Origin of the TEM-beta-lactamase gene found on plasmids

First Report of the Colistin Resistance Gene mcr-10.1 Carried by IncpA1763-KPC Plasmid pSL12517-mcr10.1 in Enterobacter cloacae in Sierra Leone

Mobile colistin resistance (mcr) gene mcr-10.1 has been distributed widely since it was initially identified in 2020. The aim of this study was to report the first mcr-10.1 in Africa and the first mcr in Sierra Leone; furthermore, we presented diverse modular structures of mcr-10.1 loci. Here, the complete sequence of one mcr-10.1-carrying plasmid in one clinical Enterobacter cloacae isolate from Sierra Leone was determined. Detailed genetic dissection and comparison were applied to this plasmid, together with a homologous plasmid carrying mcr-10.1 from GenBank. Moreover, a genetic comparison of 19 mcr-10.1 loci was performed. In this study, mcr-10.1 was carried by an Inc_pA1763-KPC plasmid from one Enterobacter cloacae isolate. A total of 19 mcr-10.1 loci displayed diversification in modular structures through complex transposition and homologous recombination. A site-specific tyrosine recombinase XerC was located upstream of mcr-10.1, and at least one insertion sequence element was inserted adjacent to a conserved xerC-mcr-10.1-orf336-orf177 region. Integration of mcr-10.1 into a different gene context and carried by various Inc plasmids contributed to the wide distribution of mcr-10.1 and enhanced the ability of bacteria to survive under colistin selection pressure.

IMPORTANCE Colistin is used as one of the last available choices of antibiotics for patients infected by carbapenem-resistant bacterial strains, but the unrestricted use of colistin aggravated the acquisition and dissemination of mobile colistin resistance (mcr) genes. So far, 10 mcr genes have been reported in four continents around the world. This study presented one mcr-10.1-carrying Enterobacter cloacae isolate from Sierra Leone. The mcr-10.1 gene was identified on an Inc_pA1763-KPC plasmid. According to the results of genetic comparison of 19 mcr-10.1 loci, the mcr-10.1 gene was found to be located in a conserved xerC-mcr-10.1-orf336-orf177 region, and at least one insertion sequence element was inserted adjacent to this region. To our knowledge, this is the first report of identifying the mcr-10.1 gene in Africa and the mcr gene in Sierra Leone.

Genetic Characterization of Four Groups of Chromosome-Borne Accessory Genetic Elements Carrying Drug Resistance Genes in Providencia

Purpose

The aim of this study was to gain a deeper genomics and bioinformatics understanding of diversification of accessory genetic elements (AGEs) in Providencia.

Methods

Herein, the complete genome sequences of five Providencia isolates from China were determined, and seven AGEs were identified from the chromosomes. Detailed genetic dissection and sequence comparison were applied to these seven AGEs, together with additional 10 chromosomal ones from GenBank (nine of them came from Providencia).

Results

These 17 AGEs were divided into four groups: Tn6512 and its six derivatives, Tn6872 and its two derivatives, Tn6875 and its one derivative, and Tn7 and its four derivatives. These AGEs display high-level diversification in modular structures that had complex mosaic natures, and particularly different multidrug resistance (MDR) regions were presented in these AGEs. At least 52 drug resistance genes, involved in resistance to 15 different categories of antimicrobials and heavy metal, were found in 15 of these 17 AGEs.

Conclusion

Integration of these AGEs into the Providencia chromosomes would contribute to the accumulation and distribution of drug resistance genes and enhance the ability of Providencia isolates to survive under drug selection pressure.

A Genomic and Bioinformatics View of the Classification and Evolution of Morganella Species and Their Chromosomal Accessory Genetic Elements Harboring Antimicrobial Resistance Genes

In this study, draft-genome sequencing was conducted for 60 Chinese Morganella isolates, and furthermore, 12 of them were fully sequenced. Then, a total of 166 global sequenced Morganella isolates, including the above 60, were collected to perform average nucleotide identity-based genomic classification and core single nucleotide polymorphism-based phylogenomic analysis. A genome sequence-based species classification scheme for Morganella was established, and accordingly, the two conventional Morganella species were redefined as two complexes and further divided into four and two genospecies, respectively. At least 88 acquired antimicrobial resistance genes (ARGs) were disseminated in these 166 isolates and were prevalent mostly in the isolates from hospital settings. IS26/IS15DI, IS10 and IS1R, and Tn3-, Tn21-, and Tn7-subfamily unit transposons were frequently presented in these 166 isolates. Furthermore, a detailed sequence comparison was applied to 18 Morganella chromosomal accessory genetic elements (AGEs) from the fully sequenced 12 isolates, together with 5 prototype AGEs from GenBank. These 23 AGEs were divided into eight different groups belonging to composite/unit transposons, transposable prophages, integrative and mobilizable elements, and integrative and conjugative elements, and they harbored at least 52 ARGs involved in resistance to 15 categories of antimicrobials. Eleven of these 23 AGEs acquired large accessory modules, which exhibited complex mosaic structures and contained many antimicrobial resistance loci and associated ARGs. Integration of ARG-containing AGEs into Morganella chromosomes would contribute to the accumulation and dissemination of ARGs in Morganella and enhance the adaption and survival of Morganella under complex and diverse antimicrobial selection pressures. IMPORTANCE This study presents a comprehensive genomic epidemiology analysis on global sequenced Morganella isolates. First, a genome sequence-based species classification scheme for Morganella is established with a higher resolution and accuracy than those of the conventional scheme. Second, the prevalence of accessory genetic elements (AGEs) and associated antimicrobial resistance genes (ARGs) among Morganella isolates is disclosed based on genome sequences. Finally, a detailed sequence comparison of eight groups of 23 AGEs (including 19 Morganella chromosomal AGEs) reveals that Morganella chromosomes have evolved to acquire diverse AGEs harboring different profiles of ARGs and that some of these AGEs harbor large accessory modules that exhibit complex mosaic structures and contain a large number of ARGs. Data presented here provide a deeper understanding of the classification and evolution of Morganella species and also those of ARG-containing AGEs in Morganella at the genomic scale.

