in plants inoculated with the bacteria, either alone or together with the fungus. Reisolation of fluorescent Pseudomonas sp. from symptomatic leaves taken from inoculated plants confirmed pathogenicity on Hebe spp. The pathogenic isolates were tentatively identified as atypical Pseudomonas viridiflava on the basis of biochemical tests (2,3), and their identity was then confirmed by sequencing of the gene encoding the 16S rRNA (3; GenBank Accession Nos. AM182933 and AM182934 for LPPA 365 and 366, respectively). To our knowledge, this is the first report of P. viridiflava as the cause of necrotic leaf spots and defoliation in Hebe spp. References: (1) H. L. Barnett and B. B. Hunter. Illustrated Genera of Imperfect Fungi. 3rd ed. Burgess Publishing Co, Minneapolis, MN, 1972. (2) A. J. González et al. Appl. Environ. Microbiol. 69:2936, 2003. (3) R. A. Lelliott et al. J. Appl. Bacteriol. 29:470. 1966.

Bacterial Wilt of Beans (Phaseolus vulgaris) Caused by Curtobacterium flaccumfaciens in Southeastern Spain

Symptoms of bacterial wilt were observed on common beans (cv. Donna) in southeastern Spain. From samples collected in four different fields (coast of Granada), a bacterium was isolated with the following characteristics: gram positive, aerobic rods with yellow colonies, strictly oxidative, oxidase negative, galactose, sucrose, erythritol, mannitol, sorbitol and m-inositol were not used as a sole carbon source, and hydrolysis of casein was positive. These results coincide with what is expected for Curtobacterium flaccumfaciens pv flaccumfaciens (3). One isolate from each field was selected for pathogenicity tests using two different methods. Bacterial suspensions (approximately 10⁸ CFU/ml) were spray inoculated on bean seedlings of cv. Andecha (10 plants with three true leaves for each isolate). Beans were covered with transparent plastic bags for 2 days and held at 25°C and 80% relative humidity with a 12-h photoperiod. In addition, 10 healthy seeds of cv. Andecha were soaked in bacterial suspensions (approximately 10⁸ CFU/ml) for 1 h and incubated at 25°C (2). Seedlings sprayed with distilled sterile water and seeds soaked in water served as controls. With both methods of inoculation, assays were conducted twice. Results were recorded after 3 weeks. Symptoms that developed on plants after infection with the four isolates were similar to those observed in the field. They included golden yellow necrotic leaf lesions and wilting. Wilting was more pronounced in the field and when inoculation was performed by spraying seedlings rather than by soaking seeds. Control plants did not develop symptoms and grew bigger than the inoculated plants. Two pathogenic isolates were identified through sequencing of the 16S rRNA gene. The genes were amplified by polymerase chain reaction (1) and their nucleotide sequences (1,418 bp) proved to be identical (Accession No. AJ879110). Comparison of these sequences with databases showed that they were also identical to those of C. flaccumfaciens strains LMG 3645 and P 259/26 (Accession Nos. AJ312209 and AJ310414) and Curtobacterium sp. strains 2384 and 3426 (Accession Nos. AY688359 and AY688360). In Spain, the bean pathogen C. flaccumfaciens was first isolated from seeds during 2001 (4). However, to our knowledge, this is the first report of damage caused by this bacterium in the field. Bacterial wilt has been recorded, but often not substantiated, in several countries from North and South America, Africa, Asia, Oceania, and Europe. References: (1) U. Edwards et al. Nucleic Acid Res. 17:7843, 1989. (2) T. F. Hsieh et al. Plant Dis. 86:1275. 2002. (3) K. Komagata and K.-I. Suzuki. Pages 1313-1317 in: Bergey's Manual of Systematic Bacteriology. Vol. 2. Williams and Wilkins, Baltimore, MD, 1986. (4) J. L. Palomo et al. Page 154 in: XI Congreso de la Sociedad Española de Fitopatología, Almería, 2002.

