Biochemical-genetic analysis and distribution of FAR-1, a class A beta-lactamase from Nocardia farcinica

Analysis of two Nocardia brasiliensis class A β-lactamases (BRA-1 and BRS-1) and related resistance to β-lactam antibiotics

OBJECTIVE

Molecular determinants of β-lactam resistance are poorly explored for most Nocardia species, such as Nocardia brasiliensis. In this study, we characterised resistance mediated by two β-lactamases in the reference strain N. brasiliensis HUJEG-1 and extended our analysis to nine N. brasiliensis clinical strains.

METHODS

The susceptibility of N. brasiliensis HUJEG-1 was determined by measuring the MIC via microdilution for five β-lactam antibiotics that were or were not associated with β-lactamase inhibitors (clavulanate and avibactam, 4 µg/mL). Two putative class A β-lactamase-encoding genes (blaBRA-1 and blaBRS-1) were identified in the HUJEG-1 genome. The kinetic parameters of purified BRA-1 and BRS-1 were determined by spectrophotometry. Measurement of β-lactam resistance was then extended to nine clinical strains. These phenotypic data were compared with the genomic diversity of whole genomes (next-generation sequencing).

RESULTS

N. brasiliensis HUJEG-1 was resistant to amoxicillin, cefuroxime, and cefotaxime, but susceptible to their combination with clavulanate or avibactam. This strain was resistant to imipenem (with or without inhibitors) and susceptible to meropenem. BRA-1 showed high catalytic efficiencies against penams (penicillin, ampicillin) and cephems (cephaloridine, cephalothin, and cefamandole), but not against penems (imipenem, meropenem), suggesting that imipenem resistance was mediated by another mechanism. The hydrolytic activity of BRS-1 was 100-1000-fold lower than that of BRA-1 for all β-lactams tested, suggesting that BRS-1 has a minor contribution to β-lactam resistance. Analysis of the nine clinical strains showed variations in susceptibility to cefotaxime, as well as diversity in genetic backgrounds and BRA-1 sequences.

CONCLUSIONS

N. brasiliensis HUJEG-1 resistance to penams and cephems is mainly due to the class A β-lactamase BRA-1.

Biochemical and structural characterization of a class A β-lactamase from Nocardia cyriacigeorgica

Nocardia are Gram-positive bacteria from the Actinobacteria phylum. Some Nocardia species can infect humans and are usually considered to be opportunist pathogens, as they often infect immunocompromised patients. Although their clinical incidence is low, many Nocardia species are now considered to be emerging pathogens. Primary sites of infection by Nocardia are the skin or the lungs, but dissemination to other body parts is very frequent. These disseminated infections are very difficult to treat and thus are tackled with multiple classes of antibiotics, in addition to the traditional treatment targeting the folate pathway. β-Lactams are often included in the regimen, but many Nocardia species present moderate or strong resistance to some members of this drug class. Genomic, microbiological and biochemical studies have reported the presence of class A β-lactamases (ABLs) in a handful of Nocardia species, but no structural investigation of Nocardia β-lactamases has yet been performed. In this study, the expression, purification and preliminary biochemical characterization of an ABL from an N. cyriacigeorgica (NCY-1) clinical strain are reported. The crystallization and the very high resolution crystal structure of NCY-1 are also described. The sequence and structural analysis of the protein demonstrate that NCY-1 belongs to the class A1 β-lactamases and show its very high conservation with ABLs from other human-pathogenic Nocardia. In addition, the presence of one molecule of citrate tightly bound in the catalytic site of the enzyme is described. This structure may provide a solid basis for future drug development to specifically target Nocardia spp. β-lactamases.

Phenotypic and genotypic analysis of antimicrobial resistance in Nocardia species

BACKGROUND

Antimicrobial resistance is common in Nocardia species but data regarding the molecular mechanisms beyond their resistance traits are limited. Our study aimed to determine the species distribution, the antimicrobial susceptibility profiles, and investigate the associations between the resistance traits and their genotypic determinants.

METHODS

The study included 138 clinical strains of Nocardia from nine Israeli microbiology laboratories. MIC values of 12 antimicrobial agents were determined using broth microdilution. WGS was performed on 129 isolates of the eight predominant species. Bioinformatic analysis included phylogeny and determination of antimicrobial resistance genes and mutations.