Lanza V, Rodríguez-Beltrán J, Galán JC, San Millán A, Cantón R, Coque TM. Evolutionary Pathways and Trajectories in Antibiotic Resistance

Evolution is the hallmark of life. Descriptions of the evolution of microorganisms have provided a wealth of information, but knowledge regarding "what happened" has precluded a deeper understanding of "how" evolution has proceeded, as in the case of antimicrobial resistance. The difficulty in answering the "how" question lies in the multihierarchical dimensions of evolutionary processes, nested in complex networks, encompassing all units of selection, from genes to communities and ecosystems. At the simplest ontological level (as resistance genes), evolution proceeds by random (mutation and drift) and directional (natural selection) processes; however, sequential pathways of adaptive variation can occasionally be observed, and under fixed circumstances (particular fitness landscapes), evolution is predictable. At the highest level (such as that of plasmids, clones, species, microbiotas), the systems' degrees of freedom increase dramatically, related to the variable dispersal, fragmentation, relatedness, or coalescence of bacterial populations, depending on heterogeneous and changing niches and selective gradients in complex environments. Evolutionary trajectories of antibiotic resistance find their way in these changing landscapes subjected to random variations, becoming highly entropic and therefore unpredictable. However, experimental, phylogenetic, and ecogenetic analyses reveal preferential frequented paths (highways) where antibiotic resistance flows and propagates, allowing some understanding of evolutionary dynamics, modeling and designing interventions. Studies on antibiotic resistance have an applied aspect in improving individual health, One Health, and Global Health, as well as an academic value for understanding evolution. Most importantly, they have a heuristic significance as a model to reduce the negative influence of anthropogenic effects on the environment.

Comparative genomics of bovine mastitis-origin Staphylococcus aureus strains classified into prevalent human genotypes

Humans may serve as a reservoir host of Staphylococcus aureus, resulting in transmission to animals. Previously, we used RNA polymerase beta subunit gene (rpoB)-based genotyping and classified S. aureus strains into rpoB sequence types (RSTs). According to our previous work, the predominant genotypes of S. aureus in humans and cows differ in Korea, but some predominant genotypes (RST4-1 and RST2-1) in humans have been isolated from bovine mastitis. Therefore, it needs to be determined whether some strains of the predominant human genotypes have adapted to or caused occasional infections in cows. We determined the whole genome sequences of 2 bovine mastitis-origin strains, PMB179 (RST4-1) and PMB196 (RST2-1), and performed comparative genomics with the corresponding RST4-1 and RST2-1 S. aureus strains in the NCBI database. We identified 257 and 180 pseudogenes among 131 RST4-1 and 54 RST2-1 strains, respectively, for the comparison of pseudogene profiles. RST4-1 strains shared more common pseudogenes than RST2-1 strains, and some epidemiologically related strains shared common pseudogenes. However, most of the pseudogenes were strain-specific, and diverse pseudogene profiles were apparent in both the RST4-1 and RST2-1 strains. Furthermore, analysis of the mobile genetic elements, virulence genes, and antibiotic resistance genes revealed no molecular markers to differentiate PMB179 and PMB196 from human strains. Interestingly, the collective comparison of RST4-1 or RST2-1 strains revealed cumulative acquisition steps of genomic islands and antibiotic resistance genes. In conclusion, our data support PMB179 and PMB196 causing occasional infections that result in bovine mastitis.

Exploring the genetic mechanisms underlying amoxicillin-clavulanate resistance in waterborne Escherichia coli

Escherichia coli is a human commensal and faecal indicator bacteria which is also the etiologic agent of several nosocomial- and community-acquired infections. Amoxicillin-clavulanate (AMC) is a widely prescribed β-lactam/β-lactamase inhibitor which is used against E. coli infections. Resistance to AMC in E. coli has been primarily attributed to point mutations in bla_TEM-1 resulting in inhibitor-resistant TEM (IRT) β-lactamases. In this study, we have explored the reasons underlying AMC-resistance in waterborne E. coli. Most of the studies regarding IRT-producing E. coli have been conducted on clinical samples and studies exploring genetic mechanisms underlying AMC-resistance in aquatic E. coli are scarce. Since, bla_TEM-1 and several antimicrobial resistance determinants are located on mobile genetic elements they can easily disseminate among other microbes inhabiting urban waterbodies. Thus, it is important to understand the underlying mechanisms to check the dissemination of AMC-resistance in other waterborne pathogens. Our results indicated that AMC-resistant E. coli were susceptible to other β-lactam/β-lactamase inhibitors like, ampicillin/sulbactam and piperacillin/tazobactam. Though, bla_TEM-1 was present, none of the strains harbored point mutations which could qualify as IRT and only one strain harbored both bla_TEM-1 and bla_OXA-1. Hyperproduction of bla_TEM-1, presence of plasimd-mediated ampC or promoter/attenuator mutations in the chromososmal ampC might not be related to IRT-like phenotype or AMC-resistance. This suggests that other mechanisms like, increased plasmid copy numbers or gene amplification or deficiency in the expression/function of porins might be responsible for AMC-resistance in waterborne E. coli.