Molecular epidemiology of emergent multidrug-resistant Salmonella enterica serotype Typhimurium strains carrying the virulence resistance plasmid pUO-StVR2

OBJECTIVES

To evaluate the incidence of a distinct multidrug-resistant (MDR) grouping of Salmonella serotype Typhimurium strains carrying the hybrid virulence resistance plasmid pUO-StVR2, and its possible evolution in the region where it was first detected [Principality of Asturias (PA), Spain].

METHODS

pUO-StVR2-containing isolates were tentatively identified by two genetic markers: the bla(OXA-30) gene and the class 1 integron InH:2000 bp/bla(OXA-30)-aadA1a. Positive isolates were examined for resistance profile (RP), plasmid content, virulence profile (VP) and genomic polymorphisms using macrorestriction-PFGE.

RESULTS

A total of 182 out of 248 Typhimurium clinical isolates recorded in the PA over 2001-02 were ampicillin-resistant and could be distributed into several MDR groupings. A MDR grouping carrying pUO-StVR2, with a defined RP (AMP/bla(OXA-30), CHL/catA1, [STR-SPT]/[strA/B,aadA1a], SUL/[sul1,sul2], TET/tet(B), qacEDelta1, merA, +/-TMP/dfrA12, and containing InH), was represented by 49 isolates. The VPs of these isolates (24 genes screened) differed from that of the type strain LT2 by the absence of the sopE1 and pef genes. Macrorestriction analysis established six combined XbaI/BlnI PFGE profiles, and supported a clonal relationship among most of the isolates.

CONCLUSIONS

During 2001-02, the isolates carrying pUO-StVR2 constituted the second most frequent S. Typhimurium MDR grouping recorded in the PA, preceded only by the pandemic pentaresistant DT104. Polymorphisms on the genomic DNA, different phage types, different plasmid profiles and the detection of trimethoprim resistance in one isolate encoded by an additional plasmid, were consistent with both intra-cluster evolution and horizontal transfer of the hybrid plasmid.

Genetic Basis of Antimicrobial Drug Resistance in Clinical Isolates ofSalmonella entericaSerotype Hadar from a Spanish Region

The genetic bases of antimicrobial drug resistance (R) of 79 Salmonella enterica serotype Hadar clinical isolates (recovered during 1995-2001 in a Spanish region) was investigated. The isolates showed a limited genomic variation, as demonstrated by PFGE analysis using XbaI (three profiles, S>or=0.77) and BlnI (seven profiles, S>or=0.49; with 95% of the isolates falling into two clusters, S>or=0.75). Thirteen R-profiles, ranging from susceptible to multidrug resistant, were recognized. All susceptible isolates (14%) were recovered before or during 1998, when multidrug resistance (MDR) was still uncommon (20% from 1995-1998). In later years, the percentage of MDR increased considerably (92% in 2001). Resistance to nalidixic acid, tetracycline, streptomycin and ampicillin-cefalotin, encoded by gyrA-Asp87/Asn, tet(A), strA/B, and bla (TEM) genes, respectively, were the most common, appearing together in 38% of the isolates. In all tetracycline- and streptomycin-resistant isolates, strA/B and tet(A) were chromosomally located, whereas bla (TEM) was plasmid-born. Five different bla (TEM) plasmids (pUO-ShR1 to pUO-ShR5, of about 9.4, 23, 30, 45, and 95 kb, respectively) were identified. pUO-ShR3 and pUO-ShR5 harbored additional R-genes: [dfrA1] and [acc(3)IV-strA/B], respectively. pUO-Sh2, pUO-Sh3, pUO-ShR4, and pUO-Sh5 were self-transferable, and the latter could also mobilize pUOShR1. The reported data constitute a useful background for further epidemiological studies of MDR in S. Hadar.