RESULTS

Among the isolates, Nocardia cyriacigeorgica was the most common species (36%), followed by Nocardia farcinica (16%), Nocardia wallacei (13%), Nocardia abscessus (9%) and Nocardia brasiliensis (8%). Linezolid was active against all isolates, followed by trimethoprim/sulfamethoxazole (93%) and amikacin (91%). Resistance to other antibiotics was species-specific, often associated with the presence of resistance genes or mutations: (1) aph(2″) in N. farcinica and N. wallacei (resistance to tobramycin); (ii) blaAST-1 in N. cyriacigeorgica and Nocardia neocaledoniensis (resistance to amoxicillin/clavulanate); (iii) blaFAR-1 in N. farcinica (resistance to ceftriaxone); (iv) Ser83Ala substitution in the gyrA gene in four species (resistance to ciprofloxacin); and (v) the 16S rRNA m1A1408 methyltransferase in N. wallacei isolates (correlating with amikacin resistance).

CONCLUSIONS

Our study provides a comprehensive understanding of Nocardia species diversity, antibiotic resistance patterns, and the molecular basis of antimicrobial resistance. Resistance appears to follow species-related patterns, suggesting a lesser role for de novo evolution or transmission of antimicrobial resistance.

Inhibition Activity of Avibactam against Nocardia farcinica β-Lactamase FARIFM10152

Nocardia farcinica, one of the most frequent pathogenic species responsible for nocardiosis, is characterized by frequent brain involvement and resistance to β-lactams mediated by a class A β-lactamase. Kinetic parameters for hydrolysis of various β-lactams by FAR_IFM10152 from strain IFM 10152 were determined by spectrophotometry revealing a high catalytic activity (k _cat/K_m ) for amoxicillin, aztreonam, and nitrocefin. For cephems, k _cat/K_m was lower but remained greater than 10⁴ M^-1 s^-1 A low catalytic activity was observed for meropenem, imipenem, and ceftazidime hydrolysis. FAR_IFM10152 inhibition by avibactam and clavulanate was compared using nitrocefin as a reporter substrate. FAR_IFM10152 was efficaciously inhibited by avibactam with a carbamoylation rate constant (k ₂/K_i ) of (1.7 ± 0.3) × 10⁴ M^-1 s^-1 The 50% effective concentrations (EC₅₀s) of avibactam and clavulanate were 0.060 ± 0.007 μM and 0.28 ± 0.06 μM, respectively. Amoxicillin, cefotaxime, imipenem, and meropenem MICs were measured for ten clinical strains in the presence of avibactam and clavulanate. At 4 μg/ml, avibactam and clavulanate restored amoxicillin susceptibility in all but one of the tested strains but had no effect on the MICs of cefotaxime, imipenem, and meropenem. At 0.4 μg/ml, amoxicillin susceptibility (MIC ≤ 8 μg/ml) was restored for 9 out of 10 strains by avibactam but only for 4 out of 10 strains by clavulanate. Together, these results indicate that avibactam was at least as potent as clavulanate, suggesting that the amoxicillin-avibactam combination could be considered as an option for the rescue treatment of N. farcinica infections if clavulanate cannot be used.

Antibiotic resistance genes in the Actinobacteria phylum

The Actinobacteria phylum is one of the oldest bacterial phyla that have a significant role in medicine and biotechnology. There are a lot of genera in this phylum that are causing various types of infections in humans, animals, and plants. As well as antimicrobial agents that are used in medicine for infections treatment or prevention of infections, they have been discovered of various genera in this phylum. To date, resistance to antibiotics is rising in different regions of the world and this is a global health threat. The main purpose of this review is the molecular evolution of antibiotic resistance in the Actinobacteria phylum.

