Precise insertion of antibiotic resistance determinants into Tn21-like transposons: nucleotide sequence of the OXA-1 beta-lactamase gene

Detection of Extended Spectrum ß-Lactamase-Producing Escherichia coli with Biofilm Formation from Chicken Meat in Istanbul

Antimicrobial resistance is one of the major public health problems worldwide. This study aimed to detect the presence of extended-spectrum β-lactamase-(ESBL-)producing Escherichia (E.) coli in chicken meat in Istanbul, Türkiye. Raw chicken meat samples (n = 208) were collected from different sale points and analyzed for ESBL-producing E. coli. In total, 101 (48.5%) isolates were confirmed as E. coli by PCR, of which 80/101 (79.2%) demonstrated multiple antibiotic resistance. Resistance against amoxicillin-clavulanic acid was most frequent (87.1%). Eighteen isolates (17.8%) demonstrated phenotypical ESBL resistance, as assessed by the double disc synergy test (DDST). Isolates were tested for the presence of β-lactamase genes and mobilized colistin-resistant genes. The blaTEM group was most frequently detected (97.02%), followed by blaCTX m (45.5%), blaSHV (9.9%), and blaOXA-2 (0.9%). However, mcr genes and blaNDM,blaKPC, blaVIM, and blaOXA-48 genes were not found in any isolate. E. coli strains were tested for biofilm formation in six different media [Nutrient broth, LB broth, Tryptone Soya broth (TSB), TSB containing 1% sucrose, TSB containing 0.6% yeast extract, and BHI]. Biofilm formation by E. coli isolates (44/101, 43.5%) was highest in TSB with 1% sucrose. It is worth noting that all biofilm-producing isolates were found to harbor the blaTEM-1 gene, which can indicate a high level of antibiotic resistance. This is the first report about ESBL-producing E. coli in poultry meat, the exposure of consumers in Istanbul metropolitan areas, and the ability of E. coli from this region to produce biofilms.

Exploiting the Carboxylate-Binding Pocket of β-Lactamase Enzymes Using a Focused DNA-Encoded Chemical Library

β-Lactamase enzymes hydrolyze and thereby provide bacterial resistance to the important β-lactam class of antibiotics. The OXA-48 and NDM-1 β-lactamases cause resistance to the last-resort β-lactams, carbapenems, leading to a serious public health threat. Here, we utilized DNA-encoded chemical library (DECL) technology to discover novel β-lactamase inhibitors. We exploited the β-lactamase enzyme-substrate binding interactions and created a DECL targeting the carboxylate-binding pocket present in all β-lactamases. A library of 106 compounds, each containing a carboxylic acid or a tetrazole as an enzyme recognition element, was designed, constructed, and used to identify OXA-48 and NDM-1 inhibitors with micromolar to nanomolar potency. Further optimization led to NDM-1 inhibitors with increased potencies and biological activities. This work demonstrates that the carboxylate-binding pocket-targeting DECL, designed based on substrate binding information, aids in inhibitor identification and led to the discovery of novel non-β-lactam pharmacophores for the development of β-lactamase inhibitors for enzymes of different structural and mechanistic classes.

Exploring multidrug-resistant Klebsiella pneumoniae antimicrobial resistance mechanisms through whole genome sequencing analysis

BACKGROUND

Antibiotic-resistant Klebsiella pneumoniae has emerged as a critical public health threat worldwide. Understanding the antimicrobial resistance mechanisms of multidrug-resistant K. pneumoniae (MDR-Kp) and its prevalence in time and space would provide clinical significance for managing pathogen infection.

METHODS

Eighteen clinical MDR-Kp strains were analyzed by whole genome sequencing (WGS), and the antimicrobial resistance genes and associated resistance mechanisms were compared with results obtained from the conventional microbiological test (CMT). The sequence homology across strains in our study and those previously collected over time from a wide geographical region was assessed by phylogenetic analysis.

RESULTS

MDR-Kp strains were collected from eighteen patients who had received empirical treatment before strain collection, with sputum (83.3%, 15/18) being the primary source of clinical samples. The commonly received treatments include β-lactamase inhibitors (55.6%, 10/18) and carbapenems (50%, 9/18). Using CMT, we found that all 18 strains were resistant to aztreonam and ciprofloxacin, while 14 (77.8%) showed resistance to carbapenem. Polymyxin B and tigecycline were the only antibiotics to which MDR-Kp strains were sensitive. A total of 42 antimicrobial resistance mechanisms were identified by WGS, surpassing the 40 detected by the conventional method, with 25 mechanisms shared between the two techniques. Despite a 100% accuracy rate of WGS in detecting penicillin-resistant strains, the accuracy in detecting cephalosporin-resistant strains was only at 60%. Among all resistance genes identified by WGS, Klebsiella pneumoniae carbapenemase-2 (KPC-2) was present in all 14 carbapenem-resistant strains. Phenotypic analysis indicated that sequence type (ST) 11 isolates were the primary cause of these MDR-Kp infections. Additionally, phylogenic clustering analysis, encompassing both the clinical and MDR-Kp strains previously reported in China, revealed four distinct subgroups. No significant difference was observed in the sequence homology between K. pneumoniae strains in our study and those previously collected in East China over time.

CONCLUSION

The application of WGS in identifying potential antimicrobial-resistant genes of MDR-Kp has demonstrated promising clinical significance. Comprehensive genomic information revealed by WGS holds the promise of guiding treatment decisions, enabling surveillance, and serving as a crucial asset in understanding antibiotic resistance.

Insights into dynamic changes in ADC-7 and P99 cephalosporinases using small angle x-ray scattering (SAXS)

To counter the emergence of β-lactamase (BL) mediated resistance, design of new β-lactamase inhibitors (BLIs) is critical. Many high-resolution crystallographic structures of BL complexed with BLIs are available. However, their impact on BLI design is struggling to keep pace with novel and emerging variants. Small angle x-ray scattering (SAXS) in combination with molecular modeling is a useful tool to determine dynamic structures of macromolecules in solution. An important application of SAXS is to determine the conformational changes that occur when BLI bind to BL. To probe if conformational dynamics occur in class C cephalosporinases, we studied SAXS profiles of two clinically relevant class C β-lactamases, Acinetobacter baumannii ADC-7 and Enterobacter cloacae P99 in apo format complexed with BLIs. Importantly, SAXS data analysis demonstrated that in solution, these representative class C enzymes remain monomeric and did not show the associated assemblies that were seen in various crystal structures. SAXS data acquired for ADC-7 and P99, in apo and inhibitor bound states, clearly showed that these enzymes undergo detectable conformational changes, and these class C β-lactamases also close upon binding inhibitors as does BlaC. Further analysis revealed that addition of inhibitor led to the compacting of a range of residues around the active site, indicating that the conformational changes that both P99 and ADC-7 undergo are central to inhibitor recognition and efficacy. Our findings support the importance of exploring conformational changes using SAXS analysis in the design of future BLIs.Communicated by Ramaswamy H. Sarma.

Analysis of antibiotic resistance gene cassettes in a newly identified Salmonella enterica serovar Gallinarum strain in Korea

Antimicrobial resistant pathogens are a global health threat driven by the indiscriminate use of antimicrobials. Antimicrobial resistance can be acquired by resistance genes encoded by mobile genetic elements. In this study, we identified a strain of Salmonella enterica serovar Gallinarum (SG4021) from an infected chicken in Korea and characterized the presence of resistance genes in its plasmid by whole genome sequencing. The sequence was then compared with that of a plasmid (P2) from strain SG_07Q015, the only other strain of S. Gallinarum isolated in Korea for which a genome sequence is available. The results revealed that both strains harbored nearly identical DNA carrying antibiotic resistance gene cassettes inserted into integron In2 of the transposable element Tn21, namely an aadA1 resistance gene conferring resistance to aminoglycosides and a sul1 resistance gene conferring resistance to sulfonamide. Interestingly, despite the presence of sul1 in SG4021, an antibiotic sensitivity test revealed that it was sensitive to sulfonamides. Further analysis revealed that this disparity was due to the insertion of a ~ 5 kb ISCR16 sequence downstream of the promoter driving sul1 expression in SG4021. Using various mutants, we showed that the insertion of ISCR16 blocked the expression of the sul1 gene from the upstream promoter. Therefore, the functionality of antimicrobial resistance genes determines phenotypic antimicrobial resistance.