Role of enterotoxigenic Escherichia coli prophage in spreading antibiotic resistance in a porcine-derived environment

Enterotoxigenic Escherichia coli (ETEC) cause acute secretory diarrhoea in pigs, posing a great economic loss to the swine industry. This study analysed the prevalence and genetic characteristics of prophages from 132 ETEC isolates from symptomatic pigs to determine their potential for spreading antibiotic resistance. A total of 1105 potential prophages were identified, and the distribution of the genome size showed three 'overlapping' trends. Similarity matrix comparison showed that prophages correlated with the ETEC lineage distribution, and further identification of these prophages corroborated the lineage specificity. In total, 1206 antibiotic resistance genes (ARGs) of 52 different categories were identified in 132 ETEC strains; among these, 2.65% (32/1206) of ARGs were found to be carried by prophages. Analysis of flanking sequences showed that almost all the ARGs could be grouped into two types: 'bla_TEM-1B ' and 'classic class 1 integron (IntI1)'. They co-occurred with a strictly conserved recombinase and transposon Tn3 family but with a difference: the 'bla_TEM-1B type' prophages exhibited a classic Tn2 transposon structure with 100% sequence identity, whereas the 'IntI1 type' co-occurred with the TnAs2 transposon with only 84% sequence identity. These results imply that ARGs might be pervasive in natural bacterial populations through transmission by transposable bacteriophages.

Extensive Gene Amplification as a Mechanism for Piperacillin-Tazobactam Resistance in Escherichia coli

Although the TEM-1 β-lactamase (Bla_TEM-1) hydrolyzes penicillins and narrow-spectrum cephalosporins, organisms expressing this enzyme are typically susceptible to β-lactam/β-lactamase inhibitor combinations such as piperacillin-tazobactam (TZP). However, our previous work led to the discovery of 28 clinical isolates of Escherichia coli resistant to TZP that contained only bla_TEM-1 One of these isolates, E. coli 907355, was investigated further in this study. E. coli 907355 exhibited significantly higher β-lactamase activity and Bla_TEM-1 protein levels when grown in the presence of subinhibitory concentrations of TZP. A corresponding TZP-dependent increase in bla_TEM-1 copy number was also observed, with as many as 113 copies of the gene detected per cell. These results suggest that TZP treatment promotes an increase in bla_TEM-1 gene dosage, allowing Bla_TEM-1 to reach high enough levels to overcome inactivation by the available tazobactam in the culture. To better understand the nature of the bla_TEM-1 copy number proliferation, whole-genome sequence (WGS) analysis was performed on E. coli 907355 in the absence and presence of TZP. The WGS data revealed that the bla_TEM-1 gene is located in a 10-kb genomic resistance module (GRM) that contains multiple resistance genes and mobile genetic elements. The GRM was found to be tandemly repeated at least 5 times within a p1ESCUM/p1ECUMN-like plasmid when bacteria were grown in the presence of TZP.IMPORTANCE Understanding how bacteria acquire resistance to antibiotics is essential for treating infected patients effectively, as well as preventing the spread of resistant organisms. In this study, a clinical isolate of E. coli was identified that dedicated more than 15% of its genome toward tandem amplification of a ~10-kb resistance module, allowing it to escape antibiotic-mediated killing. Our research is significant in that it provides one possible explanation for clinical isolates that exhibit discordant behavior when tested for antibiotic resistance by different phenotypic methods. Our research also shows that GRM amplification is difficult to detect by short-read WGS technologies. Analysis of raw long-read sequence data was required to confirm GRM amplification as a mechanism of antibiotic resistance.

The Codon Usage of Lowly Expressed Genes Is Subject to Natural Selection

Codon usage bias affects the genomes of organisms from all kingdoms of life and results from both background substitution biases and natural selection. Natural selection on codon usage to increase translation accuracy and efficiency has long been known to affect gene sequences. Such selection is stronger on highly, compared with lowly expressed genes, resulting in higher levels of codon bias within genes with higher expression levels. Additionally, selection on translation accuracy affects more strongly codons encoding conserved amino acids, since these will more often affect protein folding and/or function. By applying tests of selection on the gene sequences of the bacterium Escherichia coli, we demonstrate that both highly and lowly expressed genes display signals of selection on codon usage. Such signals are found for both conserved and less conserved amino acid positions, even within the 10% of E. coli genes expressed at the lowest levels. We further demonstrate experimentally that single synonymous codon replacements within a lowly expressed, essential gene can carry substantial effects on bacterial fitness. Combined, our results demonstrate that even within genes expressed at relatively low levels there is substantial selection on codon usage and that single synonymous codon replacements within such genes can have a marked effect on bacterial fitness.

Emergence of Antibiotic Resistance-Associated Clones Among Escherichia coli Recovered From Newborns With Early-Onset Sepsis and Meningitis in the United States, 2008-2009

BACKGROUND

Escherichia coli associated with early-onset sepsis (EOS) have historically been antibiotic-susceptible and K1-encapsulated. In the era of emerging antibiotic resistance, however, the clonal makeup of E coli associated with EOS has not been well characterized.