A Structure-Based Classification of Class A β-Lactamases, a Broadly Diverse Family of Enzymes

For medical biologists, sequencing has become a commonplace technique to support diagnosis. Rapid changes in this field have led to the generation of large amounts of data, which are not always correctly listed in databases. This is particularly true for data concerning class A β-lactamases, a group of key antibiotic resistance enzymes produced by bacteria. Many genomes have been reported to contain putative β-lactamase genes, which can be compared with representative types. We analyzed several hundred amino acid sequences of class A β-lactamase enzymes for phylogenic relationships, the presence of specific residues, and cluster patterns. A clear distinction was first made between dd-peptidases and class A enzymes based on a small number of residues (S70, K73, P107, 130SDN132, G144, E166, 234K/R, 235T/S, and 236G [Ambler numbering]). Other residues clearly separated two main branches, which we named subclasses A1 and A2. Various clusters were identified on the major branch (subclass A1) on the basis of signature residues associated with catalytic properties (e.g., limited-spectrum β-lactamases, extended-spectrum β-lactamases, and carbapenemases). For subclass A2 enzymes (e.g., CfxA, CIA-1, CME-1, PER-1, and VEB-1), 43 conserved residues were characterized, and several significant insertions were detected. This diversity in the amino acid sequences of β-lactamases must be taken into account to ensure that new enzymes are accurately identified. However, with the exception of PER types, this diversity is poorly represented in existing X-ray crystallographic data.

Resistance gene pool to co-trimoxazole in non-susceptible Nocardia strains

The soil-borne pathogen Nocardia sp. causes severe cutaneous, pulmonary, and central nervous system infections. Against them, co-trimoxazole (SXT) constitutes the mainstay of antimicrobial therapy. However, some Nocardia strains show resistance to SXT, but the underlying genetic basis is unknown. We investigated the presence of genetic resistance determinants and class 1–3 integrons in 76 SXT-resistant Nocardia strains by PCR and sequencing. By E test, these clinical strains showed SXT minimum inhibitory concentrations of ≥32:608 mg/L (ratio of 1:19 for trimethoprim: sulfamethoxazole). They belonged to 12 species, being the main representatives Nocardia farcinica (32%), followed by N. flavorosea (6.5%), N. nova (11.8%), N. carnea (10.5%), N. transvalensis (10.5%), and Nocardia sp. (6.5%). The prevalence of resistance genes in the SXT-resistant strains was as follows: sul1 and sul2 93.4 and 78.9%, respectively, dfrA(S1) 14.7%, blaTEM-1 and blaZ 2.6 and 2.6%, respectively, VIM-2 1.3%, aph(3′)-IIIa 40.8%, ermA, ermB, mefA, and msrD 2.6, 77.6, 14.4, and 5.2%, respectively, and tet(O), tet(M), and tet(L) 48.6, 25.0, and 3.9%, respectively. Detected amino acid changes in GyrA were not related to fluoroquinolone resistance, but probably linked to species polymorphism. Class 1 and 3 integrons were found in 93.42 and 56.57% strains, respectively. Class 2 integrons and sul3 genes were not detected. Other mechanisms, different than dfrA(S1), dfrD, dfrF, dfrG, and dfrK, could explain the strong trimethoprim resistance shown by the other 64 strains. For first time, resistance determinants commonly found in clinically important bacteria were detected in Nocardia sp. sul1, sul2, erm(B), and tet(O) were the most prevalent in the SXT-resistant strains. The similarity in their resistome could be due to a common genetic platform, in which these determinants are co-transferred.

Natural hot spots for gain of multiple resistances: arsenic and antibiotic resistances in heterotrophic, aerobic bacteria from marine hydrothermal vent fields

Microorganisms are responsible for multiple antibiotic resistances that have been associated with resistance/tolerance to heavy metals, with consequences to public health. Many genes conferring these resistances are located on mobile genetic elements, easily exchanged among phylogenetically distant bacteria. The objective of the present work was to isolate arsenic-, antimonite-, and antibiotic-resistant strains and to determine the existence of plasmids harboring antibiotic/arsenic/antimonite resistance traits in phenotypically resistant strains, in a nonanthropogenically impacted environment. The hydrothermal Lucky Strike field in the Azores archipelago (North Atlantic, between 11°N and 38°N), at the Mid-Atlantic Ridge, protected under the OSPAR Convention, was sampled as a metal-rich pristine environment. A total of 35 strains from 8 different species were isolated in the presence of arsenate, arsenite, and antimonite. ACR3 and arsB genes were amplified from the sediment's total DNA, and 4 isolates also carried ACR3 genes. Phenotypic multiple resistances were found in all strains, and 7 strains had recoverable plasmids. Purified plasmids were sequenced by Illumina and assembled by EDENA V3, and contig annotation was performed using the "Rapid Annotation using the Subsystems Technology" server. Determinants of resistance to copper, zinc, cadmium, cobalt, and chromium as well as to the antibiotics β-lactams and fluoroquinolones were found in the 3 sequenced plasmids. Genes coding for heavy metal resistance and antibiotic resistance in the same mobile element were found, suggesting the possibility of horizontal gene transfer and distribution of theses resistances in the bacterial population.