β-Lactamase Producing Escherichia coli Encoding blaCTX-M and blaCMY Genes in Chicken Carcasses from Egypt

Escherichia coli with multidrug resistance and β-lactamase genes may constitute a great public health hazard due to the potential for their transmission to humans through the food chain. This study determined the prevalence, antibiotic resistance profiles, phylogroups, and β-lactamase genes of E. coli isolates from chicken carcasses marketed in Mansoura, Egypt. Interestingly, E. coli was detected in 98% (98/100) of the chicken carcasses examined, which seemed among the highest contamination rates by E. coli worldwide. From the 425 genetically verified uidA gene-positive E. coli, 85 isolates were further studied for antimicrobial resistance profiles, phylogroups, and β-lactamase genes. Interestingly, 89.41% of E. coli (76/85) strains tested against 24 different antibiotics were multidrug-resistant. Of the examined 85 E. coli isolates, 22 (25.88%) isolates harbored bla_CTX-M and were resistant to ampicillin, cefazoline, and ceftriaxone, while three of them were resistant to ceftazidime besides. Nine (10.59%) E. coli strains harbored AmpC- β-lactamase bla_CMY and were resistant to ampicillin. One isolate co-carried bla_CMY and bla_CTX-M genes, though it was negative for the bla_TEM gene. Of the 35 isolates that harbored either extended-spectrum β-lactamase (ESBL) and/or AmpC β-lactamase genes, six strains (17.14%) were assigned to pathogenic phylogroup F and one to phylogroup E, whereas 28 (80%) isolates belonged to commensal phylogenetic groups.

A review on the mechanistic details of OXA enzymes of ESKAPE pathogens

The production of β-lactamases is a prevalent mechanism that poses serious pressure on the control of bacterial resistance. Furthermore, the unavoidable and alarming increase in the transmission of bacteria producing extended-spectrum β-lactamases complicates treatment alternatives with existing drugs and/or approaches. Class D β-lactamases, designated as OXA enzymes, are characterized by their activity specifically towards oxacillins. They are widely distributed among the ESKAPE bugs that are associated with antibiotic resistance and life-threatening hospital infections. The inadequacy of current β-lactamase inhibitors for conventional treatments of 'OXA' mediated infections confirms the necessity of new approaches. Here, the focus is on the mechanistic details of OXA-10, OXA-23, and OXA-48, commonly found in highly virulent and antibiotic-resistant pathogens Acinetobacter baumannii, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Enterobacter spp. to describe their similarities and differences. Furthermore, this review contains a specific emphasis on structural and computational perspectives, which will be valuable to guide efforts in the design/discovery of a common single-molecule drug against ESKAPE pathogens.

The role of Musca domestica and milk in transmitting pathogenic multidrug-resistant Escherichia coli and associated phylogroups to neonatal calves

Escherichia coli, as a global source of antimicrobial resistance, is a serious veterinary and public health concern. The transmission of pathogenic multidrug-resistant (MDR) E. coli within diarrheic calves and its correlation with Musca domestica and milk strains have been investigated. In total, 110, 80, and 26 E. coli strains were obtained from 70 rectal swabs from diarrheic calves, 60 milk samples and 20 M. domestica, respectively. Molecular pathotyping of E. coli revealed the presence of pathogenic E. coli with a higher percentage of shigatoxigenic strains within diarrheic calves and M. domestica at 46.4% and 34.6%, respectively. Phenotypic antimicrobial resistance revealed higher β-lactams resistance except for cefquinome that exhibited low resistance in M.domestica and milk strains at 30.8% and 30%, respectively. The extended-spectrum cephalosporin (ESC) resistant strains were detected within fecal, M. domestica, and milk strains at 69.1%, 73.1%, and 71.3%, respectively. All E. coli strains isolated from M. domestica exhibited MDR, while fecal and milk strains were harboring MDR at 99.1% and 85%, respectively. Molecular detection of resistant genes revealed the predominance of the bla_TEM gene, while none of these strains harbored the bla_OXA gene. The highest percentages for bla_CTXM and bla_CMYII genes were detected in M. domestica strains at 53.8% and 61.5%, respectively. Regarding colistin resistance, the mcr-1 gene was detected only in fecal and milk strains at 35.5% and 15%, respectively. A high frequency of phylogroup B2 was detected within fecal and M. domestica strains, while milk strains were mainly assigned to the B1 phylogroup. Pathogenic E. coli strains with the same phenotypic and genotypic antimicrobial resistance and phylogroups were identified for both diarrheic calves and M. domestica, suggesting that the possible role of M. domestica in disseminating pathogenic strains and antimicrobial resistance in dairy farms.

Class C β-Lactamases: Molecular Characteristics

Class C β-lactamases or cephalosporinases can be classified into two functional groups (1, 1e) with considerable molecular variability (≤20% sequence identity). These enzymes are mostly encoded by chromosomal and inducible genes and are widespread among bacteria, including Proteobacteria in particular. Molecular identification is based principally on three catalytic motifs (⁶⁴SXSK, ¹⁵⁰YXN, ³¹⁵KTG), but more than 70 conserved amino-acid residues (≥90%) have been identified, many close to these catalytic motifs. Nevertheless, the identification of a tiny, phylogenetically distant cluster (including enzymes from the genera Legionella, Bradyrhizobium, and Parachlamydia) has raised questions about the possible existence of a C2 subclass of β-lactamases, previously identified as serine hydrolases. In a context of the clinical emergence of extended-spectrum AmpC β-lactamases (ESACs), the genetic modifications observed in vivo and in vitro (point mutations, insertions, or deletions) during the evolution of these enzymes have mostly involved the Ω- and H-10/R2-loops, which vary considerably between genera, and, in some cases, the conserved triplet ¹⁵⁰YXN. Furthermore, the conserved deletion of several amino-acid residues in opportunistic pathogenic species of Acinetobacter, such as A. baumannii, A. calcoaceticus, A. pittii and A. nosocomialis (deletion of residues 304-306), and in Hafnia alvei and H. paralvei (deletion of residues 289-290), provides support for the notion of natural ESACs. The emergence of higher levels of resistance to β-lactams, including carbapenems, and to inhibitors such as avibactam is a reality, as the enzymes responsible are subject to complex regulation encompassing several other genes (ampR, ampD, ampG, etc.). Combinations of resistance mechanisms may therefore be at work, including overproduction or change in permeability, with the loss of porins and/or activation of efflux systems.

Insights Into the Inhibition of MOX-1 β-Lactamase by S02030, a Boronic Acid Transition State Inhibitor

The rise of multidrug resistant (MDR) Gram-negative bacteria has accelerated the development of novel inhibitors of class A and C β-lactamases. Presently, the search for novel compounds with new mechanisms of action is a clinical and scientific priority. To this end, we determined the 2.13-Å resolution crystal structure of S02030, a boronic acid transition state inhibitor (BATSI), bound to MOX-1 β-lactamase, a plasmid-borne, expanded-spectrum AmpC β-lactamase (ESAC) and compared this to the previously reported aztreonam (ATM)-bound MOX-1 structure. Superposition of these two complexes shows that S02030 binds in the active-site cavity more deeply than ATM. In contrast, the SO₃ interactions and the positional change of the β-strand amino acids from Lys315 to Asn320 were more prominent in the ATM-bound structure. MICs were performed using a fixed concentration of S02030 (4 μg/ml) as a proof of principle. Microbiological evaluation against a laboratory strain of Escherichia coli expressing MOX-1 revealed that MICs against ceftazidime are reduced from 2.0 to 0.12 μg/ml when S02030 is added at a concentration of 4 μg/ml. The IC₅₀ and K_i of S02030 vs. MOX-1 were 1.25 ± 0.34 and 0.56 ± 0.03 μM, respectively. Monobactams such as ATM can serve as informative templates for design of mechanism-based inhibitors such as S02030 against ESAC β-lactamases.