METHODS

Escherichia coli isolates were collected from 28 cases of EOS and early-onset meningitis (EOM) from April 2008 through December 2009, during a parent study conducted at National Institute of Child Health and Human Development Neonatal Research Network centers from February 2006 through December 2009. Clinical and microbiologic data were collected for the parent study. We applied polymerase chain reaction- and sequence-based molecular techniques to determine clonal, virulence-associated and antibiotic resistance-associated traits of the E coli isolates.

RESULTS

Among 28 E coli strains, phylogroup B2 strains predominated (68%), of which more than half were K1-encapsulated (53%). Phylogroup D strains were prominent as well (18%), but none were K1-encapsulated. Across the strain collection, the rate of ampicillin resistance was high (78%). The sole strain resistant to either extended-spectrum cephalosporins or fluoroquinolones represented ST131 H30-Rx, the multidrug-resistant subclone that has emerged worldwide in the last decade. This strain encoded extended-spectrum β-lactamase CTX-M-15 and carried an IncF plasmid of type F2:A1:B-.

CONCLUSIONS

In this collection of EOS/EOM-associated E coli isolates, we observed a high rate of ampicillin resistance, a low rate of fluoroquinolone resistance, and no aminoglycoside resistance, with resistance to third-generation cephalosporins appearing in only a single strain, from the worldwide emerging ST131 clone. Ongoing surveillance of antibiotic resistance among EOS isolates is warranted, to ensure that standard empiric regimens remain effective.

A series of medium and high copy number arabinose-inducible Escherichia coli expression vectors compatible with pBR322 and pACYC184

The original pBAD24 plasmid and the derived lower copy number (the pBAD322 series) expression vectors have been widely used in Escherichia coli, Salmonella enterica, and related bacteria. However, a flexible pBAD expression system has been available only in pMB1 (ColE1) vectors. We report a series of pBAD vectors that replicate using the origin of plasmid RSF1030 that are compatible with pMB1 (ColE1) and p15A (pACYC) vectors. Both high (≥pBAD24) and medium (~pBAD322) copy number plasmids encoding resistance to ampicillin, chloramphenicol, kanamycin, tetracycline, spectinomycin/streptomycin, gentamycin, or trimethoprim are available.

Everyman's Guide to Bacterial Insertion Sequences

The number and diversity of known prokaryotic insertion sequences (IS) have increased enormously since their discovery in the late 1960s. At present the sequences of more than 4000 different IS have been deposited in the specialized ISfinder database. Over time it has become increasingly apparent that they are important actors in the evolution of their host genomes and are involved in sequestering, transmitting, mutating and activating genes, and in the rearrangement of both plasmids and chromosomes. This review presents an overview of our current understanding of these transposable elements (TE), their organization and their transposition mechanism as well as their distribution and genomic impact. In spite of their diversity, they share only a very limited number of transposition mechanisms which we outline here. Prokaryotic IS are but one example of a variety of diverse TE which are being revealed due to the advent of extensive genome sequencing projects. A major conclusion from sequence comparisons of various TE is that frontiers between the different types are becoming less clear. We detail these receding frontiers between different IS-related TE. Several, more specialized chapters in this volume include additional detailed information concerning a number of these.

In a second section of the review, we provide a detailed description of the expanding variety of IS, which we have divided into families for convenience. Our perception of these families continues to evolve and families emerge regularly as more IS are identified. This section is designed as an aid and a source of information for consultation by interested specialist readers.

Sizes, locations, and directions of transcription of two genes on a cloned maize chloroplast DNA sequence

mRNA for the large subunit (LS) of ribulose-1,5-bisphosphate carboxylase [3-phospho-D-glycerate carboxylase (dimerizing), EC 4.1.1.39] of Zea mays is complementary to an uninterrupted 1600-base-pair-long chloroplast DNA sequence that has been mapped precisely within the 4350-base-pair-long chloroplast DNA fragment Bam 9 to which it had been traced earlier [Bedbrook, J. R., Coen, D. M., Beaton, A. R., Bogorad, L. & Rich, A. (1979) J. Biol. Chem. 254, 905-910]. An additional 1400-base-pair-long uninterrupted region that is colinear with a chloroplast RNA has been detected on Bam 9. The transcript from this region is part of a 2200-nucleotide-long RNA. The remainder of the DNA sequence for the 2200-base-pair RNA maps outside Bam 9. The 1600-base-pair LS gene and the gene for the 2200-nucleotide transcript are close to one another. They are separated by an untranscribed intercistronic "gap" about 330 base pairs long. These two closely packed genes are inverted on the chromosome-i.e., their 3' termini are at opposite ends of the untranscribed gap and they map on opposite strands.

Maize chloroplast DNA fragment encoding the large subunit of ribulosebisphosphate carboxylase

In vitro linked transcription-translation of chloroplast DNA has been used to show that the large subunit of ribulose-1,5-bisphosphate carboxylase [3-phospho-D-glycerate carboxy-lyase (dimerizing), EC 4.1.1.39] is encoded by Zea mays chloroplast DNA. A BamHI-generated chloroplast DNA sequence cloned in Escherichia coli is shown to direct the in vitro synthesis of this protein identified as large subunit by its size, serological properties, and limited proteolytic digestion products.

