Mechanisms of bacterial resistance to antibiotics

QM/MM Simulations Reveal the Determinants of Carbapenemase Activity in Class A β-Lactamases

β-lactam antibiotic resistance in Gram-negative bacteria, primarily caused by β-lactamase enzymes that hydrolyze the β-lactam ring, has become a serious clinical problem. Carbapenems were formerly considered "last resort" antibiotics because they escaped breakdown by most β-lactamases, due to slow deacylation of the acyl-enzyme intermediate. However, an increasing number of Gram-negative bacteria now produce β-lactamases with carbapenemase activity: these efficiently hydrolyze the carbapenem β-lactam ring, severely limiting the treatment of some bacterial infections. Here, we use quantum mechanics/molecular mechanics (QM/MM) simulations of the deacylation reactions of acyl-enzyme complexes of eight β-lactamases of class A (the most widely distributed β-lactamase group) with the carbapenem meropenem to investigate differences between those inhibited by carbapenems (TEM-1, SHV-1, BlaC, and CTX-M-16) and those that hydrolyze them (SFC-1, KPC-2, NMC-A, and SME-1). QM/MM molecular dynamics simulations confirm the two enzyme groups to differ in the preferred acyl-enzyme orientation: carbapenem-inhibited enzymes favor hydrogen bonding of the carbapenem hydroxyethyl group to deacylating water (DW). QM/MM simulations of deacylation give activation free energies in good agreement with experimental hydrolysis rates, correctly distinguishing carbapenemases. For the carbapenem-inhibited enzymes, free energies for deacylation are significantly higher than for the carbapenemases, even when the hydroxyethyl group was restrained to prevent interaction with the DW. Analysis of these simulations, and additional simulations of mutant enzymes, shows how factors including the hydroxyethyl orientation, the active site volume, and architecture (conformations of Asn170 and Asn132; organization of the oxyanion hole; and the Cys69-Cys238 disulfide bond) collectively determine catalytic efficiency toward carbapenems.

Distribution of β-Lactamase Genes in Clinical Isolates from California Central Valley Hospital Deviates from the United States Nationwide Trends

The evolution and dissemination of antibiotic resistance genes throughout the world are clearly affected by the selection and migration of resistant bacteria. However, the relative contributions of selection and migration at a local scale have not been fully explored. We sought to identify which of these factors has the strongest effect through comparisons of antibiotic resistance gene abundance between a distinct location and its surroundings over an extended period of six years. In this work, we used two repositories of extended spectrum β-lactamase (ESBL)-producing isolates collected since 2013 from patients at Dignity Health Mercy Medical Center (DHMMC) in Merced, California, USA, and a nationwide database compiled from clinical isolate genomes reported by the National Center for Biotechnology Information (NCBI) since 2013. We analyzed the stability of average resistance gene frequencies over the years since collection of these clinical isolates began for each repository. We then compared the frequencies of resistance genes in the DHMMC collection with the averages of the nationwide frequencies. We found DHMMC gene frequencies are stable over time and differ significantly from nationwide frequencies throughout the period of time we examined. Our results suggest that local selective pressures are a more important influence on the population structure of resistance genes in bacterial populations than migration. This, in turn, indicates the potential for antibiotic resistance to be controlled at a regional level, making it easier to limit the spread through local stewardship.

Molecular Characterization of Multidrug-resistant Bacteria Isolated From Patients With Pneumonia at Two Hospitals in North-West Nigeria