Extended-Spectrum Beta-Lactamase Producing-Escherichia coli Isolated From Irrigation Waters and Produce in Ecuador

In cities across the globe, the majority of wastewater – that includes drug resistant and pathogenic bacteria among other contaminants – is released into streams untreated. This water is often subsequently used for irrigation of pastures and produce. This use of wastewater-contaminated streams allows antibiotic-resistant bacteria to potentially cycle back to humans through agricultural products. In this study, we investigated the prevalence of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli isolated from produce and irrigation water across 17 provinces of Ecuador. A total of 117 vegetable samples, 119 fruit samples, and 38 irrigation water samples were analyzed. Results showed that 11% of the samples were positive for E. coli including 11 irrigation water samples (29%), and samples of 13 vegetables (11%), and 11 fruits (9%). Among the 165 E. coli isolates cultured, 96 (58%) had the ESBL phenotype, and 58% of ESBL producing E. coli came from irrigation water samples, 11% from vegetables, and 30% from fruits. The bla_CTX–M–55, bla_{CTX–M 65}, and bla_{CTX–M 15} genes were the most frequently found gene associated with the ESBL phenotype and coincided with the bla_CTX–M alleles associated with human infections in Ecuador. Three isolates had the mcr-1 gene which is responsible for colistin resistance. This report provides evidence of the potential role of irrigation water in the growing antimicrobial resistance crisis in Ecuador.

Application of a multiplex immunochromatographic assay for rapid identification of carbapenemases in a clinical microbiology laboratory: performance and turn-around-time evaluation of NG-test Carba 5

Background

Prompt and accurate identification of carbapenemase production is essential for appropriate treatment and infection control. NG-Test Carba 5 (termed herein “Carba 5”; NG Biotech, Guipry, France) is a multiplex immunochromatographic assay for the rapid phenotypic identification of five major carbapenemases (KPC, NDM, VIM, IMP, and OXA-48-like) from bacterial isolates. This study aimed to evaluate the diagnostic performance of Carba 5 and its impact on the turn-around-time in a clinical microbiology laboratory.

Results

Carba 5 was retrospectively evaluated using 78 carbapenemase producers and 23 non-carbapenemase producers confirmed by PCR and sequencing. The performance and time required for carbapenemase identification were prospectively evaluated using 47 carbapenem resistant Enterobacteriaceae isolates, and the results were compared to those obtained using Xpert Carba-R (Cepheid, Sunnyvale, CA, USA). For the bacterial isolates included in retrospective and prospective evaluation, the Carba 5 assay correctly identified 147 isolates except one isolate with a sensitivity of 99.13% (95% CI 95.25–99.98%) and specificity of 100% (95% CI 89.42–100%). The Carba 5 assay missed one VIM-1 among 13 VIM producers. The assay showed a sensitivity of 92.31% (95% CI 63.97–99.81%) for detecting VIM and 100% for detecting KPC, NDM, OXA-48-like, and IMP. Compared to the Xpert Carba-R assay, Carba 5 exhibited 100% agreement and was more time-efficient (median time 24 min vs. 1 h 11 min).

Conclusions

The Carba 5 assay has potential as an alternative to molecular methods for detecting major carbapenemases from bacterial isolates in a clinical microbiology laboratory. Compared to the Xpert Carba-R, Carba 5 turns out to be more affordable and time-efficient while showing a comparable performance, and may accelerate therapeutic and infection control decisions.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-021-02309-9.

Burden, Antibiotic Resistance, and Clonality of Shigella spp. Implicated in Community-Acquired Acute Diarrhoea in Lilongwe, Malawi

Although numerous studies have investigated diarrhoea aetiology in many sub-Saharan African countries, recent data on Shigella species’ involvement in community-acquired acute diarrhoea (CA-AD) in Malawi are scarce. This study investigated the incidence, antibiotic susceptibility profile, genotypic characteristics, and clonal relationships of Shigella flexneri among 243 patients presenting with acute diarrhoea at a District Hospital in Lilongwe, Malawi. Shigella spp. were isolated and identified using standard microbiological and serological methods and confirmed by identifying the ipaH gene using real-time polymerase chain reaction. The isolates’ antibiotic susceptibility to 20 antibiotics was determined using the VITEK 2 system according to EUCAST guidelines. Genes conferring resistance to sulfamethoxazole (sul1, sul2 and sul3), trimethoprim (dfrA1, dfrA12 and dfrA17) and ampicillin (oxa-1 and oxa-2), and virulence genes (ipaBCD, sat, ial, virA, sen, set1A and set1B) were detected by real-time PCR. Clonal relatedness was assessed using ERIC-PCR. Thirty-four Shigella flexneri isolates were isolated (an overall incidence of 14.0%). All the isolates were fully resistant to sulfamethoxazole/trimethoprim (100%) and ampicillin (100%) but susceptible to the other antibiotics tested. The sul1 (79%), sul2 (79%), sul3 (47%), dfrA12 (71%) and dfrA17 (56%) sulfonamide and trimethoprim resistance genes were identified; Oxa-1, oxa-2 and dfrA1 were not detected. The virulence genes ipaBCD (85%), sat (85%), ial (82%), virA (76%), sen (71%), stx (71%), set1A (26%) and set1B (18%) were detected. ERIC-PCR profiling revealed that the Shigella isolates were genetically distinct and clonally unrelated, indicating the potential involvement of genetically distinct S. flexneri in CA-AD in Malawi. The high percentage resistance to ampicillin and sulfamethoxazole/trimethoprim and the presence of several virulence determinants in these isolates emphasises a need for continuous molecular surveillance studies to inform preventive measures and management of Shigella-associated diarrhoeal infections in Malawi.

Antibiotic resistance and sensitivity pattern of Metallo-β-Lactamase Producing Gram-Negative Bacilli in ventilator-associated pneumonia in the intensive care unit of a public medical school hospital in Bangladesh

BACKGROUND

Ventilator-associated pneumonia (VAP) is the most common nosocomial infection in intensive care units (ICU), accounting for 25% of all ICU infections. Antimicrobial resistance is increasing and becoming a significant health problem worldwide, increasing hospital length of stay, mortality and costs. Identifying antibiotic resistance patterns in VAP is important as this can cause outbreaks in ICUs. To date, there have been limited studies assessing this in Bangladesh. Consequently, the primary objective of this research was to study the species of bacterial growth and to determine the antibiotic resistance patterns of Metallo-β-Lactamase (MBL) producing gram-negative bacilli among ICU patients with VAP in a public medical school hospital, Bangladesh. In addition, identify the factors associated with a positive culture to provide future guidance.

METHOD

Cross-sectional study performed in the Chattogram Medical College Hospital, Bangladesh. Mueller Hinton agar plates were used for antibiotic sensitivity testing by the Kirby-Buer disc diffusion test.

RESULTS

Among 105 clinically suspected VAP cases, qualitative cultures were positive in 95 (90%) of them. The most common bacteria identified were Acinetobacter spp. (43.2%), Klebsiella spp. (20%) and Pseudomonas spp. (18.9%). A positive culture was not associated with patients' age or gender. Among 41 isolated Acinetobacter spp., 38 (92.7%) were resistant to gentamicin followed by 36 (87.8%) to ceftriaxone. Among 24 isolated Klebsiella spp., 22 (83.3%) were resistant to ceftriaxone. Among 18 isolated Pseudomonas spp., 16 (88.8%) were resistant to ciprofloxacin, and 13 (72.2%) were resistant to ceftriaxone. Among nine isolated E. coli, all were resistant to ceftriaxone and ciprofloxacin. All four Proteus spp. (100%) isolated were resistant to ciprofloxacin. Additionally, phenotype MBL producing was 65.22% and genotype was 45.65% among imipenem resistant pathogens. Imipenem resistant pathogens were sensitive to amoxyclav, amikacin¸ azithromycin, ceftazidime, ceftriaxone, colistin and gentamycin.