International spread and persistence of TEM-24 is caused by the confluence of highly penetrating enterobacteriaceae clones and an IncA/C2 plasmid containing Tn1696::Tn1 and IS5075-Tn21

TEM-24 remains one of the most widespread TEM-type extended-spectrum beta-lactamases (ESBLs) among Enterobacteriaceae. To analyze the reasons influencing its spread and persistence, a multilevel population genetics study was carried out on 28 representative TEM-24 producers from Belgium, France, Portugal, and Spain (13 Enterobacter aerogenes isolates, 6 Escherichia coli isolates, 6 Klebsiella pneumoniae isolates, 2 Proteus mirabilis isolates, and 1 Klebsiella oxytoca isolate, from 1998 to 2004). Clonal relatedness (XbaI pulsed-field gel electrophoresis [PFGE] and E. coli phylogroups) and antibiotic susceptibility were determined by standard procedures. Plasmid analysis included determination of the incompatibility group (by PCR, hybridization, and/or sequencing) and comparison of restriction fragment length polymorphism (RFLP) patterns. Characterization of genetic elements conferring antibiotic resistance included integrons (classes 1, 2, and 3) and transposons (Tn3, Tn21, and Tn402). Similar PFGE patterns were identified among E. aerogenes, K. pneumoniae, and P. mirabilis isolates, while E. coli strains were diverse (phylogenetic groups A, B2, and D). Highly related 180-kb IncA/C2 plasmids conferring resistance to kanamycin, tobramycin, chloramphenicol, trimethoprim, and sulfonamides were identified. Each plasmid contained defective In0-Tn402 (dfrA1-aadA1, aacA4, or aacA4-aacC1-orfE-aadA2-cmlA1) and In4-Tn402 (aacA4 or dfrA1-aadA1) variants. These integrons were located within Tn21, Tn1696, or hybrids of these transposons, with IS5075 interrupting their IRtnp and IRmer. In all cases, blaTEM-24 was part of an IS5075-DeltaTn1 transposon within tnp1696, mimicking other genetic elements containing blaTEM-2 and blaTEM-3 variants. The international dissemination of TEM-24 is fuelled by an IncA/C2 plasmid acquired by different enterobacterial clones which seem to evolve by gaining diverse genetic elements. This work highlights the risks of a confluence between highly penetrating clones and highly promiscuous plasmids in the spread of antibiotic resistance, and it contributes to the elucidation of the origin and evolution of TEM-2 ESBL derivatives.

The Fortunate Professor

My professional life can be summarized by a quote from the Talmud.

Much have I learned from my teachers, More from my colleagues, But most from my students.

It is the fortunate professor who learns from the student.

Bacterial plasmids: their extraordinary contribution to molecular genetics

Reviewed here are certain of the extraordinary contributions to molecular genetics that have resulted from the study of bacterial plasmids. Work with plasmids has led to both the 'operon' and 'replicon' concepts, and has provided seminal information about bacterial conjugation and fertility, recombination, transposable genetic elements, genome evolution and antisense RNA. Studies of plasmid functions have yielded important findings about the regulation of DNA replication, DNA topology and partitioning, gene control signals and restriction/modification enzymes. Plasmids have had a central role in the development of DNA cloning (recombinant DNA) methods; additionally, they have provided a paradigm for both the co-transformation of non-selected DNA into eukaryotic cells and the creation of the artificial chromosomes.

Antibiotic resistance in Haemophilus influenzae: mechanisms, clinical importance and consequences for therapy

Invasive and non-invasive infections caused by Haemophilus influenzae are frequently diagnosed in children below the age of 5 years. The treatment of choice for these infections was ampicillin. However, since the early 1970s the increasing prevalence of resistance to ampicillin and other antibiotics has necessitated major changes in antibiotic therapy. This article summarizes some of the important clinical features of diseases caused by H. influenzae. The epidemiology, the problems with in vitro susceptibility testing and the mechanisms of resistance to major antibiotics are reviewed. The consequences of antibiotic resistance for the treatment of diseases caused by H. influenzae are discussed.

The future contribution of transposition to antimicrobial resistance

Antibiotic resistance is commonplace in clinical bacterial isolates. Many of the resistance genes are transposon-borne and have the potential for rapid dispersal throughout the bacterial kingdom. Resistance genes are constantly subject to mutation and reassortment. Given appropriate selection pressure, the new resistance determinants can emerge rapidly to pose significant treatment problems. It seems likely that in the future bacterial resistance will continue to be a problem, both with respect to current antibiotics and to new ones and that transposon-borne resistance genes will continue to figure prominently.

Cloning and expression in Escherichia coli of the Azospirillum brasilense Sp7 gene encoding ampicillin resistance

The Azospirillum brasilense ATCC 29145 gene coding for beta-lactamase was cloned in Escherichia coli. The gene was expressed in E. coli from its own promoter as a 30-kilodalton protein, conferring resistance to high levels of beta-lactam antibiotics. The DNA sequence containing the beta-lactamase gene was found to be highly amplified in the Azospirillum genome, scattered in the chromosomal as well as in the plasmidic DNA.

Rapid chemiluminescent nucleic acid assays for detection of TEM-1 beta-lactamase-mediated penicillin resistance in Neisseria gonorrhoeae and other bacteria

Two new assays for the detection of TEM-1 beta-lactamase-mediated bacterial penicillin resistance were developed that involve the use of specific nucleic acid hybridization. Both techniques are based on a solution-phase hybridization of oligonucleotide probes to the target DNA sequence, solid-phase capture of the probe-target complex, and an amplified chemiluminescent labeling method. One configuration of hybridization probes detected the presence of TEM-1 in Neisseria gonorrhoeae (45 strains), Haemophilus spp., Escherichia coli, Shigella sonnei and Salmonella typhi. A second configuration (TEM-1NH) detected TEM-1 beta-lactamase-mediated penicillin resistance only in N. gonorrhoeae (97 strains) and Haemophilus (6 strains) isolates in which TEM-1 is inserted in a pFA7-type plasmid. Both methods were 100 times more sensitive than a commercially available colorimetric beta-lactamase activity test and approximately 5 times more sensitive than radioisotopic dot blot screening for the gene. The assays are particularly well suited to the analysis of large numbers of samples, can be performed in a total of 4 h, and are sensitive to 10(4) to 10(5) CFU.