Cytotoxin and pyrogenic toxin superantigen gene profiles of Staphylococcus aureus associated with subclinical mastitis in dairy cows and relationships with macrorestriction genomic profiles

A set of 84 Staphylococcus aureus isolates collected from the milk of cows with subclinical mastitis in Asturias (a cattle region of Spain) and six control strains were tested for sequences of genes encoding hemolysins (hla, hlb, hld, hlg, and hlg-2), leukotoxins (lukPV, lukM, and lukED), toxic shock syndrome toxin (tst), and enterotoxins (sea to see, seg to ser, and seu) by conventional and multiplex PCR. It was found that 84, 83, 11, and 39 isolates carried some type of hl, luk, tst, or se gene, respectively, which were arranged in 14 exotoxin genotypes. All of the isolates were negative for lukPV, hlg, sea, sed, see, sej, sek, sep, seq, and ser. Two gene groupings could be related with pathogenicity islands-[lukED, seg, sei, sem, sen, seo +/- seu] with Sabeta-1 and [tst, sec, sel] with SaPIbov, present in 45 and 13.1% of the isolates, respectively-while 11.9% of them carried both islands. Only one contained seb (together with upsilonSabeta-1), and another contained seh (together with lukED). The isolates were also analyzed by pulsed-field gel electrophoresis performed with SmaI. Thirty-nine SmaI profiles (similarity coefficient [S] = 0.94 to 0.21) were differentiated; 12, 1, and 10 of these, respectively, were generated by isolates presumptively carrying Sabeta-1, SaPIbov, or both. Five SmaI profiles (S > or = 0.8) formed a cluster, which contained 20 and 10 isolates carrying one (upsilonSabeta-1) or both islands. These data show the high frequency of genes encoding cytotoxins and pyrogenic toxin superantigens, their relationship with pathogenicity islands, and their distribution among a diversity of genetic types of S. aureus related to subclinical mastitis.

Structural and functional characterization of the recR gene of Streptomyces

The recR gene product is necessary for homologous recombination and recombinational DNA repair in eubacteria. We report the isolation and sequencing of the recR gene from Streptomyces coelicolor. It encodes a protein of 198 amino acids, with a predicted molecular mass of 22 kDa. The deduced amino acid sequence shows significant similarity to that of RecR proteins from other bacteria, including Escherichia coli and Bacillus subtilis. Like these, Streptomyces RecR contains potential helix-hairpin-helix, zinc finger and ATP-binding motifs, as well as the Toprim domain which is present also in topoisomerases of Types IA and II, primases and nucleases of the OLD family. The recR genes of Escherichia coli and Bacillus subtilis are immediately preceded by a small ORF (orf12 and orf107, respectively). An equivalent ORF (orf1) is also found in Streptomyces. S. lividans recR mutants, obtained either by insertional inactivation of recR or by deletion of the gene together with the preceding ORF, displayed increased sensitivity to DNA-damaging agents (such as UV light and methylmethanesulfonate), when compared with the wild-type strain. Both mutants could be complemented by the wild-type orflrecR genes and also by the recR gene alone. Based on these results, orf1 appears to be dispensable for the repair function of Streptomyces RecR. In studies of heterologous complementation, the B. subtilis recR region (orf107recR) was found to complement the S. lividans deltaorflrecR mutant, but the equivalent region from E. coli (orf12recR) could not. However, in the absence of orf107, B. subtilis recR was unable to restore the wild-type phenotype to the Streptomyces deletion mutant.

Identification of a growth phase-dependent promoter in the rplJL operon of Streptomyces coelicolor A3(2)