Molecular identification and susceptibility pattern of clinical Nocardia species: Emergence of Nocardia crassostreae as an agent of invasive nocardiosis

BACKGROUND

Nocardia species are rare, opportunistic organisms that cause disease in both immunocompetent and immunocompromised individuals.

OBJECTIVE

To investigate the clinical presentations of various Nocardia infections based on the 16S ribosomal RNA gene of the isolate, as well as related risk factors and susceptibility patterns to antimicrobial agents.

METHODS

Thirteen patients with a diagnosis of nocardiosis were included in the present study. Seven Nocardia species were identified by 16S ribosomal RNA. Susceptibility testing was performed using six antimicrobial agents.

RESULTS

Five patients were immunocompromised, and eight were immunocompetent with predisposing factors including cystic fibrosis, tuberculosis and ophthalmic infections. Nocardia caused pulmonary infections in eight patients (61.5%), invasive systemic infections in three patients (23%) and local (ophthalmic) infections in two patients (15.4%). In the patients with pulmonary disease, nocardiosis was caused by six species (Nocardia cyriacigeorgica, Nocardia otitidiscaviarum, Nocardia farcinica, Nocardia carnea, Nocardia testacea and Nocardia asiatica). The seventh species identified in the present study was Nocardia crassostreae.

DISCUSSION

N crassostreae is a multidrug-resistant organism that was reported to be an emerging human pathogen causing invasive nocardiosis in a patient with non-Hodgkin's lymphoma. N farcinica was isolated from blood in a patient with breast cancer. None of the Nocardia isolates were resistant to linezolid. One N otitidiscaviarum isolate was a multidrug-resistant organism. All patients in the present study were treated with the appropriate antibiotics and their condition resolved without further sequelae.

CONCLUSIONS

The present study is the first report on N crassostreae as a human pathogen. The detection of multidrug-resistant species necessitate molecular identification and susceptibility testing, and should be performed for all Nocardia infections. Nocardiosis manifests various clinical features depending on the Nocardia species and underlying conditions.

Multisite reproducibility of the broth microdilution method for susceptibility testing of Nocardia species

Antimicrobial susceptibility testing (AST) of clinical isolates of Nocardia is recommended to detect resistance to commonly used antimicrobial agents; such testing is complicated by difficulties in inoculum preparation and test interpretation. In this study, six laboratories performed repetitive broth microdilution testing on single strains of Nocardia brasiliensis, Nocardia cyriacigeorgica, Nocardia farcinica, Nocardia nova, and Nocardia wallacei. For each isolate, a total of 30 microdilution panels from three different lots were tested at most sites. The goal of the study was to determine the inter- and intralaboratory reproducibility of susceptibility testing of this group of isolates. Acceptable agreement (>90% agreement at ±1 dilution of the MIC mode) was found for amikacin, ciprofloxacin, clarithromycin, and moxifloxacin. After eliminating MIC values from single laboratories whose results showed the greatest deviation from those of the remaining laboratories, acceptable agreement was also found for amoxicillin-clavulanic acid, linezolid, minocycline, and tobramycin. Results showed unsatisfactory reproducibility of broth microdilution testing of ceftriaxone with N. cyriacigeorgica and N. wallacei, tigecycline with N. brasiliensis and N. cyriacigeorgica, and sulfonamides with N. farcinica and N. wallacei. N. nova ATCC BAA-2227 is proposed as a quality control organism for AST of Nocardia sp., and the use of a disk diffusion test for sulfisoxazole is proposed as a check of the adequacy of the inoculum and to confirm sulfonamide MIC results.