Background and aims: The spread of antimicrobial resistance (AMR) is a serious public health threat complicating treatment and resulting in prolonged hospitalization. The prevalence of AMR threat is not well defined due to the dearth of appropriate surveillance systems. This study sought to assess the prevalence of AMR among bacterial isolates from sputum specimens obtained from patients with pneumonia presenting at two secondary healthcare facilities in Zaria from June 1 to August 31, 2018. Methods: Standard methodology was followed in processing sputum samples that met the acceptance criteria. The antibiotic susceptibility patterns of bacterial pathogens cultured from sputum specimens obtained from June 1 to August 31, 2018) were evaluated using the recommendation of the Clinical and Laboratory Standards Institute. Finally, data were analyzed using descriptive statistics. Results: Acinetobacter spp. were the predominant pathogens accounting for 32% of recovered isolates, followed by Staphylococcus spp. (18%) and Klebsiella spp. (17%), respectively. AMR was found in 91% of the isolates. Most isolates were resistant to erythromycin (ERY) (80%) and amoxicillin (83.3%). Eventually, the multiple antibiotic resistance index ≥0.3 was observed in 76% of the isolates. Conclusion: Based on the findings, AMR rates were observed to be high, and may display a serious therapeutic challenge to the management of community-acquired pneumonia. Concerted efforts are needed to combat the worrisome AMR trends revealed in this study.

Extended Spectrum β-Lactamase (ESBL) Producing Escherichia coli in Pigs and Pork Meat in the European Union

The aim of this article is to review the fast and worldwide distribution of ESBL enzymes and to describe the role of the pork production chain as a reservoir and transmission route of ESBL-producing Escherichia coli and ESBLs in the European Union (EU). The use of β-lactam antibiotics in swine production and the prevalence of ESBL producing E. coli in fattening pigs and pork meat across Europe is analyzed. Overall, an increasing trend in the prevalence of presumptive ESBL producing E. coli in fattening pigs in the EU has been observed in the last decade, although with major differences among countries, linked to different approaches in the use of antimicrobials in pork production within the EU. Moreover, the various dissemination pathways of these bacteria along the pork production chain are described, along with factors at farm and slaughterhouse level influencing the risk of introducing or spreading ESBL producing bacteria throughout the food chain.

A Genotype-Phenotype Correlation Study of SHV β-Lactamases Offers New Insight into SHV Resistance Profiles

The SHV β-lactamases (BLs) have undergone strong allele diversification that has changed their substrate specificities. Based on 147 NCBI entries for SHV alleles, in silico mathematical models predicted 5 positions as relevant for the β-lactamase inhibitor (BLI)-resistant (2br) phenotype, 12 positions as relevant for the extended-spectrum BL (ESBL) (2be) phenotype, and 2 positions as related solely to the narrow-spectrum (2b) phenotype. These positions and six additional positions described in other studies (including one promoter mutation) were systematically substituted and investigated for their substrate specificities in a BL-free Escherichia coli background, representing, to our knowledge, the most comprehensive substrate and substitution analysis for SHV alleles to date. An in vitro analysis confirmed the essentiality of positions 238 and 179 for the 2be phenotype and of position 69 for the 2br phenotype. The E240K and E240R substitutions, which do not occur alone in known 2br SHV variants, led to a 2br phenotype, indicating a latent BLI resistance potential of these substitutions. The M129V, A234G, S271I, and R292Q substitutions conferred latent resistance to cefotaxime. In addition, seven positions that were found not always to be associated with the ESBL phenotype resulted in increased resistance to ceftaroline. We also observed that coupling of a strong promoter (IS26) to an A146V mutant with the 2b phenotype resulted in highly increased resistance to BLIs, cefepime, and ceftaroline but not to third-generation cephalosporins, indicating that SHV enzymes represent an underestimated risk for empirical therapies that use piperacillin-tazobactam or cefepime to treat different infectious diseases caused by Gram-negative bacteria.

