Metallo-β-lactamase inhibitors: A continuing challenge for combating antibiotic resistance

β-lactam antibiotics are the most successful and commonly used antibacterial agents, but the emergence of resistance to these drugs has become a global health threat. The expression of β-lactamase enzymes produced by pathogens, which hydrolyze the amide bond of the β-lactam ring, is the major mechanism for bacterial resistance to β-lactams. In particular, among class A, B, C and D β-lactamases, metallo-β-lactamases (MBLs, class B β-lactamases) are considered crucial contributors to resistance in gram-negative bacteria. To combat β-lactamase-mediated resistance, great efforts have been made to develop β-lactamase inhibitors that restore the activity of β-lactams. Some β-lactamase inhibitors, such as diazabicyclooctanes (DBOs) and boronic acid derivatives, have also been approved by the FDA. Inhibitors used in the clinic can inactivate mostly serine-β-lactamases (SBLs, class A, C, and D β-lactamases) but have not been effective against MBLs until now. In order to develop new inhibitors particularly for MBLs, various attempts have been suggested. Based on structural and mechanical studies of MBL enzymes, several MBL inhibitor candidates, including taniborbactam in phase 3 and xeruborbactam in phase 1, have been introduced in recent years. However, designing potent inhibitors that are effective against all subclasses of MBLs is still extremely challenging. This review summarizes not only the types of β-lactamase and mechanisms by which β-lactam antibiotics are inactivated, but also the research finding on β-lactamase inhibitors targeting these enzymes. These detailed information on β-lactamases and their inhibitors could give valuable information for novel β-lactamase inhibitors design.

Synergistic antimicrobial effect of the combination of beta-lactam antibiotics and chitosan derivative on multidrug-resistant bacteria

Dissemination of multidrug-resistant (MDR) bacteria with CTX-M-type extended-spectrum β-lactamases (blaCTX-M) has become the greatest challenge in public health care. This study aimed to investigate the synergistic antibacterial potential of N-alkylaminated chitosan nanoparticles (CNPs) combined with conventional β-lactam antibiotics (BLAs) against multidrug-resistant pathogen with blaCTX-M gene. The results of this study showed that the developed nano-formulation resensitized the studied E. coli MDR strain (E001) to ampicillin (AMP) and piperacillin (PIP) by causing a 1000-10,000-fold decrease in their MIC values (5000-50,000 mg/L to 5 mg/L). The conjugation of CNPs with cefoxitin (FOX) and ceftazidime (CAZ) showed a comparatively lower synergistic inhibitory effect owing to the higher susceptibility (MIC value = 0.5 mg/L-5 mg/L) of E001 to these antibiotics. The results indicate that CNPs could be effectively employed as an additive to augment the antibacterial effect of the BLAs for which MDR strains exhibit higher MIC values.

Prevalence of β-lactamase-encoding genes and molecular typing of Acinetobacter baumannii isolates carrying carbapenemase OXA-24 in children

Background

β-Lactam antibiotics have been broadly used for the treatment of Acinetobacter baumannii infections, resulting in development of β-lactam inactivating β-lactamases. Here, we described antibiotic resistance rate, prevalence of β-lactamase-encoding genes, and clonal relationships of A. baumannii strains isolated from children referred to Children’s Medical Center in Tehran, Iran, during 2019–2020.

Methods

A total of 60 non-replicate A. baumannii isolates were recovered from clinical specimens of pediatric patients. Antibiotic susceptibility testing was done by the disc diffusion method. Colistin susceptibility of isolates was performed by the broth microdilution method. β-lactamase-encoding genes were characterized by PCR. The presence of ISAba1 element upstream of the several oxacillinase genes was also checked. Genetic relatedness of isolates was determined by using random amplification of polymorphic DNA (RAPD) typing.

Results

The antimicrobial susceptibility tests showed that 83.3% of A. baumannii isolates were MDR, and 40% XDR. Both MDR and XDR A. baumannii isolates were susceptible to colistin. The frequency of bla_OXA-51-like, bla_OXA-23-like, bla_TEM, bla_OXA-24-like, bla_PER, bla_SHV, bla_CTX-M, bla_OXA-58-like, and bla_IMP was 100, 93.33, 60, 36.67, 28.33, 8.33, 5, 3.33, and 1.67%, respectively. Coexistence of ISAba1/bla_OXA-23-like and ISAba1/bla_OXA-51-like was observed in 65% and 85% of isolates, respectively. RAPD analysis revealed 4 common types and 2 single types of A. baumannii isolates.