A single promoter, rplJp (P(L10)), has been identified in the rplJL operon from Streptomyces coelicolor A3(2) by promoter probe and primer extension analyses. P(L10) is located upstream of the rplL gene and of the DNA encoding the mRNA leader region that contains the putative L10 (or L10.L12(4)) binding site for translational autogenous regulation. The potential start point for transcription was found 239 nucleotides upstream of the predicted translational start codon of rplJ. The promoter sequence shows -35 and -10 hexamers that resemble those of Streptomyces consensus Escherichia coli sigma(70)-like promoters and the rplJp from Streptomyces griseus. The amount of the transcript detected by primer extension analysis decreases during growth immediately after the transition phase, a slowdown in growth occurring during exponential phase associated with increases in ppGpp level. The temporal pattern of transcripts shows a clear correlation with the temporal pattern of L10 and L7/L12 protein synthesis reported in previous kinetic studies. This indicates that P(L10) is a growth phase-dependent promoter which may contribute, together with translational regulation, to the decrease in the synthesis of L10 and L7/L12 observed in liquid minimal medium. This is supported by results of promoter probe experiments. Although no significant promoter activity has been found by promoter probing in the rplJ and rplL intergenic region, an additional 5'-transcript end was detected by primer extension, probably as a result of mRNA processing event from a longer transcript. This may be required to maintain the 1:4 ratio observed for L10 and L7/L12 in the ribosomes.

Characterization of IS1389, a new member of the IS3 family of insertion sequences isolated from Xanthomonas campestris pv. amaranthicola

IS1389, a new insertion sequence belonging to the IS3 family, has been identified in Xanthomonas campestris pv. amaranthicola. The genome of this bacterium contains at least 11 copies of the element, whereas no hybridizing sequences were detected in other Xanthomonas species [X. axonopodis, X. fragaridae, X. phaseoli, and X. (Stenotrophomonas) maltophila]. Two nearly identical copies of the element (IS1389-A and IS1389-B) were characterized. According to analysis of sequence alignments and similar structural features, IS1389 belongs to the IS407 subgroup of the IS3 family, which duplicates 4 bp of target DNA upon insertion. IS1389-A was found in the proximity of the modification gene of the XamI restriction-modification system.

Establishment of a hybrid SalI-HgiDII type II restriction-modification system

In the SalI system, endonuclease activity can be only achieved in the presence of a functional modification gene. Thus, the DNA methyltransferase is involved in the control of restriction. By fusion of the restriction gene of the SalI system to the modification gene of the isospecific HgiDII system a hybrid type II restriction-modification system was created. Although in the hybrid situation the level of endonuclease activity was significantly lower than in the natural system, the HgiDII modification enzyme clearly supports SalI restriction. The mechanism by which the two isospecific methyltransferases control restriction is currently under study.

Isolation and nucleotide sequence of the gene encoding the XamI DNA methyltransferase of Xanthomonas campestris pv. amaranthicola

The gene (xamIM) encoding the DNA methyltransferase of the XamI restriction-modification system from Xanthomonas campestris pv. amaranithicola (M.XamI) has been cloned in Escherichia coli and its nucleotide sequence determined. The sequence predicts a protein of 527 amino acids that contains nine conserved motifs characteristic of DNA amino methyltransferases. In fact, M.XamI shows significant similarity with N6-adenine methyltransferases of the gamma group of amino methyltransferases, including M.SalI (from the isoschizomeric SalI restriction-modification system) and M.TaqI (the only N6-adenine methyltransferase for which a three-dimensional structure is available). M.XamI and M.SalI share two highly conserved regions within the C-terminal domain, one of which aligns with one of the DNA recognition loops proposed for M.TaqI. Analysis of the chromosomal DNA adjacent to xamIM led to the identification of an additional ORF (275 codons), downstream, in the same transcriptional orientation. Although some limited similarities between the SalI restriction enzyme and the product deduced from this ORF were found, the clone carrying xamIM did not express the expected endonuclease function.

Comparative analysis of expression of the SalI restriction-modification system in Escherichia coli and Streptomyces

The salIR and salIM genes encode the endonuclease and methyltransferase components of the SalI restriction-modification system from Streptomyces albus G. Expression of the salI genes in Escherichia coli was investigated and major differences with Streptomyces were found. In E. coli there is no detectable expression of the salI R gene due to inactivity of the sal-pR promoter region. In the natural host of the system this region directs transcription of the salI genes as a bicistronic message. In contrast to salIR, salIM is transcribed in the heterologous host from a promoter within the salI DNA. Since sal-pR is not active, the gene cannot be expressed as part of the salI operon. It is probably transcribed from sal-pM, a promoter internal to the operon which allows independent expression of the modification gene in Streptomyces. Replacement of sal-pR by the strong pLac promoter allows expression of salIR in E. coli and enhances expression of salIM. The resulting strain produces about 10 times more endonuclease than a Streptomyces clone containing the SalI system under the control of sal-pR.