Past and Present Perspectives on β-Lactamases

β-Lactamases, the major resistance determinant for β-lactam antibiotics in Gram-negative bacteria, are ancient enzymes whose origins can be traced back millions of years ago. These well-studied enzymes, currently numbering almost 2,800 unique proteins, initially emerged from environmental sources, most likely to protect a producing bacterium from attack by naturally occurring β-lactams. Their ancestors were presumably penicillin-binding proteins that share sequence homology with β-lactamases possessing an active-site serine. Metallo-β-lactamases also exist, with one or two catalytically functional zinc ions. Although penicillinases in Gram-positive bacteria were reported shortly after penicillin was introduced clinically, transmissible β-lactamases that could hydrolyze recently approved cephalosporins, monobactams, and carbapenems later became important in Gram-negative pathogens. Nomenclature is based on one of two major systems. Originally, functional classifications were used, based on substrate and inhibitor profiles. A later scheme classifies β-lactamases according to amino acid sequences, resulting in class A, B, C, and D enzymes. A more recent nomenclature combines the molecular and biochemical classifications into 17 functional groups that describe most β-lactamases. Some of the most problematic enzymes in the clinical community include extended-spectrum β-lactamases (ESBLs) and the serine and metallo-carbapenemases, all of which are at least partially addressed with new β-lactamase inhibitor combinations. New enzyme variants continue to be described, partly because of the ease of obtaining sequence data from whole-genome sequencing studies. Often, these new enzymes are devoid of any phenotypic descriptions, making it more difficult for clinicians and antibiotic researchers to address new challenges that may be posed by unusual β-lactamases.

Klebsiella: a long way to go towards understanding this enigmatic jet-setter

Klebsiella pneumoniae is the causative agent of a variety of diseases, including pneumonia, urinary tract infections, septicemia, and the recently recognized pyogenic liver abscesses (PLA). Renewed efforts to identify and understand the bacterial determinants required to cause disease have come about because of the worldwide increase in the isolation of strains resistant to a broad spectrum of antibiotics. The recent increased isolation of carbapenem-resistant strains further reduces the available treatment options. The rapid geographic spread of the resistant isolates and the spread to other pathogens are of particular concern. For many years, the best characterized virulence determinants were capsule, lipopolysaccharide, siderophores, and types 1 and 3 fimbriae. Recent efforts to expand this list include in vivo screens and whole-genome sequencing. However, we still know little about how this bacterium is able to cause disease. Some recent clonal analyses of K. pneumoniae strains indicate that there are distinct clonal groups, some of which may be associated with specific disease syndromes. However, what makes one clonal group more virulent and what changes the disease pattern are not yet clear and remain important questions for the future.

Characterization of the inhibitor-resistant SHV β-lactamase SHV-107 in a clinical Klebsiella pneumoniae strain coproducing GES-7 enzyme

The clinical Klebsiella pneumoniae INSRA6884 strain exhibited nonsusceptibility to all penicillins tested (MICs of 64 to >2,048 μg/ml). The MICs of penicillins were weakly reduced by clavulanate (from 2,048 to 512 μg/ml), and tazobactam restored piperacillin susceptibility. Molecular characterization identified the genes bla(GES-7) and a new β-lactamase gene, bla(SHV-107), which encoded an enzyme that differed from SHV-1 by the amino acid substitutions Leu35Gln and Thr235Ala. The SHV-107-producing Escherichia coli strain exhibited only a β-lactam resistance phenotype with respect to amoxicillin, ticarcillin, and amoxicillin-clavulanate combination. The kinetic parameters of the purified SHV-107 enzyme revealed a high affinity for penicillins. However, catalytic efficiency for these antibiotics was lower for SHV-107 than for SHV-1. No hydrolysis was detected against oxyimino-β-lactams. The 50% inhibitory concentration (IC(50)) for clavulanic acid was 9-fold higher for SHV-107 than for SHV-1, but the inhibitory effects of tazobactam were unchanged. Molecular dynamics simulation suggested that the Thr235Ala substitution affects the accommodation of clavulanate in the binding site and therefore its inhibitory activity.