Genetic and biochemical characterization of CAD-1, a chromosomally encoded new class A penicillinase from Carnobacterium divergens

Carnobacterium divergens clinical isolates BM4489 and BM4490 were resistant to penicillins but remained susceptible to combinations of amoxicillin-clavulanic acid and piperacillin-tazobactam. Cloning and sequencing of the responsible determinant from BM4489 revealed a coding sequence of 912 bp encoding a class A beta-lactamase named CAD-1. The bla(CAD-1) gene was assigned to a chromosomal location in the two strains that had distinct pulsed-field gel electrophoresis patterns. CAD-1 shared 53% and 42% identity with beta-lactamases from Bacillus cereus and Staphylococcus aureus, respectively. Alignment of CAD-1 with other class A beta-lactamases indicated the presence of 25 out of the 26 isofunctional amino acids in class A beta-lactamases. Escherichia coli harboring bla(CAD-1) exhibited resistance to penams (benzylpenicillin and amoxicillin) and remained susceptible to amoxicillin in combination with clavulanic acid. Mature CAD-1 consisted of a 34.4-kDa polypeptide. Kinetic analysis indicated that CAD-1 exhibited a narrow substrate profile, hydrolyzing benzylpenicillin, ampicillin, and piperacillin with catalytic efficiencies of 6,600, 3,200, and 2,900 mM(-1) s(-1), respectively. The enzyme did not interact with oxyiminocephalosporins, imipenem, or aztreonam. CAD-1 was inhibited by tazobactam (50% inhibitory concentration [IC(50)] = 0.27 microM), clavulanic acid (IC(50) = 4.7 microM), and sulbactam (IC(50) = 43.5 microM). The bla(CAD-1) gene is likely to have been acquired by BM4489 and BM4490 as part of a mobile genetic element, since it was not found in the susceptible type strain CIP 101029 and was adjacent to a gene for a resolvase.

Determination of antimicrobial susceptibility patterns of Nocardia spp. from clinical specimens by Etest

Susceptibilities to 11 antimicrobial agents were determined by Etest for 93 Nocardia isolates from clinical specimens and 15 type strains belonging to different Nocardia spp. All isolates were susceptible to trimethoprim-sulphamethoxazole, amikacin and linezolid, but susceptibilities of the various Nocardia spp. to beta-lactams, aminoglycosides, ciprofloxacin and clarithromycin varied markedly. Overall, there was a good correlation between the drug resistance patterns and the species identification established by conventional phenotypic tests and 16S rDNA sequencing. Among the different species encountered, Nocardia farcinica and Nocardia brasiliensis displayed the most multiresistant profiles, with resistance to imipenem occurring mainly among isolates of N. brasiliensis and Nocardia abscessus. The species variability in susceptibility profiles and the numerous recent taxonomic changes means that in-vitro susceptibility tests may be a complementary tool for the identification of Nocardia isolates from human clinical specimens. Further studies on a larger number of species from more diverse geographical sources, including species that are found less commonly among clinical isolates, are required to validate and extend the results.

Chromosome-borne class A BOR-1 beta-Lactamase of Bordetella bronchiseptica and Bordetella parapertussis

A narrow-spectrum clavulanic acid-inhibited class A beta-lactamase, BOR-1, was identified in a Bordetella bronchiseptica clinical isolate. It shared 45% amino acid identity with L-2 from Stenotrophomonas maltophilia. An identical beta-lactamase gene was found in B. bronchiseptica and Bordetella parapertussis reference strains that may contribute only in part to their resistance phenotype.

The complete genomic sequence of Nocardia farcinica IFM 10152

We determined the genomic sequence of Nocardia farcinica IFM 10152, a clinical isolate, and revealed the molecular basis of its versatility. The genome consists of a single circular chromosome of 6,021,225 bp with an average G+C content of 70.8% and two plasmids of 184,027 (pNF1) and 87,093 (pNF2) bp with average G+C contents of 67.2% and 68.4%, respectively. The chromosome encoded 5,674 putative protein-coding sequences, including many candidate genes for virulence and multidrug resistance as well as secondary metabolism. Analyses of paralogous protein families suggest that gene duplications have resulted in a bacterium that can survive not only in soil environments but also in animal tissues, resulting in disease.

Promoters P3, Pa/Pb, P4, and P5 upstream from bla(TEM) genes and their relationship to beta-lactam resistance

Using an isogenic system, we have determined the impact that the four promoters known to control bla(TEM) gene expression have on beta-lactamase activity. For both TEM-1 and TEM-30, this activity gradually increased in relation to the presence of promoters P3, Pa/Pb, and P4 upstream of the corresponding gene. Promoter P5, only found upstream of the bla(TEM-1B) gene, was related to the highest expression of this gene.