Expression of the SalI restriction-modification system of Streptomyces albus G in Escherichia coli

The salIR and salIM genes of Streptomyces albus G encode the restriction endonuclease (ENase) and DNA methyltransferase (MTase) of the SalI restriction-modification (R-M) system. In S. albus G, the genes constitute an operon that is mainly transcribed from a promoter located upstream from salIR, the first gene of the operon. In addition, a second promoter, at the 3' end of salIR, allows independent transcription of the MTase gene. Expression of salIR and salIM in Escherichia coli was investigated. The ENase gene was not expressed in the heterologous host, probably due to inactivity of the main promoter of the salI operon. In contrast to salIR, salIM was functional in E. coli. Preliminary S1 nuclease mapping experiments suggest that the alternative promoter of the MTase gene can initiate transcription in the heterologous, as well as in the homologous host.

Organization and sequence of the SalI restriction-modification system

The organization and nucleotide (nt) sequences were determined for the genes encoding the SalI restriction and modification (R-M) system (recognition sequence 5'-GTCGAC-3') from Streptomyces albus G. The system comprises two genes, salIR, coding for the restriction endonuclease (ENase, R.SalI; probably 315 amino acids (aa), a predicted M(r) of 35,305; product, G'TCGAC) and salIM, coding for the methyltransferase (MTase, M.SalI; probably 587 aa, a predicted M(r) of 64,943; product, GTCGm6AC). The genes are adjacent, they have the same orientation, and they occur in the order salIR then salIM. R.SalI contains a putative magnesium-binding motif similar to those at the active sites of R.EcoRI and R.EcoRV, but otherwise it bears little aa sequence similarity to other ENases. M.SalI is a member of the m6A gamma class of MTases. In aa sequence it resembles M.AccI, another m6A gamma-MTase whose recognition sequence includes the SalI recognition sequence as a subset.

Structural changes induced by glycine on Streptomyces antibioticus

Germination and vegetative growth of Streptomyces antibioticus in liquid medium with different concentrations of glycine was examined. Both processes proved to be sensitive to the amino acid, being inhibited by 5 and 2.5% glycine, respectively. At concentrations of 5% or more, lysis of the vegetative mycelium occurred. Subinhibitory concentrations of glycine induced structural changes on germinating spores. These included an increase in the number of germ tubes produced by spore, in relation to the control. Moreover, soon after outgrowth the tubes bifurcate, giving rise to germinated spores with a characteristic aspect, and anomalous formation of cross-walls that appear both within the spores and in the newly formed germinative tubes, at or close to the region of outgrowth. The branching effect of glycine was also observed during vegetative growth of S. antibioticus.

Synthesis of ribosomal proteins during growth of Streptomyces coelicolor

Changes in expression of ribosomal protein genes during growth and stationary phase of Streptomyces coelicolor A3(2) in liquid medium were studied. Proteins being synthesized were pulse-labelled with [35S]-methionine, separated by two-dimensional polyacrylamide gel electrophoresis, and quantified using the BioImage computer software. Most of the ribosomal proteins were synthesized throughout the life cycle. Exceptions were two proteins whose synthesis drastically decreased at the approach of stationary phase. These two proteins were identified in purified ribosomes as homologues of Escherichia coli ribosomal proteins L10 and L7/L12, using antibodies raised against fusion proteins between these ribosomal proteins and Escherichia coli beta-galactosidase. The genes (rplJ and rplL) encoding the L10 and L7/L12 proteins were contained in a 1.2 kb BamHI fragment that was cloned and sequenced. The linkage and order of the genes coincide with other L10-L7/L12 operons. However, L11 and L1 genes were not present immediately upstream of the L10 gene, as is the case for E. coli and other bacteria. Instead, two open reading frames of unknown function were found immediately upstream of the L10 gene, in an adjacent 1.9 kb BamHI fragment.