SHV-1 beta-lactamase is mainly a chromosomally encoded species-specific enzyme in Klebsiella pneumoniae

The nature of the SHV-1 beta-lactamase gene was analyzed in 97 epidemiologically unrelated Klebsiella pneumoniae strains isolated from clinical samples. beta-Lactamase bands that focused at a pI of 7.6 (SHV-1-type) in 74 strains, at a pI of 7.1 (LEN-1-type) in 13 strains, and at a pI of 5.4 (TEM-1-type) in 10 strains were detected by analytical isoelectric focusing (IEF). Among the 74 SHV-1-producing strains, 40 had, in addition to the pI 7.6 band, an additional band on IEF: 20 had a band with a pI of 7.1 and 20 had a band with a pI of 5.4. Most of the 74 SHV-1-producing strains (76.7%) carried plasmids. Transfer of beta-lactam resistance by conjugation was possible in only 9.3% of the strains tested. SHV-1 gene-specific PCR-restriction fragment length polymorphism (PCR-RFLP) analysis of the chromosomal DNA was positive for 93 of the 97 strains and negative for only 4 of the 10 samples with K. pneumoniae TEM-1 producers. In an attempt to approximate the location of the SHV gene locus by endonuclease restriction analysis, RFLP analysis with Southern blotting of chromosomal DNA with a labeled SHV-1 fragment as a probe was used to study the 97 strains. A trial with EcoRI showed at least one positive hybridization band for 96 strains; two bands were detected for 8 strains. The hybridization was negative for only one TEM-1 beta-lactamase-producing strain. DNA sequence analysis showed no differences in promoter regions or extra stop-triplet sequences; only point mutations determined different allelic variants. The novel SHV-type variants are designated SHV-32 and SHV-33. As a result of the RFLP and sequencing analyses, it can be postulated that the loci for SHV-1 and LEN-1 genes are arranged in tandem. Our results strongly support the hypothesis that the ancestor of the SHV-1 beta-lactamase originated from the K. pneumoniae chromosome.

An allelic variant of the chromosomal gene for class A beta-lactamase K2, specific for Klebsiella pneumoniae, is the ancestor of SHV-1

Fecal Klebsiella isolates from neonates in 22 Swedish special care units were examined by a PCR we developed for detection of the SHV-1 beta-lactamase gene. All 105 K. pneumoniae isolates and all 11 K. pneumoniae reference strains (including the K. pneumoniae subsp. pneumoniae, ozaenae, and rhinoscleromatis type strains) tested were positive, whereas all 67 K. oxytoca isolates and the K. oxytoca, K. planticola, and K. terrigena type strains tested were negative. Resistance to beta-lactams in K. pneumoniae was not transferable by conjugation, and the beta-lactamase gene was never found on a plasmid. Southern blot analysis showed that the gene had a defined chromosomal location. Isoelectric focusing and sequencing of 231-bp PCR amplicons from different isolates revealed many variants of the enzyme, with the two main groups being SHV-1 like (pI 7.6; 68 isolates) and LEN-1 like (pI 7.1; 14 isolates). Clavulanic acid markedly reduced the MICs of ampicillin for all the K. pneumoniae isolates tested. This fact, MIC profiles (penicillin rather than cephalosporin resistance), pIs, and sequence data showed that the chromosomal beta-lactamase of K. pneumoniae is a class A, group 2 enzyme distinct from the chromosomal AmpC enzymes found in several other gram-negative bacteria and from the chromosomal beta-lactamase K1 of K. oxytoca. We propose that the chromosomal beta-lactamase of K. pneumoniae be designated K2 and suggest that an allelic pI 7.6 variant of this enzyme is the ancestor of the SHV family of plasmid-mediated beta-lactamases.

Complete amino acid sequence of p453-plasmid-mediated PIT-2 beta-lactamase (SHV-1)

The complete amino acid sequence of the p453-plasmid-mediated PIT-2 beta-lactamase (SHV-1) was determined. The protein contains 265 residues. Peptides resulting from digestions with trypsin, Staphylococcus aureus V8 proteinase, chymotrypsin and Lys-C proteinase and cleavage with CNBr were separated and purified by using reverse-phase h.p.l.c. The amino acid sequence of each peptide was manually determined with the dimethylaminoazobenzene isothiocyanate/phenyl isothiocyanate double-coupling method. The primary structure of PIT-2 beta-lactamase was compared with those of two closely related enzymes, namely TEM-1 beta-lactamase and the beta-lactamase of Klebsiella pneumoniae strain LEN-1. The PIT-2 beta-lactamase amino acid sequence was strongly retained, with respectively 68% and 88% homology. Thus PIT-2 enzyme could represent an evolutionary step between a chromosomally encoded beta-lactamase and the plasmid-mediated TEM beta-lactamases.

