Small Non-conjugative Plasmid Research Articles

A Streamlined Approach for Fluorescence Labelling of Low-Copy-Number Plasmids for Determination of Conjugation Frequency by Flow Cytometry.

Bacterial conjugation plays a major role in the dissemination of antibiotic resistance and virulence traits through horizontal transfer of plasmids. Robust measurement of conjugation frequency of plasmids between bacterial strains and species is therefore important for understanding the transfer dynamics and epidemiology of conjugative plasmids. In this study, we present a streamlined experimental approach for fluorescence labelling of low-copy-number conjugative plasmids that allows plasmid transfer frequency during filter mating to be measured by flow cytometry. A blue fluorescent protein gene is inserted into a conjugative plasmid of interest using a simple homologous recombineering procedure. A small non-conjugative plasmid, which carries a red fluorescent protein gene with a toxin-antitoxin system that functions as a plasmid stability module, is used to label the recipient bacterial strain. This offers the dual advantage of circumventing chromosomal modifications of recipient strains and ensuring that the red fluorescent protein gene-bearing plasmid can be stably maintained in recipient cells in an antibiotic-free environment during conjugation. A strong constitutive promoter allows the two fluorescent protein genes to be strongly and constitutively expressed from the plasmids, thus allowing flow cytometers to clearly distinguish between donor, recipient, and transconjugant populations in a conjugation mix for monitoring conjugation frequencies more precisely over time.

Methicillin-Resistant Staphylococcus Aureus in Community Settings: Spread of Drug Resistance and Uncontrollable Infections

Abstract Methicillin-resistant Staphylococcus aureus (MRSA) is a major multidrug-resistant bacterial pathogen. The evolution of MRSA is dynamic posing an ongoing threat to humans. The evolution of MRSA includes horizontal gene transfer, which is mediated by mobile genetic elements, plasmids, and bacteriophages, and also mutations. In this review, we clarify the recent trends in MRSA from the perspectives of drug-resistance transfer and uncontrollable infections, particularly those occurring in community settings. We first address the role of MRSA as a disseminator of multidrug resistance. We have studied the cell-to-cell transfer of drug resistance, in which transfer frequencies range from 10-3 to 10-8. The mechanisms of drug-resistance transfers include the self-transmission of large plasmids, the mobilization of small nonconjugative plasmids, the generalized transduction of phages, and the transfer of transposons with circular intermediates. We then discuss uncontrollable infections. Although several anti-MRSA agents have been developed, uncontrollable cases of MRSA infections are still reported. Examples include a case of uncontrollable sepsis arising from a community-associated MRSA (CA-MRSA) with the ST8/SCCmecIVl genotype, and a relapsing severe invasive infection of ST30/SCCmecIVc CA-MRSA in a student athlete. Some of these cases may be attributable to unique adhesins, superantigens, or cytolytic activities. The delayed diagnosis of highly adhesive and toxic infections in community settings may result in CA-MRSA diseases that are difficult to treat. Repeated relapse, persistent bacteremia, and infections of small-colony variants may occur. To treat MRSA infections in community settings, these unique features of MRSA must be considered to ensure that diagnostic delay is avoided.

Specialization of small non-conjugative plasmids in Escherichia coli according to their family types.

We undertook a comprehensive comparative analysis of a collection of 30 small (<25 kb) non-conjugative Escherichia coli plasmids previously classified by the gene sharing approach into 10 families, as well as plasmids found in the National Center for Biotechnology Information (NCBI) nucleotide database sharing similar genomic sequences. In total, 302 mobilizable (belonging to 2 MOBrep and 5 MOBRNA families) and 106 non-transferable/relaxase-negative (belonging to three ReLRNA families) plasmids were explored. The most striking feature was the specialization of the plasmid family types that was not related to their transmission mode and replication system. We observed a range of host strain specificity, from narrow E. coli host specificity to broad host range specificity, including a wide spectrum of Enterobacteriaceae . We found a wide variety of toxin/antitoxin systems and colicin operons in the plasmids, whose numbers and types varied according to the plasmid family type. The plasmids carried genes conferring resistance spanning almost all of the antibiotic classes, from those to which resistance developed early, such as sulphonamides, to those for which resistance has only developed recently, such as colistin. However, the prevalence of the resistance genes varied greatly according to the family type, ranging from 0 to 100 %. The evolutionary history of the plasmids based on the family type core genes showed variability within family nucleotide divergences in the range of E. coli chromosomal housekeeping genes, indicating long-term co-evolution between plasmids and host strains. In rare cases, a low evolutionary divergence suggested the massive spread of an epidemic plasmid. Overall, the importance of these small non-conjugative plasmids in bacterial adaptation varied greatly according to the type of family they belonged to, with each plasmid family having specific hosts and genetic traits.