Biochemical-genetic analysis and distribution of DES-1, an Ambler class A extended-spectrum beta-lactamase from Desulfovibrio desulfuricans

Desulfovibrio spp. are gram-negative anaerobes phylogenetically related to Bacteroides spp., which are rarely isolated and which are mostly isolated from intra-abdominal abscesses. Desulfovibrio desulfuricans clinical isolate D3 had a clavulanic acid-inhibited beta-lactam resistance profile and was resistant to some expanded-spectrum cephalosporins. A beta-lactamase gene, bla(DES-1), was cloned from whole-cell DNA of isolate D3 and expressed in Escherichia coli. Purified beta-lactamase DES-1, with a pI value of 9.1, had a relative molecular mass of ca. 31 kDa and a mature protein of 288 amino acids. DES-1 was distantly related to Ambler class A beta-lactamases and most closely related to PenA from Burkholderia pseudomallei (48% amino acid identity). It was weakly related to class A beta-lactamases CblA, CepA, CfxA, and CfxA2 from other anaerobic species, Bacteroides spp. and Prevotella intermedia. Its hydrolysis spectrum included amino- and ureidopenicillins, narrow-spectrum cephalosporins, ceftriaxone, and cefoperazone. bla(DES-1)-like genes were not identified in phylogenetically related Desulfovibrio fairfieldensis isolates. However, they were found in some but not all D. desulfuricans strains, thus suggesting that these genes may be present in a given D. desulfuricans subspecies.

Molecular and biochemical analysis of AST-1, a class A beta-lactamase from Nocardia asteroides sensu stricto

A beta-lactamase gene was cloned from a Nocardia asteroides sensu stricto clinical isolate. A recombinant plasmid, pAST-1, expressed the beta-lactamase AST-1 in Escherichia coli JM109. Its pI was 4.8, and its relative molecular mass was 31 kDa. E. coli JM109(pAST-1) was resistant to penicillins and narrow-spectrum cephalosporins. The beta-lactamase AST-1 had a restricted hydrolytic activity spectrum. Its activity was partially inhibited by clavulanic acid but not by sulbactam and tazobactam. AST-1 is an Ambler class A beta-lactamase sharing 65% amino acid identity with beta-lactamase FAR-1, the most closely related enzyme.

Genetic-biochemical analysis and distribution of the Ambler class A beta-lactamase CME-2, responsible for extended-spectrum cephalosporin resistance in Chryseobacterium (Flavobacterium) meningosepticum

In vitro synergy between extended-spectrum cephalosporins and either clavulanic acid or cefoxitin was found for Chryseobacterium meningosepticum isolates during a double-disk assay on an agar plate. An extended-spectrum beta-lactamase (ESBL) gene from a C. meningosepticum clinical isolate was cloned and expressed in Escherichia coli DH10B. Its protein conferred resistance to most beta-lactams including extended-spectrum cephalosporins but not to cephamycins or to imipenem. Its activity was strongly inhibited by clavulanic acid, sulbactam, and tazobactam, as well as by cephamycins and imipenem. Sequence analysis of the cloned DNA fragment revealed an open reading frame (ORF) of 891 bp with a G+C content of 33.9%, which lies close to the expected range of G+C contents of members of the Chryseobacterium genus. The ORF encoded a precursor protein of 297 amino acids, giving a mature protein with a molecular mass of 31 kDa and a pI value of 9.2 in E. coli. This gene was very likely chromosomally located. Amino acid sequence comparison showed that this beta-lactamase, named CME-2 (C. meningosepticum ESBL), is a novel ESBL of the Ambler class A group (Bush functional group 2be), being weakly related to other class A beta-lactamases. It shares only 39 and 35% identities with the ESBLs VEB-1 from E. coli MG-1 and CBL-A from Bacteroides uniformis, respectively. The distribution of bla(CME-2) among unrelated C. meningosepticum species isolates showed that bla(CME-2)-like genes were found in the C. meningosepticum strains studied but were absent from strains of other C. meningosepticum-related species. Each C. meningosepticum strain produced at least two beta-lactamases, with one of them being a noninducible serine ESBL with variable pIs ranging from 7.0 to 8.5.