Spread of SHV-1 beta-lactamase in Escherichia coli isolated from fecal samples in Africa

Ninety-seven (42%) Escherichia coli strains isolated in Senegal from fecal samples produced beta-lactamases. Among them, 29 (30%) isolates produced SHV-1 beta-lactamase that was plasmid mediated. The plasmids belonged to four incompatibility groups. Various degrees of TEM-1 expression in the presence of SHV-1 were observed.

What do beta-lactamases mean for clinical efficacy?

beta-Lactamases have proved to be extremely important in influencing therapy with penicillins and cephalosporins against gram-positive and gram-negative aerobic and anaerobic species. Both plasmid mediated beta-lactamases which are primarily of a constitutive penicillinase type and the inducible chromosomal enzymes which are primarily cephalosporinases are important. The use of penicillins to treat Haemophilus, Neisseria gonorrhoeae, Escherichia coli, Klebsiella, Salmonella, Shigella and Pseudomonas infections must be based upon the relative incidence of beta-lactamase producing strains. In the same manner cephalosporins can be used to treat infections due to Enterobacter, Serratia and Bacteroides only if the compounds are beta-lactamase stable and not good inducers of beta-lactamase activity. Although altered permeability is important in the resistance of some Pseudomonas and Enterobacter to beta-lactams, the resistance really is due to a combination of reduced entry of molecules and strategically placed beta-lactamases. It is only in some Streptococcus pneumoniae, methicillin-resistant Staphylococcus aureus and Streptococcus faecalis strains that altered penicillin-binding proteins make a significant contribution to the resistance to beta-lactams. beta-lactamases will continue to be the most important factor in clinically significant resistance of bacteria to both penicillins and cephalosporins.

Principal beta-lactamases responsible for resistance to beta-lactam antibiotics in urinary tract infections

Two independent surveys have been conducted to determine the prevalent bacterial species and beta-lactamase types present in clinical populations of gram-negative, ampicillin-resistant isolates. A total of 208 isolates (112 from Nottingham Hospital and 96 from Charing Cross Hospital), all of which had been collected from out-patients suffering from urinary tract infections, were investigated. The incidence of ampicillin-resistant isolates (minimum inhibitory concentrations, 8 micrograms/ml) was 24.1% and 18.8% within the Nottingham and Charing Cross samples, respectively. The surveys gave similar results within the ampicillin-resistant samples. Escherichia coli was the prevalent bacterial species (52.9%), followed by Klebseilla pneumoniae (30.3%). The majority of isolates, at least 54.8% and possibly as high as 74.5%, owed their principal beta-lactamase activity to enzymes mediated by R-plasmids. The most prevalent beta-lactamases were TEM-1 (53.3%), SHV-1 (30.9%), and OXA-1 (11.5%). Positive associations were found between E. coli and TEM-1 or OXA-1 and between K. pneumoniae and SHV-1.

Types of beta-lactamase determined by plasmids in gram-negative bacteria

Two species of beta-lactamase determined by plasmids in enteric bacteria that show some resemblance to TEM enzymes are described. Both are distinct from all other plasmid-mediated beta-lactamases and differ from the TEM beta-lactamases in ability to hydrolyze some substrates, in isoelectric point, in immunological specificity, and in susceptibility to inhibition. One of the enzyme species, mediated by plasmid p453, has been briefly described previously. We have discovered that this beta-lactamase, designated SHV-1, is unique in its response to inhibition by the sulfhydryl group reagent p-chloromercuribenzoate, because the hydrolysis of cephaloridine but not that of benzylpenicillin is affected. This enzyme is found in a variety of plasmid types which were transferred from several bacterial species collected from a wide geographic range. The other enzyme species is novel; only a single plasmid determining this kind of beta-lactamase (designated HMS-1) has been detected.