Conclusions

The multiple clones harboring bla_OXA-23-like, ISAba1-bla_OXA-51-like, and ISAba1-bla_OXA-23-like were responsible for the spread of A. baumannii isolates in our clinical wards. Dissemination of the well-established clones is worrisome and would become therapeutic challenges due to the possible transferring genetic elements associated with resistance.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12941-021-00480-5.

Destination shapes antibiotic resistance gene acquisitions, abundance increases, and diversity changes in Dutch travelers

BACKGROUND

Antimicrobial-resistant bacteria and their antimicrobial resistance (AMR) genes can spread by hitchhiking in human guts. International travel can exacerbate this public health threat when travelers acquire AMR genes endemic to their destinations and bring them back to their home countries. Prior studies have demonstrated travel-related acquisition of specific opportunistic pathogens and AMR genes, but the extent and magnitude of travel's effects on the gut resistome remain largely unknown.

METHODS

Using whole metagenomic shotgun sequencing, functional metagenomics, and Dirichlet multinomial mixture models, we investigated the abundance, diversity, function, resistome architecture, and context of AMR genes in the fecal microbiomes of 190 Dutch individuals, before and after travel to diverse international locations.

RESULTS

Travel markedly increased the abundance and α-diversity of AMR genes in the travelers' gut resistome, and we determined that 56 unique AMR genes showed significant acquisition following international travel. These acquisition events were biased towards AMR genes with efflux, inactivation, and target replacement resistance mechanisms. Travel-induced shaping of the gut resistome had distinct correlations with geographical destination, so individuals returning to The Netherlands from the same destination country were more likely to have similar resistome features. Finally, we identified and detailed specific acquisition events of high-risk, mobile genetic element-associated AMR genes including qnr fluoroquinolone resistance genes, blaCTX-M family extended-spectrum β-lactamases, and the plasmid-borne mcr-1 colistin resistance gene.

CONCLUSIONS

Our results show that travel shapes the architecture of the human gut resistome and results in AMR gene acquisition against a variety of antimicrobial drug classes. These broad acquisitions highlight the putative risks that international travel poses to public health by gut resistome perturbation and the global spread of locally endemic AMR genes.

Detection of multi-drug resistance and AmpC β-lactamase/extended-spectrum β-lactamase genes in bacterial isolates of loggerhead sea turtles (Caretta caretta) from the Mediterranean Sea

Sea turtles are useful sentinels to monitor the dissemination of antimicrobial resistance (AMR) in the marine coastal ecosystems. Forty Gram negative bacteria were isolated from wounds of 52 injured Caretta caretta, living in the Mediterranean Sea. Bacteria were identified using 16S rRNA gene sequencing and tested for susceptibility to 15 antibiotics. In addition, NGS amplicon sequencing was performed to detect the presence of AmpC β-lactamase genes (bla_AmpC) and extended-spectrum β-lactamase (ESBL) genes (bla_CTX-M,bla_SHV,bla_TEM). Seventy-five percent of the isolates (30/40 isolates) exhibited multidrug resistance (MDR) phenotypes and 32.5% (13/40 isolates) were confirmed to be positive for at least one gene. The variants of ESBLs genes were bla_CTX-M-3,bla_TEM-236 and bla_SHV-12. Variants of the bla_AmpCβ-lactamase gene i.e., bla_ACT-24, bla_ACT-2, bla_ACT-17, bla_DHA-4 and bla_CMY-37, were also detected. In addition, 4 isolates were found simultaneously harboring CTX and AmpC genes while 2 strains harbored 3 genes (bla_{ACT-2+TEM-236+SHV-12}, and bla_{CTX-M-3+ACT-24+TEM-236}).