CONCLUSION

A positive culture was detected in 90% of VAP patients, but it was not associated with the patients' age and gender. The most common bacteria identified were Acinetobacter spp., Klebsiella spp. and Pseudomonas spp., where the majority of these were resistant to ceftriaxone. The results are being used to provide future guidance on the empiric management of VAP in this hospital.

A surface loop modulates activity of the Bacillus class D β-lactamases

The expression of β-lactamases is a major mechanism of bacterial resistance to the β-lactam antibiotics. Four molecular classes of β-lactamases have been described (A, B, C and D), however until recently the class D enzymes were thought to exist only in Gram-negative bacteria. In the last few years, class D enzymes have been discovered in several species of Gram-positive microorganisms, such as Bacillus and Clostridia, and an investigation of their kinetic and structural properties has begun in earnest. Interestingly, it was observed that some species of Bacillus produce two distinct class D β-lactamases, one highly active and the other with only basal catalytic activity. Analysis of amino acid sequences of active (BPU-1 from Bacillus pumilus) and inactive (BSU-2 from Bacillus subtilis and BAT-2 from Bacillus atrophaeus) enzymes suggests that presence of three additional amino acid residues in one of the surface loops of inefficient β-lactamases may be responsible for their severely diminished activity. Our structural and docking studies show that the elongated loop of these enzymes severely restricts binding of substrates. Deletion of the three residues from the loops of BSU-2 and BAT-2 β-lactamases relieves the steric hindrance and results in a significant increase in the catalytic activity of the enzymes. These data show that this surface loop plays an important role in modulation of the catalytic activity of Bacillus class D β-lactamases.

Oral amoxicillin and amoxicillin-clavulanic acid: properties, indications and usage

BACKGROUND

Amoxicillin has been in use since the 1970s; it is the most widely used penicillin both alone and in combination with the β-lactamase clavulanic acid.

OBJECTIVES

In this narrative review, we re-examine the properties of oral amoxicillin and clavulanic acid and provide guidance on their use, with emphasis on the preferred use of amoxicillin alone.

SOURCES

Published medical literature (MEDLINE database via Pubmed).

CONTENT

While amoxicillin and clavulanic acid have similar half-lives, clavulanic acid is more protein bound and even less heat stable than amoxicillin, with primarily hepatic metabolism. It is also more strongly associated with gastrointestinal side effects, including Clostridium difficile infection, and, thus, in oral combination formulations, limits the maximum daily dose of amoxicillin that can be given. The first ratio for an amoxicillin-clavulanic acid combination was set at 4:1 due to clavulanic acid's high affinity for β-lactamases; ratios of 2:1, 7:1, 14:1 and 16:1 are currently available in various regions. Comparative effectiveness data for the different ratios are scarce. Amoxicillin-clavulanic acid is often used as empiric therapy for many of the World Health Organization's Priority Infectious Syndromes in adults and children, leading to extensive consumption, when some of these syndromes could be handled with a delayed antibiotic prescription approach or amoxicillin alone.

IMPLICATIONS

Using available epidemiological and pharmacokinetic data, we provide guidance on indications for amoxicillin versus amoxicillin-clavulanic acid and on optimal oral administration, including choice of combination ratio. More data are needed, particularly on heat stability, pharmacodynamic effects and emergence of resistance in 'real-world' clinical settings.

The Complete Nucleotide Sequence of pZM3, a 1970 FIA:FIB:FII Plasmid Carrying Antibiotic Resistance and Virulence Determinants

The multiresistance plasmid, pZM3, from a 1970 Salmonella enterica serovar Wien isolate from Algeria represents the multiresistance FIme-type plasmids conferring resistance to ampicillin, chloramphenicol, kanamycin, neomycin, sulfonamides, streptomycin, spectinomycin, tetracycline, and mercuric ions circulating in the Middle East in the 1970s. pZM3 was sequenced to determine the relationship between IS1936, the IS26-like insertion sequence it carries, and IS26. IS1936 is identical to IS26. pZM3 is a 166.8-kb plasmid with three replicons typed as FIA-1, FIB-1, and FII-1, consistent with other FIme plasmids. However, Tn3, containing the bla_TEM-1a ampicillin resistance gene, disrupts the FII repA gene. pZM3 also contains an IS1-flanked virulence region, including the sit and aerobactin operons, shared with many other FIB-1 virulence plasmids. The remaining resistance genes are located in a 44.7-kb complex resistance island that includes the Tn21-like transposon, Tn1935, identified previously. Relative to Tn21, Tn1935 includes an additional gene cassette, oxa1, and Tn4352 in tniA. Tn1935 is in the same Tn2670 context as Tn21 in NR1, and identity to NR1 extends beyond the IS1 flanking the catA1 gene. On the other side, IS1-mediated events have brought in a Tn10 remnant and inverted part of it, highlighting the role of IS1 in resistance region evolution. The backbone of pZM3 was found to be almost identical to that of pRSB225, recovered in Germany in 2013, and their resistance islands are in the same position. The pRSB225 resistance island has evolved in situ from the pZM3 configuration through an insertion, a replacement, and an inversion.

IID572: A New Potentially Best-In-Class β-Lactamase Inhibitor

Resistance in Gram-negative bacteria to β-lactam drugs is mediated primarily by the expression of β-lactamases, and co-dosing of β-lactams with a β-lactamase inhibitor (BLI) is a clinically proven strategy to address resistance. New β-lactamases that are not impacted by existing BLIs are spreading and creating the need for development of novel broader spectrum BLIs. IID572 is a novel broad spectrum BLI of the diazabicyclooctane (DBO) class that is able to restore the antibacterial activity of piperacillin against piperacillin/tazobactam-resistant clinical isolates. IID572 is differentiated from other DBOs by its broad inhibition of β-lactamases and the lack of intrinsic antibacterial activity.

The resistomes of six carbapenem-resistant pathogens - a critical genotype-phenotype analysis

Carbapenem resistance is a rapidly growing threat to our ability to treat refractory bacterial infections. To understand how carbapenem resistance is mobilized and spread between pathogens, it is important to study the genetic context of the underlying resistance mechanisms. In this study, the resistomes of six clinical carbapenem-resistant isolates of five different species – Acinetobacter baumannii, Escherichia coli, two Klebsiella pneumoniae, Proteus mirabilis and Pseudomonas aeruginosa – were characterized using whole genome sequencing. All Enterobacteriaceae isolates and the A. baumannii isolate had acquired a large number of antimicrobial resistance genes (7–18 different genes per isolate), including the following encoding carbapenemases: bla_KPC-2, bla_OXA-48, bla_OXA-72, bla_NDM-1, bla_NDM-7 and bla_VIM-1. In addition, a novel version of bla_SHV was discovered. Four new resistance plasmids were identified and their fully assembled sequences were verified using optical DNA mapping. Most of the resistance genes were co-localized on these and other plasmids, suggesting a risk for co-selection. In contrast, five out of six carbapenemase genes were present on plasmids with no or few other resistance genes. The expected level of resistance – based on acquired resistance determinants – was concordant with measured levels in most cases. There were, however, several important discrepancies for four of the six isolates concerning multiple classes of antibiotics. In conclusion, our results further elucidate the diversity of carbapenemases, their mechanisms of horizontal transfer and possible patterns of co-selection. The study also emphasizes the difficulty of using whole genome sequencing for antimicrobial susceptibility testing of pathogens with complex genotypes.