Emergence of Plasmid-Borne dfrA14 Trimethoprim Resistance Gene in Shigella sonnei.

The most common mechanism of trimethoprim (TMP)-resistance is the acquisition of dihydrofolate reductase enzyme resistant to this drug. Previous molecular characterization of TMP-genes resistance in Chilean isolates of Shigella sonnei searching for dfrA1 and dfrA8, showed solely the presence of dfrA8 (formerly dhfrIIIc). However, these genetic markers were absent in S. sonnei strains further isolated during an outbreak in 2009. To identify the TMP-resistance gene in these strains, a genomic DNA library from a TMP-resistant (TMPR) S. sonnei representative strain for the outbreak was used to clone, select and identify a TMP-resistance marker. The TMPR clone was sequenced by primer walking, identifying the presence of the dfrA14 gene in the sul2-strA'-dfrA14-‘strA-strB gene arrangement, harbored in a native 6779-bp plasmid. The same plasmid was isolated by transforming with a ~4.2 MDa plasmid extracted from several TMPR S. sonnei strains into Escherichia coli. This plasmid, named pABC-3, was present only in dfrA14-positive strains and was homologous to a previously described pCERC-1, but different due to the absence of an 11-bp repetitive unit. The distribution of dfrA1, dfrA8, and dfrA14 TMP-resistance genes was determined in 126 TMPR S. sonnei isolates. Most of the strains (96%) carried only one of the three TMP-resistance genes assessed. Thus, all strains obtained during the 2009-outbreak harbored only dfrA14, whereas, dfrA8 was the most abundant gene marker before outbreak and, after the outbreak dfrA1 seems have appeared in circulating strains. According to PFGE, dfrA14-positive strains were clustered in a genetically related group including some dfrA1- and dfrA8-positive strains; meanwhile other genetic group included most of the dfrA8-positive strains. This distribution also correlated with the isolation period, showing a dynamics of trimethoprim genetic markers prevalent in Chilean S. sonnei strains. To our knowledge, dfrA14 gene associated to a small non-conjugative plasmid was detected for the first time in Shigella. Apparently, the strain causing the outbreak must have been introduced, changing drastically the genetic distribution of trimethoprim resistance in Chilean S. sonnei strains.

Prevalence and Plasmid Characterization of theqnrDDeterminant inEnterobacteriaceaeIsolated from Animals, Retail Meat Products, and Humans

qnrD, unlike other qnr genes, is mainly located on small nonconjugative plasmids. We investigated the presence of qnrD among 1,373 Enterobacteriaceae isolates in China. Twelve qnrD-positive strains were detected, and all were nonsusceptible to fluoroquinolones. The complete sequence of plasmids showed that the qnrD determinants were located on two plasmids with a respective size of ~4.2 and 2.7 k-bp. Interestingly, the identification of qnrD in this study revealed the highest prevalence of Proteeae among Enterobacteriaceae identified.

Description of a 2,683-Base-Pair Plasmid Containing qnrD in Two Providencia rettgeri Isolates

qnr genes are plasmid-mediated quinolone resistance genes mainly harbored on large conjugative multiresistant plasmids. The qnrD gene was recently observed in Salmonella enterica on a small nonconjugative plasmid (p2007057). We describe two strains of Providencia rettgeri harboring qnrD on nonconjugative plasmids. The plasmids were 99% identical, with 2,683 bp and four open reading frames, including qnrD, but exhibited only 53% identity with the plasmid found in S. enterica.

A phenomenon of plasmid retrotransfer in conjugation of Bacillus subtilis

A conjugal retrotransfer-retromobilization of a small nonconjugative plasmid pUB110 was established in Bacillus subtilis. This process involves a large conjugative plasmid p19.

First identification of an SHV-12 extended-spectrum beta-lactamase in Klebsiella pneumoniae isolated in Italy.