Characterization of yeast DNA sequences capable of directing transcription in Streptomyces and Escherichia coli

Random genomic DNA fragments from Saccharomyces cerevisiae were tested for their ability to activate transcription of a promoterless aminoglycoside phosphotransferase-encoding gene in Streptomyces. About 10% of the insertions led to kanamycin resistance when selected at low concentration (5 micrograms ml-1). The nucleotide sequences of five insertions that allowed growth at different concentrations of the antibiotic were determined. Three of them contained -10 and -35 consensus sequences for the major class of eubacterial promoters. In two others, a -10 sequence could be identified, but a -35 element was absent at the appropriate distance. All of the five inserts were also transcriptionally active in Escherichia coli and therefore probably belong to the major class of eubacterial promoters. Three of the characterized insertions found to match known yeast sequences did not derive from promoter regions. We conclude that sequences that function as eubacterial promoters occur at random in the yeast genome.

Complex transcription of an operon encoding the SalI restriction-modification system of Streptomyces albus G

High-resolution S1 nuclease mapping of mRNA synthesised in vivo, in vitro run-off transcription with RNA polymerase from Streptomyces lividans and gene fusions were used to analyse the transcriptional organization of the SalI restriction-modification system of Streptomyces albus G. The salIR and salIM genes that encode the restriction endonuclease and its cognate methyltransferase constitute an operon which is mainly transcribed from sal-pR1, a promoter located immediately upstream of salIR, with two possible minor promoters further upstream. Another promoter, sal-pM, is within the 3' end of the salIR coding region, and allows expression of the modification gene in the absence of sal-pR1. The sal-pM promoter might be involved in the establishment of modification prior to restriction endonuclease activity. Sequences upstream of the apparent transcriptional start sites for sal-pR1 and sal-pM show similarity with the -10 region of typical vegetatively expressed eubacterial promoters, but appropriately centered -35 regions are absent.

Characterization of the temperate actinophage phi A7 DNA and its deletion derivatives

A restriction map of phi A7 DNA (46.7 kb) was established for nine endonucleases (BclI, ClaI, EcoRI, EcoRV, HpaI, PvuI, SacII, SphI and XbaI) which cut the phage genome up to 11 times. There was no sites for BamHI, BglII, HindIII, PstI, PvuII, SacI or SalI. phi A7 DNA, circularized through its cohesive ends, could integrate into the genome of several Streptomyces hosts, to form stable lysogens. Integration occurred by recombination between unique attachment sites on the phage (attP) and the host (attB) genomes. The attP site has been located on the phi A7 restriction map. Deletion mutants of phi A7 DNA were obtained by selecting for pyrophosphate- or EDTA-resistant clones. The deletions occurred either near the left-hand end of the conventional restriction map, or about 18 kb from the right-hand end, close to, but not affecting the unique SacII site. Together, the deletions defined at least 7.9 kb of DNA (16.9% of the phage genome) non-essential for plaque formation. phi A7 DNA was introduced into S. lividans protoplasts by liposome-assisted transfection. Since the phage does not adsorb to intact cells of this strain, and therefore does not form plaques, an overlay of S. antibioticus spores was used to detect the infectious progeny released by the protoplasts. Using this technique, phi A7 could be introduced into S. antibioticus with an efficiency of about 6 x 10(6) p.f.u. per micrograms DNA (equivalent to 3 x 10(-4) p.f.u. per DNA molecule).