Systematic Identification and Classification of β-Lactamases Based on Sequence Similarity Criteria: β-Lactamase Annotation

β-lactamases, the enzymes responsible for resistance to β-lactam antibiotics, are widespread among prokaryotic genera. However, current β-lactamase classification schemes do not represent their present diversity. Here, we propose a workflow to identify and classify β-lactamases. Initially, a set of curated sequences was used as a model for the construction of profiles Hidden Markov Models (HMM), specific for each β-lactamase class. An extensive, nonredundant set of β-lactamase sequences was constructed from 7 different resistance proteins databases to test the methodology. The profiles HMM were improved for their specificity and sensitivity and then applied to fully assembled genomes. Five hierarchical classification levels are described, and a new class of β-lactamases with fused domains is proposed. Our profiles HMM provide a better annotation of β-lactamases, with classes and subclasses defined by objective criteria such as sequence similarity. This classification offers a solid base to the elaboration of studies on the diversity, dispersion, prevalence, and evolution of the different classes and subclasses of this critical enzymatic activity.

New STs in multidrug-resistant Acinetobacter baumannii harbouring β-lactamases encoding genes isolated from Brazilian soils

AIMS

We investigated the resistance profile, presence of β-lactamases encoding genes and the clonal relationships in Acinetobacter baumannii isolated from Brazilian soils.

METHODS AND RESULTS

Soil isolates of A. baumannii were subjected to antimicrobial susceptibility testing by disk diffusion and minimum inhibitory concentration methods. Different β-lactamases encoding genes were screened by PCR and the molecular typing of these isolates was performed through the multilocus sequence typing. Non-susceptibility to different antibiotics was found, since environmental isolates were classified as multidrug-resistant. The bla_SHV gene was the most prevalent, followed by bla_GES. All sequence types (STs) found (ST1584, ST1607, ST1608, ST1609, ST1610, ST1611 and ST1612) were described for the first time in this study.

CONCLUSION

The wide variety of new alleles and new STs detected in the present study indicates a divergent population compared to studies that are carried out in the clinical environment and points to an even larger genetic diversity within the species than was anticipated.

SIGNIFICANCE AND IMPACT OF THE STUDY

A number of the environmental isolates represented multidrug-resistant strains, a phenotype that has been more commonly reported for clinical isolates of A. baumannii; the detection of several β-lactamase encoding genes in the investigated isolates is of great concern suggesting that there is a large reservoir of these resistance genes in the environment.

Integron-mediated multidrug resistance in extended-spectrum β-lactamase-producing Escherichia coli and Klebsiella pneumoniae isolated from fecal specimens in Egypt

BACKGROUND

The increasing incidence of hospital-acquired infections due to extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae represent a major health problem because of few therapeutic alternatives. The fecal flora can represent a reservoir for ESBL genes. Integrons are genetic structures capable of capturing gene cassettes that usually encode antibiotic-resistance determinants.

OBJECTIVES

To investigate the antimicrobial susceptibility of fecal isolates of ESBL-producing Escherichia coli and Klebsiella pneumoniae from hospitalized and nonhospitalized Egyptian patients and to determine the prevalence of class 1 and class 2 integrons together with the most common ESBL-producing genes (bla TEM, SHV, CTX-M, and OXA) among the collected isolates.

MATERIALS AND METHODS

Ninety-six fecal samples were collected: 48 samples from hospitalized patients admitted at Kasr Al-Ainy University Hospital, Cairo and 48 from outpatient clinics. Samples were inoculated on MacConkey agar and identified. All isolates were tested for their susceptibility to different antimicrobial agents using a standard disk diffusion method. The double-disk synergy test was applied for screening ESBL. All ESBL-producing isolates were confirmed by molecular testing to detect ESBL-encoding genes (SHV, TEM, CTX-M, and OXA). To identify the strains carrying integrons 1 and 2, the conserved regions of integron-encoded integrase gene intI1 and intI2 were amplified.

RESULTS

E. coli isolates accounted for 52.1% of the isolates collected from hospitalized patients and 60.4% of those collected from outpatient clinics. Results of the double-disk synergy test were positive in all E. coli and K. pneumoniae isolates, indicating the presence of ESBL production. Isolates of both groups showed variably high degrees of resistance to ciprofloxacin and co-trimoxazole. The most predominant ESBL gene in both groups was the bla CTX-M gene (93.8%) and the least prevalent was the bla OXA gene, which was not detected in any of the study isolates. Between the other two genes, the bla TEM gene was more common than the bla SHV gene in the two study groups. Class 1 integron was more prevalent among hospitalized patients, being detected in 64.6% of isolates from this group. Class 1 integron was linked with the bla CTX-M gene (P=0.039). Class 2 integron was more prevalent in the nonhospitalized group (85.4%) compared with the hospitalized group (50%) (P<0.001).

CONCLUSION AND RECOMMENDATIONS

ESBL-producing E. coli and K. pneumoniae showed a marked degree of antibiotic resistance in both hospitalized and nonhospitalized study groups. The high prevalence of class 1 and 2 integrons among isolates of both groups has a serious impact on the spread of antibiotic resistance.

Role of the Conserved Disulfide Bridge in Class A Carbapenemases

Some members of the class A β-lactamase family are capable of conferring resistance to the last resort antibiotics, carbapenems. A unique structural feature of these clinically important enzymes, collectively referred to as class A carbapenemases, is a disulfide bridge between invariant Cys69 and Cys238 residues. It was proposed that this conserved disulfide bridge is responsible for their carbapenemase activity, but this has not yet been validated. Here we show that disruption of the disulfide bridge in the GES-5 carbapenemase by the C69G substitution results in only minor decreases in the conferred levels of resistance to the carbapenem imipenem and other β-lactams. Kinetic and circular dichroism experiments with C69G-GES-5 demonstrate that this small drop in antibiotic resistance is due to a decline in the enzyme activity caused by a marginal loss of its thermal stability. The atomic resolution crystal structure of C69G-GES-5 shows that two domains of this disulfide bridge-deficient enzyme are held together by an intensive hydrogen-bonding network. As a result, the protein architecture and imipenem binding mode remain unchanged. In contrast, the corresponding hydrogen-bonding networks in NMCA, SFC-1, and SME-1 carbapenemases are less intensive, and as a consequence, disruption of the disulfide bridge in these enzymes destabilizes them, which causes arrest of bacterial growth. Our results demonstrate that the disulfide bridge is essential for stability but does not play a direct role in the carbapenemase activity of the GES family of β-lactamases. This would likely apply to all other class A carbapenemases given the high degree of their structural similarity.

Antibiotic Resistance in Long-Term Care Facilities

Long-term care facilities are comprised of a heterogeneous group of institutions caring for residential patients over prolonged periods of time. Included as long-term care facilities in this review are private and Veterans' Affairs (VA) nursing homes, rehabilitation centers, institutions for the developmentally disabled, and hospital wards for both long-term and intermediate care. Patients in long-term care facilities incur bacterial infections at a prevalence of 10% to 16%. These infections usually are caused by common bacterial pathogens that invade the compromised host residing within a complex physical environment. The high prevalence of institutional infections leads, in turn, to the need for multiple courses of antimicrobials or for hospitalization. This process selects strains more resistant to antibiotics, which are then available for repeated dispersal in the long-term care facility.

Self-resistance in Streptomyces, with Special Reference to β-Lactam Antibiotics

Antibiotic resistance is one of the most serious public health problems. Among bacterial resistance, β-lactam antibiotic resistance is the most prevailing and threatening area. Antibiotic resistance is thought to originate in antibiotic-producing bacteria such as Streptomyces. In this review, β-lactamases and penicillin-binding proteins (PBPs) in Streptomyces are explored mainly by phylogenetic analyses from the viewpoint of self-resistance. Although PBPs are more important than β-lactamases in self-resistance, phylogenetically diverse β-lactamases exist in Streptomyces. While class A β-lactamases are mostly detected in their enzyme activity, over two to five times more classes B and C β-lactamase genes are identified at the whole genomic level. These genes can subsequently be transferred to pathogenic bacteria. As for PBPs, two pairs of low affinity PBPs protect Streptomyces from the attack of self-producing and other environmental β-lactam antibiotics. PBPs with PASTA domains are detectable only in class A PBPs in Actinobacteria with the exception of Streptomyces. None of the Streptomyces has PBPs with PASTA domains. However, one of class B PBPs without PASTA domain and a serine/threonine protein kinase with four PASTA domains are located in adjacent positions in most Streptomyces. These class B type PBPs are involved in the spore wall synthesizing complex and probably in self-resistance. Lastly, this paper emphasizes that the resistance mechanisms in Streptomyces are very hard to deal with, despite great efforts in finding new antibiotics.