Haemophilus influenzae: antibiotic susceptibility

Ampicillin resistance was first reported among clinical isolates of Haemophilus influenzae in 1972. Reports of chloramphenicol resistance followed shortly thereafter. The principal mechanism of resistance to these two antibiotics is enzymatic. Although other mechanisms have been described, they are found in comparatively few strains. The genetic information for the inactivating enzymes is plasmid mediated and therefore readily transmissible to susceptible strains. Consequently, effective therapy for invasive disease caused by this pathogen has been seriously compromised. As antibiotic susceptibility became less predictable, in vitro testing became increasingly important. Unfortunately, the standardization of methods for laboratory testing has been slow and complicated by the fastidious nature of the organisms. This review traces the development of antibiotic resistance in H. influenzae, discusses the mechanisms which appear to be important in mediating resistance, explores newer antimicrobial agents which might be useful in the treatment of infection, and analyzes the various approaches to in vitro testing.

Nucleotide sequence comparisons of plasmids pHD131, pJB1, pFA3, and pFA7 and beta-lactamase expression in Escherichia coli, Haemophilus influenzae, and Neisseria gonorrhoeae

The sites of initiation for beta-lactamase mRNA transcription and the nucleotide sequences of beta-lactamase plasmids derived from Haemophilus and Neisseria species were determined. In N. gonorrhoeae, transcription from plasmid pFA3 was initiated from two sites, one located about 20 base pairs (bp) and the other 210 bp upstream of the beta-lactamase initiating codon, whereas in H. influenzae, transcriptional initiation from plasmid pHD131 occurred at two different sites, approximately 150 and 170 bp upstream of the initiating codon. When these plasmids were transformed into Escherichia coli, transcription was initiated at the 150- and 170-bp upstream sites in both plasmids. The nucleotide sequences of both plasmids within the noncoding region upstream of the transcriptional initiation site were identical and, except at two or three nucleotide positions, the sequences were also identical to the corresponding region of Tn3. At one of these positions there is a TA for CG substitution, which correlates in E. coli and Haemophilus sp. with the presence of two strong, overlapping beta-lactamase promoters, initiating transcription at the 150- and 170-bp upstream sites. Over a larger (875-bp) segment comprising most of the sequences of the tnpR and bla genes, the nucleotide sequences of both plasmids were also identical, and although this sequence differed from the corresponding Tn3 sequence at 18 sites, it was identical to that of Tn2, except at one site. The sequence of a second Haemophilus plasmid, pJB1, was identical to that of pHD131 in the same region, except at two nucleotides. All three plasmids were identical in nucleotide sequence in other TnA regions, as well as in regions flanking the TnA sequence, except that the Neisseria plasmid lacked a TnA segment of 3,298 bp [comprising the IR(L) and proximal sequences] together with approximately 273 bp of the non-TnA region adjacent to IR(L). The sequence of a second N. gonorrhoeae plasmid, pFA7, was identical to pFA3, except that the terminal, 3,299 TnA nucleotides were missing.

Variations between the nucleotide sequences of Tn1, Tn2, and Tn3 and expression of beta-lactamase in Pseudomonas aeruginosa and Escherichia coli

Using S1 nuclease assays, we located the sites of initiation of transcription of the beta-lactamase gene on Tn1 and Tn2. Transcription in Tn2, like that in Tn3, occurred from the P3 promoter, whereas transcription in Tn1 was initiated by two stronger and overlapping promoters, Pa and Pb. The nucleotide sequences of Tn1 and Tn2 were determined over a 1,195-base-pair segment constituting most of the sequences of the tnpR and bla genes and the intervening region. There were six base-pair differences between Tn1 and Tn3. One in the bla regulatory region accounted for the presence of the Pa and Pb promoters, and another in the bla structural gene is consistent with the isoelectric focusing difference found between the Tn1 and Tn3 enzymes. In contrast, there were 24 base-pair differences between Tn2 and Tn3, most of them clustered in one segment of the tnpR gene.

Close evolutionary relationship between the chromosomally encoded beta-lactamase gene of Klebsiella pneumoniae and the TEM beta-lactamase gene mediated by R plasmids

Sixty-three percent homology of nucleotide sequence and 67% homology of deduced amino acid sequence were found between the chromosomally encoded beta-lactamase gene of Klebsiella pneumoniae and the TEM beta-lactamase of transposon Tn3. Moreover, 22 out of 24 amino acid residues are identical around the predicted active site. It is therefore suggested that these two kinds of beta-lactamases share a common evolutionary origin. The 0.5 kb DNA fragment of the cloned gene hybridized specifically with the chromosomal DNA of all the K. pneumoniae strains tested which had been isolated in Japan, USA and Europe.

Variability of IncHI1 plasmids from Salmonella typhi with special reference to Peruvian plasmids encoding resistance to trimethoprim and other antibiotics

In spite of extensive DNA homology among IncHI1 plasmids, ApaI and XbaI restriction digests of plasmids from Peruvian Salmonella typhi varied considerably from other IncHI1 plasmids isolated previously. IncHI1 plasmids appear to be undergoing a process of modular evolution, probably by sequential acquisition of resistance determinants.