Parameters of acquired resistance and their role in the evaluation of new chemotherapeutic drugs

Acquired resistance can be defined as a qualitative alteration of the genetic material of a cell which is phenotypically correlated with a measurable decrease of the cell's sensitivity against one or several chemotherapeutic agents. There are two basic genetic mechanisms which can lead to the emergence of resistance: mutation and the acquisition of additional genetic material from another cell. Both forms of resistance play an important role in clinical situations: the emergence of resistance by mutation occurs in tumor cells and can also lead to therapeutic problems in antimicrobial chemotherapy. In bacteria, however, acquisition of resistance plasmids represents the dominating mechanism which is responsible for most therapeutic problems in the clinical environment. The different genetic mechanisms involved in the emergence of resistance are paralleled -- at least in bacteria -- by two principally different groups of biochemical mechanisms implementing resistance. Mutations lead to alterations of single cell constituents such as the cell membrane or cellular receptors necessary for the binding of the antimicrobial agent. This form of resistance is biochemically characterized by the inaccessibility of the cell interior for a particular compound or by the modification of an intracellular binding site which loses its affinity for the chemotherapeutic agent. Resistance plasmids on the other hand code for enzymes which inactivate the antibiotic (beta-lactamases, aminoglycosideinactivating enzymes, chloramphenicol-acetyltransferase); In some cases, they direct the synthesis of proteins which affect cell permeability (tetracycline) or isoenzymes which have a lower affinity for the inhibitor (trimethoprim). Resistance against antibiotics can be inducible; In these cases the regulatory mechanisms involved are stable genetical traits as resistance itself; Using chloramphenicol, beta-lactam-antibiotics and aminoglycosides as examples, it is demonstrated that resistance data gathered early in the development of a new drug are of little value in estimating the clinical potential of a new compound. Information on the rate at which resistance develops, on the pattern according to which it emerges ("single step" or "multi step") and on cross-resistance patterns is important in the characterization of a new drug but is often invalidated by later findings obtained in the clinical environment; The problem appears somewhat simpler if a new drug is a member of an already known class of compounds, e.g. a beta-lactam or an aminoglycoside. In such cases our knowledge of frequent enzymatic inactivation mechanisms provides a basis not only for the evaluation of an existing drug, but also for the synthesis of new derivatives.

Immunogical study of anti-beta-lactamase antibodies by acidimetric methods

A beta-lactamase was extracted from an Escherichia coli K-12 strain carrying the R-TEM plasmid and has been purified by affinity chromatography. Antisera to this enzyme were prepared in the rabbit, and the enzyme-antibody neutralization reaction has been evaluated with acidimetric methods (pH stat or pH meter). Under defined experimental conditions, it is now possible to clearly illustrate the enzyme-antibody reaction by means of accurate, rapid, and simple-to-perform methods. These methods are in accord with the specificity of the two reactive partners and allow the detection of the enzyme in a crude bacterial extract which would eventually contain more than one beta-lactamase.

R factor-mediated and chromosomal resistance to ampicillin in Escherichia coli

Sixty-four ampicillin-resistant strains of Escherichia coli were studied. Six characters were examined: (i) resistance to ampicillin, cephalothin, and carbenicillin, (ii) synergy between ampicillin and cloxacillin, (iii) level of beta-lactamase activity after osmotic shock, (iv) transferability of ampicillin resistance, (v) immunological characterization of the enzyme, and (vi) determination of substrate profiles. One class of strains was found in which synthesis of beta-lactamase is inferred to be plasmid mediated; these strains are highly resistant to ampicillin and carbenicillin, sensitive to cephalothin, do not show synergism between ampicillin and cloxacillin, and reveal a high enzymatic activity after osmotic shock. A second class is formed by strains for which beta-lactamase synthesis is inferred to be chromosomal; these strains present a low resistance level to ampicillin, are sensitive to carbenicillin and resistant to cephalothin, show a synergism between ampicillin and cloxacillin, and reveal a very low enzymatic activity after osmotic shock. These characters may be used to differentiate periplasmic and cell-bound beta-lactamases.