Isolation and genetic structure of IS112, an insertion sequence responsible for the inactivation of the SalI restriction-modification system of Streptomyces albus G

IS112 is a transposable element identified in Streptomyces albus G by its frequent mutagenic insertion into the genes for the SalI restriction-modification system. IS112 is present in several copies in the genome of S. albus G. Homologous sequences were detected in other Streptomyces strains. Sequence analysis revealed that IS112 has a length of 883 bp with a GC content of 67.4%. The copy that was isolated contained imperfect inverted repeats (16/20 match) at its ends and was flanked by a 2 bp duplication at the target site, which was located within the gene (salIR) for the SalI endonuclease. A long open reading frame (ORF) encoding a putative polypeptide of 256-253 amino acids spans almost the entire sequence. Significant homology was detected between this polypeptide and that corresponding to ORFB of IS493, an insertion sequence recently isolated from Streptomyces lividans 66.

The SalI (SalGI) restriction-modification system of Streptomyces albus G

The salIR and salM genes of Streptomyces albus G specify the SalGI (SalI) restriction enzyme and its cognate methyltransferase, respectively. These enzymes are responsible for restriction and modification of bacteriophages. Some phages carry genes that interfere with SalI-specific modification. The sal genes have been cloned in a Streptomyces host-vector system. Use of the cloned DNA as a hybridization probe reveals that sal mutants frequently arise from transposition of a DNA segment of approx. 1 kb into the sal genes. Some, but not all, other bacteria that produce SalGI isoschizomers contain nucleotide sequences that hybridize with sal DNA.

New derivatives of the Streptomyces temperate phage phi C31 useful for the cloning and functional analysis of Streptomyces DNA

The thiostrepton resistance gene (tsr) of Streptomyces azureus, and a synthetic oligonucleotide adapter sequence, were introduced into the DNA of attP-site-deleted phage phi C31-based cloning vectors. The DNA of two of the new derivatives, KC515 and KC516, contains single sites for the enzymes BamHI, BglII, PstI, PvuII, SstI (two sites close together) and XhoI, available for the insertion of DNA of up to 4 kb. The two vectors also contain a cloned, promoterless viomycin phosphotransferase gene (vph) from Streptomyces vinaceus. When an internal segment of the Streptomyces coelicolor glycerol (gyl) operon was inserted at the appropriate position and in the correct orientation next to vph, it could bring about in vivo recombination leading to fusion of vph of the chromosomally located gyl operon, resulting in glycerol-regulated expression of viomycin resistance. Two other new phi C31 derivatives, KC505 and KC518, are PstI and BamHI replacement vectors, respectively, for 2-8-kb DNA fragments, and allow simple screening for the presence of inserted DNA.

Small DNA-free liposomes stimulate transfection of streptomyces protoplasts

DNA of the bacteriophage phi C31 was rendered DNase resistant by entrapment in liposomes. Liposome-entrapped phi C31 DNA transfected Streptomyces protoplasts in the presence of 50% polyethylene glycol (PEG), providing a potential alternative route to conventional PEG-mediated transfection of protoplasts. However, probably partially because of low entrapment of DNA, this system did not result in an effective increase in transfection efficiency over the conventional transfection procedure. A more effective use of liposomes for stimulating transfection was provided by the discovery that supernatants obtained during the washing of DNA-free liposome preparations stimulated PEG-mediated transfection of protoplasts. This effect appeared to involve small (0.1- to 0.3-micrometer diameter) poorly sedimented liposomes. It was most effective (more than 100-fold stimulation) with positively charged liposome supernatants and high (about 50% [wt/vol]) PEG concentrations. Stimulation of transfection was also observed with cloning ligation mixtures containing phi C31 DNA as the vector. Transformation by plasmids (but not by chromosomal DNA fragments) was also significantly more efficient in these conditions than in conventional protoplast transformation.

Protoplast-like structures formation from two species of Enterobacteriaceae by fosfomycin treatment

A procedure for protoplasts formation from Escherichia coli and Serratia marcescens by treatment with fosfomycin alone is described. This method gives high and low yields of stable protoplasts from E. coli and S. marcescens respectively. In the last case numerous spheroplasts were obtained. Electron micrographs of intact cells, protoplasts and spheroplasts are shown.