Genesis of a complex transposon encoding the OXA-1 (type II) beta-lactamase gene

Plasmid R753-1-encoded resistance to ampicillin (by production of OXA-1 [type II] beta-lactamase), streptomycin, and sulfonamide was analyzed functionally and physically. The OXA-1 beta-lactamase gene on R753-1 could not transpose, whereas on some plasmids this gene was capable of transposition as part of transposon Tn2603. By using the nontransposable gene on R753-1 with Tn21 on a separate plasmid, we observed the genesis of a complex transposon with a structure similar to that of Tn2603. This finding confirms our previous hypothesis that Tn2603 has evolved directly from Tn21 through acquisition of the OXA-1 beta-lactamase gene by substitution of DNA segments. Furthermore, the mechanism of mobilization of pACYC184 derivatives by RecA-dependent homologous recombination was demonstrated.

A gene probe for TEM type beta-lactamases

A restriction fragment of plasmid pBR322 bearing the TEM-1 beta-lactamase structural gene was electroeluted from agarose gels after digestion with EcoRI and HinfI. The 1-kilobase fragment was 32P-labeled and used to examine genetic relationships with nucleic acids encoding seven other beta-lactamase classes. The probe hybridized only with TEM-2 and OXA-2 class plasmids.

Elimination of multicopy plasmid R6K by bleomycin

Bleomycin eliminated multicopy plasmid R6K from growing cells of Escherichia coli AB1157 but failed to cure either of the low-copy plasmids R1 or R46. Measurements of R6K-encoded beta-lactamase and of covalently closed plasmid DNA indicated that the drug causes a progressive reduction in plasmid copy number.

Plasmid mode of propagation of the genetic element P4

The satellite bacteriophage P4, in the presence of a helper phage, can enter either the lytic or the lysogenic cycle. In the absence of the helper, P4 can integrate in the bacterial chromosome. In addition, the partially immunity-insensitive mutant P4 vir1 can be maintained as a plasmid. We have found that in the absence of the helper, P4 wt also can be maintained as a plasmid, and that both P4 wt and P4 vir1 have two options for their intracellular propagation: a repressed-integrated or a derepressed-high copy number plasmid mode of maintenance. In the repressed mode, the P4 wt genome is only found integrated into the bacterial chromosome, while the P4 vir1 is found also as a low copy number plasmid coexisting with the integrated P4 vir1 genome. The clones carrying P4 in the derepressed-high copy number plasmid state are obtained at low frequency (0.3%) upon infection with P4 wt, while the vir1 mutation increases this frequency about 300-fold. Such clones can be distinguished easily because of their typical colony morphology (rosettes), due to the presence of filamentous cells. Filamentation of the bacterial host suggests that the presence of derepressed P4 genomes in high copy number interferes with the normal cell division mechanism. The derepressed clones are rather stable, but may revert spontaneously to the repressed state. Spontaneous transition from the repressed to the derepressed state was not observed; however, it can be induced by P2 or P4 vir1 superinfection of P4 wt and P4 vir1 lysogens or by growing the P4 vir1 lysogens up to the late exponential phase. The ability of P4 to choose either of two stable states and the potential to shift between these two modes of propagation indicate that the synthesis of the immunity repressor is regulated.

Two improved promoter sequences for the beta-lactamase expression arising from a single base-pair substitution

A mutation in the transposon Tn2660 derived from the plasmid R6K, and resulting in an approximate tenfold increase in penicillin resistance is shown to be a single GC to AT substitution 177 base pairs 'upstream' of the initiation codon of the structural beta-lactamase (bla) gene. This substitution leads to the transcription of two new mRNAs which can be ascribed to the creation of two new overlapping promoter sequences. All the sequences (450bp) examined in the wild-type Tn2660 are identical to those reported in Tn3.

Absence of direct repeats flanking transposons resulting from intramolecular transposition

Tn2660 is an ampicillin-resistance-conferring transposon with a high degree of homology for the transposon Tn3. The nucleotide sequences flanking the termini of Tn2660 have been determined on plasmids inferred to have resulted from both inter- and intramolecular transposition of Tn2660. In all cases, transposition of Tn2660, as of Tn3, creates 5-bp flanking direct repeats, except following intramolecular transposition resulting from trans ligation. In this case, in R6K replicons, the nucleotide sequence between the two Tn2660 elements is stably inverted from the normal orientation, and 5-bp direct repeats do not flank each transposon, but instead flank opposite ends of the two transposon copies.

Escherichia coli RNA polymerase binding sites and transcription initiation sites in the transposon Tn3

We have identified the Escherichia coli RNA polymerase-binding sites and the transcription initiation sites in the transposon Tn3. Results from nitrocellulose filter-binding assays indicate that there are two regions within Tn3 capable of forming stable binary complexes with RNA polymerase. The two regions are a 208-bp region containing the N-terminal coding sequence of the transposase (tnpA) and repressor (tnpR) genes, and a 332-bp region containing the N-terminal coding sequence for the beta-lactamase (bla) gene. DNase I footprint analysis of the 208-bp and 332-bp fragments further defined an extended region of protection, approx. 110 bp long, located between the transposase and repressor coding regions, and an 80-bp region of protection near the N-terminal coding sequence of the beta-lactamase gene. In vitro transcription studies with fragments containing these protected regions allowed us to determine the precise transcription initiation sites for the transposase, repressor, and beta-lactamase mRNAs. The transposase and repressor mRNAs are transcribed divergently and their transcription initiation sites are separated by 80 bp. The -35 homology regions for the transposase and repressor promoters are separated by 10 bp and the -10 homology region of the transposase promoter is coincident with the recombination site (res) for the site-specific recombinase activity (resolvase) of the repressor protein, which is required for resolution of Tn3 cointegrates. We discuss the significance of this complex divergently transcribed promoter region with respect to regulation of Tn3 transposition and we propose a model for coordinated regulation of the tnpA and tnpR genes. We also compare the Tn3 tnpA-tnpR intercistronic region with that of the closely related transposon gamma delta.