OXA β-lactamases

The OXA β-lactamases were among the earliest β-lactamases detected; however, these molecular class D β-lactamases were originally relatively rare and always plasmid mediated. They had a substrate profile limited to the penicillins, but some became able to confer resistance to cephalosporins. From the 1980s onwards, isolates of Acinetobacter baumannii that were resistant to the carbapenems emerged, manifested by plasmid-encoded β-lactamases (OXA-23, OXA-40, and OXA-58) categorized as OXA enzymes because of their sequence similarity to earlier OXA β-lactamases. It was soon found that every A. baumannii strain possessed a chromosomally encoded OXA β-lactamase (OXA-51-like), some of which could confer resistance to carbapenems when the genetic environment around the gene promoted its expression. Similarly, Acinetobacter species closely related to A. baumannii also possessed their own chromosomally encoded OXA β-lactamases; some could be transferred to A. baumannii, and they formed the basis of transferable carbapenem resistance in this species. In some cases, the carbapenem-resistant OXA β-lactamases (OXA-48) have migrated into the Enterobacteriaceae and are becoming a significant cause of carbapenem resistance. The emergence of OXA enzymes that can confer resistance to carbapenems, particularly in A. baumannii, has transformed these β-lactamases from a minor hindrance into a major problem set to demote the clinical efficacy of the carbapenems.

Class D β-lactamases do exist in Gram-positive bacteria

Production of β-lactamases of the four molecular classes (A, B, C, and D) is the major mechanism of bacterial resistance to β-lactams, the largest class of antibiotics that have saved countless lives since their inception 70 years ago. Although several hundred efficient class D enzymes have been identified in Gram-negative pathogens over the last four decades, they have not been reported in Gram-positive bacteria. Here we demonstrate that efficient class D β-lactamases capable of hydrolyzing a wide array of β-lactam substrates are widely disseminated in various species of environmental Gram-positive organisms. Class D enzymes of Gram-positive bacteria have a distinct structural architecture and employ a unique substrate binding mode quite different from that of all currently known class A, C, and D β-lactamases. They constitute a novel reservoir of antibiotic resistance enzymes.

Conformational Change Observed in the Active Site of Class C β-Lactamase MOX-1 upon Binding to Aztreonam

We solved the crystal structure of the class C β-lactamase MOX-1 complexed with the inhibitor aztreonam at 1.9Å resolution. The main-chain oxygen of Ser315 interacts with the amide nitrogen of aztreonam. Surprisingly, compared to that in the structure of free MOX-1, this main-chain carboxyl changes its position significantly upon binding to aztreonam. This result indicates that the interaction between MOX-1 and β-lactams can be accompanied by conformational changes in the B3 β-strand main chain.

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.

Genetic characterization of fluoroquinolone resistant Escherichia coli from urban streams and municipal and hospital effluents

Escherichia coli with reduced susceptibility to ciprofloxacin, isolated from urban streams, wastewater treatment plants and hospital effluent between 2004 and 2012, were compared based on multilocus sequence typing (MLST), quinolone and beta-lactam resistance determinants and plasmid replicon type. Isolates from the different types of water and isolation dates clustered together, suggesting the persistence and capacity to propagate across distinct aquatic environments. The most prevalent MLST groups were ST10 complex and ST131. Almost all isolates (98%) carried mutations in the chromosomal genes gyrA and/or parC, and 10% possessed the genes qepA, aac(6('))-Ib-cr and/or qnrS1. Over 80% of the isolates were resistant to three or more classes of antibiotics (MDR ≥ 3). The most prevalent beta-lactamase encoding gene was blaTEM, followed by blaCTX-M-15, co-existing with plasmid mediated quinolone resistance. The plasmid replicon types of the group IncF were the most prevalent and distributed by different MLST groups. The genes aac(6('))-Ib-cr and/or qnrS1 could be transferred by conjugation in combination with the genes blaTEM,blaSHV-12 or blaOXA-1 and the plasmid replicon types I1-Iγ, K, HI2 and/or B/O. The potential of multidrug resistant E. coli with reduced susceptibility to ciprofloxacin, harboring mobile genetic elements and with ability to conjugate and transfer resistance genes, to spread and persist across different aquatic environments was demonstrated.

The resistome of Pseudomonas aeruginosa in relationship to phenotypic susceptibility

Many clinical isolates of Pseudomonas aeruginosa cause infections that are difficult to eradicate due to their resistance to a wide variety of antibiotics. Key genetic determinants of resistance were identified through genome sequences of 390 clinical isolates of P. aeruginosa, obtained from diverse geographic locations collected between 2003 and 2012 and were related to microbiological susceptibility data for meropenem, levofloxacin, and amikacin. β-Lactamases and integron cassette arrangements were enriched in the established multidrug-resistant lineages of sequence types ST111 (predominantly O12) and ST235 (O11). This study demonstrates the utility of next-generation sequencing (NGS) in defining relevant resistance elements and highlights the diversity of resistance determinants within P. aeruginosa. This information is valuable in furthering the design of diagnostics and therapeutics for the treatment of P. aeruginosa infections.

Acquired Class D β-Lactamases

The Class D β-lactamases have emerged as a prominent resistance mechanism against β-lactam antibiotics that previously had efficacy against infections caused by pathogenic bacteria, especially by Acinetobacter baumannii and the Enterobacteriaceae. The phenotypic and structural characteristics of these enzymes correlate to activities that are classified either as a narrow spectrum, an extended spectrum, or a carbapenemase spectrum. We focus on Class D β-lactamases that are carried on plasmids and, thus, present particular clinical concern. Following a historical perspective, the susceptibility and kinetics patterns of the important plasmid-encoded Class D β-lactamases and the mechanisms for mobilization of the chromosomal Class D β-lactamases are discussed.

Studies on structure-based sequence alignment and phylogenies of beta-lactamases

The β-lactamases enzymes cleave the amide bond in β-lactam ring, rendering β-lactam antibiotics harmless to bacteria. In this communication we have studied structure-function relationship and phylogenies of class A, B and D beta-lactamases using structure-based sequence alignment and phylip programs respectively. The data of structure-based sequence alignment suggests that in different isolates of TEM-1, mutations did not occur at or near sequence motifs. Since deletions are reported to be lethal to structure and function of enzyme. Therefore, in these variants antibiotic hydrolysis profile and specificity will be affected. The alignment data of class A enzyme SHV-1, CTX-M-15, class D enzyme, OXA-10, and class B enzyme VIM-2 and SIM-1 show sequence motifs along with other part of polypeptide are essentially conserved. These results imply that conformations of betalactamases are close to native state and possess normal hydrolytic activities towards beta-lactam antibiotics. However, class B enzyme such as IMP-1 and NDM-1 are less conserved than other class A and D studied here because mutation and deletions occurred at critically important region such as active site. Therefore, the structure of these beta-lactamases will be altered and antibiotic hydrolysis profile will be affected. Phylogenetic studies suggest that class A and D beta-lactamases including TOHO-1 and OXA-10 respectively evolved by horizontal gene transfer (HGT) whereas other member of class A such as TEM-1 evolved by gene duplication mechanism. Taken together, these studies justify structure-function relationship of beta-lactamases and phylogenetic studies suggest these enzymes evolved by different mechanisms.

Crystal structure analysis of EstA from Arthrobacter sp. Rue61a--an insight into catalytic promiscuity

In this article we analyze the reasons for catalytic promiscuity of a type VIII esterase with β-lactamase fold and the ability to cleave β-lactams. We compared the structure of this enzyme to those of an esterase of the same type without any lactamase ability, an esterase with moderate lactamase ability, and a class C β-lactamase with similar fold. Our results show that for these enzymes, the difference in the substrate specificity is sterically driven.