A clinical isolate of Klebsiella pneumoniae highly resistant to third- and fourth-generation cephalosporins, cephamycins and aminoglycosides, was isolated in 1991 from urine. Analysis of a crude extract showed the presence of three beta-lactamases with isoelectric points of 6.6, 7.5 and 8.2. The enzyme with pI 8.2 was transferred by conjugation into Escherichia coli K-12 J53 and was responsible for the resistance to third-generation cephalosporins and monobactams, but not to other antibiotics. Kinetic studies of partially purified beta-lactamase from the transconjugant strain confirmed that the enzyme was able to hydrolyse ceftazidime, cefotaxime and aztreonam but not cephamycins. Analysis of the transconjugant showed the presence of two small non-conjugative plasmids of 14 and 6 kb. A polymerase chain reaction was performed using primers specific for the bla(SHV) gene and a fragment of the expected size (about 961 bp) was obtained with both the K. pneumoniae clinical isolate and the transconjugant. Nucleotide sequence analysis of the fragment showed that it encoded the enzyme SHV-12, derived from SHV-5 (with Gln-35 to Leu). This is the first report of an SHV-12-like enzyme isolated in Italy.

Intergeneric natural plasmid transformation between E. coli and a marine Vibrio species.

Natural transformation is the mechanism of procaryotic gene transfer that involves the uptake and expression of genetic information encoded in extracellular DNA. This process has been regarded as a mechanism to transfer genes (primarily chromosomal markers) between closely related strains or species. Here we demonstrate the cell-contact-dependent transfer of a non-conjugative plasmid from a laboratory E. coli strain to a marine Vibrio species, the first report of intergeneric natural plasmid transformation involving a marine bacterium. The nucleic acid synthesis inhibitors nalidixic acid and rifampicin inhibited the ability of the E. coli to function as a donor. However, dead cells also served as efficient donors. There was an obligate requirement for cell contact. No transfer occurred in the presence of DNase I, when donors and recipients were separated by a 0.2-micron filter, or when spent medium alone was used as a source of transforming DNA. These results indicate that contact-mediated intergeneric plasmid exchange can occur in the absence of detectable viable donor cells and that small non-conjugative plasmids can be spread through heterogeneous microbial communities by a process previously not recognized, natural plasmid transformation. These findings are important in the assessment of genetic risk to the environment, particularly from wastewater treatment systems and the use of genetically engineered organisms in the environment.

Conjugative plasmid transfer from Escherichia coli to Clostridium acetobutylicum

The conjugation mechanism of IncP plasmids may be employed to mobilize small non-conjugative plasmids from Escherichia coli to a wide range of different organisms. This strategy has been adapted for use with the Gram-positive anaerobe, Clostridium acetobutylicum NCIB 8052. Several shuttle vectors containing replicons from pAM beta 1 (Enterococcus faecalis), pCB101 (Clostridium butyricum) or pWV01 (Streptococcus cremoris), together with the cis-acting oriT region of RK2, have been constructed, and transferred to and established in this organism. One of the vectors apparently contains a hot spot for insertion of IS1. Conjugative mobilization of plasmids from E. coli will provide a useful alternative to electroporation for effecting gene transfer to this industrially important anaerobe.

Conjugal transfer of a small plasmid fromBacillus subtilistoClostridium acetobutylicumby cointegrate formation with plasmid pAMβ1

Plasmid pAMβ1 is transferred at low efficiency in filter matings between Bacillus subtilis and Clostridium acetobutylicum. We have constructed a small non-conjugative plasmid, pOD1 (7.2 kbp; ApR, CmR, EmR) that becomes established in pAMβ1-containing strains of B. subtilis in the form of a cointegrate (pAMβ1::pOD1). The cointegrate plasmid is transferred to, and maintained in C. acetobutylicum, with an efficiency similar to that of pAMβ1. We have also constructed derivatives of plasmid pOD1, with single sites for several commonly used restriction endonucleases. They can be used to transfer foreign genes to C. acetobutylicum via B. subtilis.

Heterogeneity of tetracycline resistance determinants in Streptococcus.

We found that naturally occurring tetracycline resistance in streptococci is encoded by more than one genetic determinant. Two of these distinct determinants were cloned, and the regions that are necessary and sufficient for expression of tetracycline resistance were defined by deletion analysis. These cloned determinants were further characterized by DNA-DNA hybridization experiments which also identified a third genetically unrelated tetracycline resistance determinant. Some of these genetic differences appear to represent mechanistic differences. The tetL determinant was associated with small nonconjugative plasmids and mediated resistance to tetracycline. The tetM determinant was most often "nonplasmid" associated and mediated resistance to minocycline as well as tetracycline. The tetN determinant was represented on a large conjugative plasmid and was genetically distinct from tetL and tetM, although phenotypically it resembled tetM.

The maintenance of Plasmid-containing organisms in populations of Escherichia coli.

Populations of Escherichia coli containing a small non-conjugative plasmid were grown in carbon-limited continuous culture. For all plasmids tested the presence of the plasmid lowered the growth rate of the host bacterium, and the proportion of plasmid-containing organisms in the total population declined initially. However, periodically, adaptive changes occurred in plasmid-containing organisms which increased their growth rate. This resulted in oscillations in the proportion of plasmid-containing organisms, and the delayed loss of the plasmid from the population.