Properties of IncP-2 plasmids of Pseudomonas spp

Thirty IncP-2 R plasmids from isolates of Pseudomonas spp. of diverse geographical origins were examined for the production of resistance properties. All the plasmids determined resistance to tellurite and all inhibited the propagation of certain DNA phages, although several patterns of phage inhibition were detected. Of the 30 plasmids, 29 determined resistance to streptomycin, 28 determined resistance to mercuric ion, and 24 determined resistance to sulfonamide. Resistance to other antibiotics, to compounds of arsenic, boron, or chromium, and to UV irradiation was less common. The degradative plasmid CAM also belonged to this group. When CAM was introduced into recipients carrying an IncP-2 R plasmid, recombinant plasmids were often formed in which antibiotic resistance and the ability to grow on camphor were transferred together to further recipients or were lost together in a strain in which IncP-2 plasmids were unstable. Such hybrid plasmid formation was rec dependent. CAM and other IncP-2 plasmids that determine UV light resistance demonstrated UV-enhanced, nonpolarized transfer of the Pseudomonas aeruginosa chromosome. By agarose gel electrophoresis, all IncP-2 R plasmids and CAM were ca. 300 X 10(6) in molecular weight.

R46 encodes a site-specific recombination system interchangeable with the resolution function of TnA

Transposition of Tn4 onto the IncN plasmic R46 generates unstable DNA molecules. The R46::TnA recombinant plasmids undergo further DNA rearrangements which depend on the orientation in which the TnA element is inserted into the plasmid, and deletions and inversions of R46 and TnA sequences have been observed. Both types of rearrangement have the same specific endpoints, one within TnA and one located between the R46 coordinates, 36.0 and 37.0. The results are consistent with the operation of a recA-independent, site-specific recombination system utilizing, at least in part, the transposon cointegrate resolution system of TnA, together with R46-encoded functions. Data are presented that indicate that R46 encodes analogs of both the res site of TnA and its tnpR gene, although little homology between this element and the plasmid is apparent. Models for the TnA-induced generation of site-specific deletions and inversions upon transposition of TnA to R46 are presented.

Heteroduplex analysis of P-plasmid evolution: the role of insertion and deletion of transposable elements

DNA homology of thirteen R-plasmids of group P was examined by heteroduplex analysis and Southern blotting. Ten of these plasmids showed homology for extensive regions including all genes reported as necessary for replication and conjugational transfer. The differences between these plasmids could be explained by gain or loss of DNA sequences, many of which have been shown to be transposons. Of the other three plasmids, two showed unambiguous homology with the typical P-plasmids but this homology was imperfect, implying that these plasmids are products of lines which have evolved separately for long periods. One plasmid failed to produce heteroduplexes with the reference P plasmid.

Tn2610, a transposon involved in the spread of the carbenicillin-hydrolyzing beta-lactamase gene

We have found a new transposon, Tn2610, on pCS200 in clinical isolates of Escherichia coli, which encodes the carbenicillin-hydrolyzing beta-lactamase gene in combination with the resistance determinants to streptomycin and sulfonamide. Tn2610 has a molecular size of 24 kilobase pairs and is flanked by long inverted repeat sequences of 3 kilobase pairs in length. Genetical and physical analyses indicate that Tn2610 is a single transposable unit encoding the multiple resistance determinants and that is different from any previously described transposon. The characteristic DNA structure observed in various complex resistance transposons involved in the transposition of the carbenicillin-hydrolyzing beta-lactamase gene is discussed.

Tn2011, a new transposon encoding oxacillin-hydrolyzing beta-lactamase

The type II penicillinase (oxacillin-hydrolyzing beta-lactamase, OXA-1) gene on plasmid Rms213 was transposed to various plasmids or to the host chromosome. The transposon bearing this gene, designated Tn2011, conferred resistance to ampicillin, streptomycin, sulfonamide, and mercuric chloride. By restriction endonuclease digestion and agarose gel electrophoresis, the molecular weight of Tn2011 was estimated to be 12.5 X 10(6). The transposition frequency of Tn2011 was about 10(-4) to 10(-5). The activity of type II penicillinase is related to the copy number of the replicon bearing Tn2011.

pMS76, a plasmid capable of amplification by treatment with chloramphenicol

pMS76 is a nonconjugative, 5.54-megadalton plasmid. This plasmid is present in Escherichia coli K12 cells at about 20 copies per chromosome. In addition, the pMS76 plasmid can be mobilized by conjugative plasmids and it shares a number of other properties with the amplifiable ColE1 plasmid, including the ability to amplify copy number in the presence of chloramphenicol. However, pMS76 is compatible with ColE1-like replicons, pBR313, and with other multicopy plasmids, RSF1030 and pACYC184. Also the replication of pMS76 is rifampicin sensitive and requires DNA polymerase 1.