Molecular evaluations of extended spectrum β-lactamase producing strains of Serratia isolated from blood samples of the patients in Namazi Hospital, Shiraz, Southern Iran

BACKGROUND AND OBJECTIVE

Nowadays, the presence of extended-spectrum β-lactamases (ESBLs) producing strains in Serratia genus causes the emergence of resistance to many antibiotics. So, the lack of proper diagnosis of ESBLs strains can lead to failure in the treatment. The objective of the present study was to investigate ESBLs production in Serratia strains isolated from the clinical blood samples in Shiraz, Iran.

MATERIALS AND METHODS

In this study, 39 Serratia strains isolated from the patients referred to Namazi Hospital, during a 2 year period were tested. The antimicrobial resistance of the isolates to 21 antibiotics was evaluated using Kirby-Bauer disk diffusion method. Combination disk method was used to determine the ESBL phenotype among the isolates. PCR was performed to investigate the presence of ESBL genes of SHV, OXA and TEM types.

RESULTS

The lowest antibiotic resistance rates belonged to meropenem (7.69%) and imipenem (5.12%). Overall, positive ESBL phenotype was identified in 69% (n = 27) of the isolates, 70.37% (n = 19) for S. marcescens and 29.62% (n = 8) for S. liquefaciens. Results obtained by PCR showed that only 20.51% carried OXA gene and 15.38% carried SHV-1 gene. TEM gene was detected in none of the isolates.

CONCLUSION

This study showed a high prevalence of the emerging ESBL producing strains among clinical isolates of Serratia that could lead to an increase in antibiotic resistance. However, ESBLs genes other than those tested here may be more responsible for the emergence of ESBL phenotype among Serratia clinical isolates in our region.

Identification of 50 class D β-lactamases and 65 Acinetobacter-derived cephalosporinases in Acinetobacter spp

Whole-genome sequencing of a collection of 103 Acinetobacter strains belonging to 22 validly named species and another 16 putative species allowed detection of genes for 50 new class D β-lactamases and 65 new Acinetobacter-derived cephalosporinases (ADC). All oxacillinases (OXA) contained the three typical motifs of class D β-lactamases, STFK, (F/Y)GN, and K(S/T)G. The phylogenetic tree drawn from the OXA sequences led to an increase in the number of OXA groups from 7 to 18. The topologies of the OXA and RpoB phylogenetic trees were similar, supporting the ancient acquisition of blaOXA genes by Acinetobacter species. The class D β-lactamase genes appeared to be intrinsic to several species, such as Acinetobacter baumannii, Acinetobacter pittii, Acinetobacter calcoaceticus, and Acinetobacter lwoffii. Neither blaOXA-40/143- nor blaOXA-58-like genes were detected, and their origin remains therefore unknown. The phylogenetic tree analysis based on the alignment of the sequences deduced from blaADC revealed five main clusters, one containing ADC belonging to species closely related to A. baumannii and the others composed of cephalosporinases from the remaining species. No indication of blaOXA or blaADC transfer was observed between distantly related species, except for blaOXA-279, possibly transferred from Acinetobacter genomic species 6 to Acinetobacter parvus. Analysis of β-lactam susceptibility of seven strains harboring new oxacillinases and cloning of the corresponding genes in Escherichia coli and in a susceptible A. baumannii strain indicated very weak hydrolysis of carbapenems. Overall, this study reveals a large pool of β-lactamases in different Acinetobacter spp., potentially transferable to pathogenic strains of the genus.

Molecular surveillance and clinical outcomes of carbapenem-resistant Escherichia coli and Klebsiella pneumoniae infections

BACKGROUND/PURPOSE

The emergence of carbapenem-resistant Enterobacteriaceae (CRE) is a cause for great concern. The aim of this study was to evaluate antimicrobial susceptibility, mechanisms of carbapenem-resistance in two members of the Enterobacteriaceae family (Escherichia coli and Klebsiella pneumoniae), and clinical outcomes of their infections.

METHODS

The susceptibility tests of 16 E. coli and 60 K. pneumoniae isolates, collected from 2010 to 2011, were assessed. The minimal inhibitory concentrations of eight antimicrobial agents were assessed by the broth microdilution method according to the recommendations of the Clinical and Laboratory Standards Institute. The detection of beta-lactamase genes was performed by polymerase chain reaction. The genetic relatedness of these isolates was determined by pulsed-field gel electrophoresis (PFGE) fingerprinting.

RESULTS

The carbapenemase genes blaKPC-2 and blaOxA were detected in one and five K. pneumoniae isolates, respectively. The genetic combinations blaSHV-5-blaDHA and blaSHV-5-blaCTx-M-G9 were prevalent in 45% and 26.7% of 60 K. pneumoniae isolates, respectively. The susceptibility rates of 60 K. pneumoniae isolates to colistin and tigecycline were 58.3% and 50.0%, respectively. The 30-day mortality rates of the patients treated with carbapenem, colistin, or tigecycline were as high as 60.6%. Nine clusters of K. pneumoniae isolates were identified by PFGE fingerprinting.

CONCLUSION

The findings of carbapenemase genes in a few isolates and small clusters of CRE indicated the emerging problems in the hospital. The high mortality rates were observed in the patients treated by colistin and tigecycline, although they were the only alternative treatment options for CRE infections. Active surveillance and an effective infection control strategy should be implemented to control the spread of CRE infections.

Novel gene cassettes and integrons in antibiotic-resistant bacteria isolated from urban wastewaters

In this study, the occurrence and diversity of integrons were evaluated in 697 isolates belonging to Enterobacteriaceae and Aeromonas spp. isolated from urban wastewaters. Screening of integrons was performed by dot blot hybridization and intI-positive strains were further characterized. The global prevalence of integrons was 3.73%. Three new gene cassettes were identified: a novel aadA variant (aadA17), a gene putatively involved in cell signaling (dcyA) and an open reading frame of unknown function interrupted by a novel insertion sequence (orfER.17::ISAs12). In total, thirteen different gene cassette arrays were detected, 4 representing novel integrons: intI1-dcyA-tniC, intI1-orfER.1.7::ISAs12-aadA13-qacEΔ1-sul1, intI1-aacA4-catB3-bla(OxA-10)-aadA1-qacEΔ1-sul1 and intI1-catB8-aadA17-qacEΔ1-sul1. Approximately 80% of strains were resistant to at least 3 antibiotics of different classes. The presence of novel integron structures in treated effluents suggests that domestic wastewaters may favor the formation of novel combinations of gene cassettes. Moreover, the high prevalence of multiresistant strains highlights the urgent need to employ effective means of effluent disinfection to avoid dissemination of antibiotic-resistant bacteria.

Current challenges in antimicrobial chemotherapy: focus on ß-lactamase inhibition

The use of the three classical beta-lactamase inhibitors (clavulanic acid, tazobactam and sulbactam) in combination with beta-lactam antibacterials is currently the most successful strategy to combat beta-lactamase-mediated resistance. However, these inhibitors are efficient in inactivating only class A beta-lactamases and the efficiency of the inhibitor/antibacterial combination can be compromised by several mechanisms, such as the production of naturally resistant class B or class D enzymes, the hyperproduction of AmpC or even the production of evolved inhibitor-resistant class A enzymes. Thus, there is an urgent need for the development of novel inhibitors. For serine active enzymes (classes A, C and D), derivatives of the beta-lactam ring such as 6-beta-halogenopenicillanates, beta-lactam sulfones, penems and oxapenems, monobactams or trinems seem to be potential starting points to design efficient molecules (such as AM-112 and LK-157). Moreover, a promising non-beta-lactam molecule, NXL-104, is now under clinical development. In contrast, an ideal inhibitor of metallo-beta-lactamases (class B) remains to be found, despite the huge number of potential molecules already described (biphenyl tetrazoles, cysteinyl peptides, mercaptocarboxylates, succinic acid derivatives, etc.). The search for such an inhibitor is complicated by the absence of a covalent intermediate in their catalytic mechanisms and the fact that beta-lactam derivatives often behave as substrates rather than as inhibitors. Currently, the most promising broad-spectrum inhibitors of class B enzymes are molecules presenting chelating groups (thiols, carboxylates, etc.) combined with an aromatic group. This review describes all the types of molecules already tested as potential beta-lactamase inhibitors and thus constitutes an update of the current status in beta-lactamase inhibitor discovery.