Tn2301, a transposon construct carrying the entire transfer region of the F plasmid.

The largest R . BamHI fragment of the plasmid F, which carries the entire F conjugation system, has been cloned into the single R . BamHI site of the ampicillin (Ap) resistance transposon TN1. pDS1106 (ColE1 mob::Tn1) was the vector plasmid, and the resultant conjugative plasmid, pED830, was characterized both genetically and by restriction enzyme analysis. The transposon construct, denoted Tn2301, was transposable at frequencies similar to Tn1 to small nonconjugative plasmids or to the Escherichia coli host chromosome. In the former case, Apr conjugative plasmids were obtained, whereas in the latter case, Hfr strains resulted. Representative Hfr strains were characterized by quantitative and interrupted mating experiments. Extension of this technique for Hfvr formation should aid chromosome mapping both in E. coli and in other bacterial genera.

Trans-complementable copy-number mutants of plasmid ColE1.

Plasmid ColE1, like many other small non-conjugative plasmids, is present in multiple copies (about 15 per chromsome equivalent) in Escherichia coli cells. Because of their high copy number, the replication of such plasmids has been described as 'relaxed', even though there is good evidence that it is strictly controlled: ColE1 derivatives have characteristic but different copy numbers and ColE1 copy-number mutants have been characterised. No plasmid-specified protein is essential for the replication of ColE1 and related plasmids, as extensive replication can occur in chloramphenicol-treated cells, in plasmid-free chloramphenicol-treated cells transfected with a hybrid ColE1/phage replicon and in vitro in extracts derived from plasmid-free cells. Nevertheless, it is possible that a plasmid-specified protein is involved in ColE1 replication control in viable cells. Here we show that deletion of a given non-essential region from ColE1-like plasmids results in a raised copy number. Such plasmids are stably maintained and have their copy number returned to normal when a complementing plasmid is present in the same cell, indicating that a plasmid-specified diffusible gene product regulates the plasmid content of ColE1-containing cells. Deletion of the equivalent region from the cloning vector pBR322 gives a derivative which has a raised copy number and which has also lost its origin for conjugal transfer; unlike pBR322, it cannot be mobilised.

Transposition of a plasmid deoxyribonucleic acid sequence that mediates ampicillin resistance: identity of laboratory-constructed plasmids and clinical isolates.

The structural gene for ampicillin resistance resides upon a 3.2 X 10(6)-dalton sequence of deoxyribonucleic acid, TnA that can be transposed from replicon to replicon in laboratory experiments. TnA was transposed from a large conjugative plasmid to a small nonconjugative plasmid, RSF1010. Several RSF1010::TnA plasmids isolated in these laboratory experiments have been shown to be identical to plasmids found in clinical isolates. These data provide direct support to the theory that transposition of drug resistance genes play a key role in the evolution of R plasmids.

Involvement of multiple translocating DNA segments and recombinational hotspots in the structural evolution of bacterial plasmids

Previous studies from our laboratory (Kopecko & Cohen, 1975) have shown that two different antibiotic resistance-coding segments of the pSC50 plasmid are capable of recA-independent translocation to the small non-conjugative plasmid pSC101. Both of the transposable units are structurally defined DNA segments containing 130 to 145-nucleotide long inverted repeat DNA sequences at each end. The present electron microscope heteroduplex investigations indicate that one of the transposable genetic elements (TnA) is contained within the length of the other (TnS) on both the parental and recombinant plasmids. The movement of TnA and TnS among plasmids as discrete structural units implies that specific sites at their termini are involved in the translocation process. Although multiple insertion sites for these elements exist on the pSC101 plasmid, the non-random distribution of recipient loci suggests that insertion is site-specific and that it may involve recognition of a frequently recurring nucleotide sequence. In addition to their role in the intergenomic transfer of DNA sequences, the termini of transposable genetic elements can serve as hotspots for other types of recombinational events: in the R1-19 plasmid, a Km-Nm resistance segment that separates the right terminus of TnS from an IS1 (insertion sequence) element can be deleted spontaneously, bringing the termini of TnS and IS1 in juxtaposition. Recombination of another DNA segment containing inverted repeats and a gene for Km-Nm resistance occurs at the left terminus of TnS. Our findings suggest that evolutionary divergence of several groups of related cointegrated antibiotic resistance plasmids has occurred segmentally by a series of site specific recombinational events involving the translocation, insertion, and/or deletion of structurally defined segments of DNA.