Design, synthesis, and crystal structures of 6-alkylidene-2'-substituted penicillanic acid sulfones as potent inhibitors of Acinetobacter baumannii OXA-24 carbapenemase

Class D β-lactamases represent a growing and diverse class of penicillin-inactivating enzymes that are usually resistant to commercial β-lactamase inhibitors. As many such enzymes are found in multi-drug resistant (MDR) Acinetobacter baumannii and Pseudomonas aeruginosa, novel β-lactamase inhibitors are urgently needed. Five unique 6-alkylidene-2'-substituted penicillanic acid sulfones (1-5) were synthesized and tested against OXA-24, a clinically important β-lactamase that inactivates carbapenems and is found in A. baumannii. Based upon the roles Tyr112 and Met223 play in the OXA-24 β-lactamase, we also engineered two variants (Tyr112Ala and Tyr112Ala,Met223Ala) to test the hypothesis that the hydrophobic tunnel formed by these residues influences inhibitor recognition. IC(50) values against OXA-24 and two OXA-24 β-lactamase variants ranged from 10 ± 1 (4 vs WT) to 338 ± 20 nM (5 vs Tyr112Ala, Met223Ala). Compound 4 possessed the lowest K(i) (500 ± 80 nM vs WT), and 1 possessed the highest inactivation efficiency (k(inact)/K(i) = 0.21 ± 0.02 μM(-1)  s(-1)). Electrospray ionization mass spectrometry revealed a single covalent adduct, suggesting the formation of an acyl-enzyme intermediate. X-ray structures of OXA-24 complexed to four inhibitors (2.0-2.6 Å) reveal the formation of stable bicyclic aromatic intermediates with their carbonyl oxygen in the oxyanion hole. These data provide the first structural evidence that 6-alkylidene-2'-substituted penicillin sulfones are effective mechanism-based inactivators of class D β-lactamases. Their unique chemistry makes them developmental candidates. Mechanisms for class D hydrolysis and inhibition are discussed, and a pathway for the evolution of the BlaR1 sensor of Staphylococcus aureus to the class D β-lactamases is proposed.

Diversity and strength of internal outward-oriented promoters in group IIC-attC introns

Integrons are genetic elements that incorporate mobile gene cassettes by site-specific recombination and express them as an operon from a promoter (Pc) located upstream of the cassette insertion site. Most gene cassettes found in integrons contain only one gene followed by an attC recombination site. We have recently shown that a specific lineage of group IIC introns, named group IIC-attC introns, inserts into the bottom strand sequence of attC sites. Here, we show that S.ma.I2, a group IIC-attC intron inserted in an integron cassette array of Serratia marcescens, impedes transcription from Pc while allowing expression of the following antibiotic resistance cassette using an internal outward-oriented promoter (P_out). Bioinformatic analyses indicate that one or two putative P_out, which have sequence similarities with the Escherichia coli consensus promoters, are conserved in most group IIC-attC intron sequences. We show that P_out with different versions of the −35 and −10 sequences are functionally active in expressing a promoterless chloramphenicol acetyltransferase (cat) reporter gene in E. coli. P_out in group IIC-attC introns may therefore play a role in the expression of one or more gene cassettes whose transcription from Pc would otherwise be impeded by insertion of the intron.

Updated functional classification of beta-lactamases

Two classification schemes for beta-lactamases are currently in use. The molecular classification is based on the amino acid sequence and divides beta-lactamases into class A, C, and D enzymes which utilize serine for beta-lactam hydrolysis and class B metalloenzymes which require divalent zinc ions for substrate hydrolysis. The functional classification scheme updated herein is based on the 1995 proposal by Bush et al. (K. Bush, G. A. Jacoby, and A. A. Medeiros, Antimicrob. Agents Chemother. 39:1211-1233, 1995). It takes into account substrate and inhibitor profiles in an attempt to group the enzymes in ways that can be correlated with their phenotype in clinical isolates. Major groupings generally correlate with the more broadly based molecular classification. The updated system includes group 1 (class C) cephalosporinases; group 2 (classes A and D) broad-spectrum, inhibitor-resistant, and extended-spectrum beta-lactamases and serine carbapenemases; and group 3 metallo-beta-lactamases. Several new subgroups of each of the major groups are described, based on specific attributes of individual enzymes. A list of attributes is also suggested for the description of a new beta-lactamase, including the requisite microbiological properties, substrate and inhibitor profiles, and molecular sequence data that provide an adequate characterization for a new beta-lactam-hydrolyzing enzyme.

Diversity, epidemiology, and genetics of class D beta-lactamases

Class D beta-lactamase-mediated resistance to beta-lactams has been increasingly reported during the last decade. Those enzymes also known as oxacillinases or OXAs are widely distributed among Gram negatives. Genes encoding class D beta-lactamases are known to be intrinsic in many Gram-negative rods, including Acinetobacter baumannii and Pseudomonas aeruginosa, but play a minor role in natural resistance phenotypes. The OXAs (ca. 150 variants reported so far) are characterized by an important genetic diversity and a great heterogeneity in terms of beta-lactam hydrolysis spectrum. The acquired OXAs possess either a narrow spectrum or an expanded spectrum of hydrolysis, including carbapenems in several instances. Acquired class D beta-lactamase genes are mostly associated to class 1 integron or to insertion sequences.

Characterization of Salmonella enterica isolates from infants and toddlers in Wuhan, China

BACKGROUND

Extended-spectrum cephalosporins and fluoroquinolones are important antimicrobials for treating invasive salmonellosis, and emerging resistance to these antimicrobials is of paramount concern. This study reports on the antimicrobial susceptibility and molecular characterization of Salmonella enterica isolates recovered in 2006 from 0- to 3-year-old outpatients in China.

METHODS

The isolates were subjected to serotyping, antimicrobial susceptibility testing, screening for beta-lactamase genes, mutations in the quinolone resistance determining regions (QRDRs), qnr alleles and aac-(6')-Ib-cr by PCR followed by DNA sequence analysis. All Salmonella Typhimurium isolates and 43 selected non-Typhimurium isolates were further characterized by PFGE to determine the genetic relatedness.

RESULTS

From 3746 paediatric outpatient stool samples, 221 (5.9%) S. enterica isolates of 29 distinct serotypes were recovered. The antimicrobial resistance profiles differed among serotypes. Ciprofloxacin-resistant isolates were concentrated in serotype Typhimurium that were resistant to at least four additional non-quinolone antimicrobials. Nineteen out of 22 ciprofloxacin-resistant Salmonella Typhimurium isolates were grouped into one PFGE cluster. Plasmid-mediated quinolone resistance determinant aac-(6')-Ib-cr was detected in 18 S. enterica isolates and 4 isolates also carried qnr alleles. Plasmid-mediated blaCTX-M-14-like genes were found in seven ceftriaxone-resistant isolates, and two isolates also exhibited reduced susceptibility to ciprofloxacin.

CONCLUSIONS

Based on these results, fluoroquinolones should not be used to treat the invasive Salmonella Typhimurium infections in this local community. The monitoring programme should stay vigilant for ceftriaxone-resistant S. enterica isolates with reduced fluoroquinolone susceptibility.

Ciprofloxacin-resistant Salmonella enterica serotype Typhimurium, China

We characterized 44 Salmonella enterica serotype Typhimurium isolates from Tongji Hospital outpatients in Wuhan, China, May 2002–October 2005. All 31 ciprofloxacin-resistant isolates were also resistant to >8 other antimicrobial drugs and carried >2 mutations in GyrA and 1 mutation in ParC. Class 1 integrons were identified in 37 isolates.