Diversity of L1/L2 genes and molecular epidemiology of high-level carbapenem resistance Stenotrophomonas maltophilia isolates from animal production environment in China

Stenotrophomonas maltophilia is emerging as a significant cause of human and animal disease worldwide. A total of 3400 samples were collected from animal farms and adjacent environments in China. The bla_L1 and bla_L2 genes were identified using whole genome sequence analyses and examined by phylogenetics. Isolates were also tested for susceptibility to 18 antibiotics. We isolated 118 strains of S. maltophilia from 3400 samples. The positive rates of bla_L1 and bla_L2 genes were 75% (89/118) and 22% (26/118) and we identified 11 L1 and 6 L2 amino acid sequence variants. S. maltophilia has at least two inducible β-lactamases (L1 and L2) that can hydrolyze almost all classes of β-lactams and these genes are suspected to confer carbapenem resistance. This represents a significant public health threat especially for hospitalized patients. We conducted a molecular surveillance study on the prevalence and characteristics of the bla_L1 and bla_L2 genes of S. maltophilia.

Co-harboring of mcr-1 and β-lactamase genes in Pseudomonas aeruginosa by high-resolution melting curve analysis (HRMA): Molecular typing of superbug strains in bloodstream infections (BSI)

Background Colistin resistance in P. aeruginosa (CRPA) is due to the appearance of superbug strains. As this pathogen gains more transferrable resistance mechanisms and continues to adapt to acquire additional resistance mechanisms during antimicrobial therapy rapidly, we face the growing threat of CRPA in bloodstream infections (BSI). This study designed to evaluate the frequency of CRPA strains producing different β-lactamases by the High-Resolution Melting Curve Analysis (HRMA) method in BSI and to characterize the different types by multilocus sequence typing (MLST).

MATERIAL AND METHODS

Sixty-nine (69) P. aeruginosa isolates were collected from blood culture. MIC E-test methods examined the antimicrobial susceptibilities of the bacterial isolates. Detection of resistant strains performed by using HRMA assay.

RESULTS

The strains resistant to amikacin (n = 11; 15.94%) and colistin (n = 10; 14.49%) were the least abundant and the gentamicin (n = 56; 82.6%) and ciprofloxacin (n = 67; 97.10%) resistant strains were the most frequent. Also, 39 isolates (56.52%) considered as multidrug-resistant (MDR), 20 isolates (28.98%) as extensively drug resistant (XDR), and 11 isolates (15.94%) as Pandrug Resistance (PDR). Further, 32 isolates (46.37%) considered as AmpC producer, and 28 isolates (40.57%) were considered an MBL producer. According to HRMA results, the blaSPM gene was detected in 19 isolates (27.53%), blaNDM gene in 11 isolates (15.94%), blaFOX gene in 31 isolates (44.92%), mcr-1 gene in 10 isolates (14.49%), blaACC and blaVIM genes in 27 isolates (39.13%), and blaTEM gene was reported in 20 isolates (28.98%). Furthermore, P. aeruginosa PASGNDM699, ST3340, and ST235 identified in 1.44%, 11.59% and 17.39% isolates, respectively.

CONCLUSION

CRPA strains play an essential role in the spread of antibiotic resistance in BSI. Likewise, the HRMA method was sensitive and specific for the detection of superbugs. Moreover, MLST analysis of a diverse collection of P. aeruginosa from blood culture suggests that particular strains or clonal complexes are associated with antibiotic resistance profile.

Occurrence and abundance of clinically relevant antimicrobial resistance genes in environmental samples after the Brumadinho dam disaster, Brazil

On January 25th 2019, the structure damming a pond containing ore mining wastes and iron burst at Brumadinho City, Brazil. About 11.7 million m³ of a tailings-mud mixture was released from the dam, causing destruction along 300 km of the Paraopeba River toward the São Francisco River. The environments with a high content of metals may provide a suitable environment for horizontal gene transfer, including antimicrobial resistance genes (ARGs). Therefore, this study aimed to detect and quantify clinically relevant ARGs in environmental samples after the Brumadinho dam disaster. Soil, sediment, and water samples were collected within 300 km of the Brumadinho dam disaster at unaffected and affected sites. Physical-chemical parameters of water samples were measured. Total DNA was extracted and 65 clinically relevant ARGs were researched by PCR. The most prevalent ARGs were selected for real-time quantitative PCR analysis. The average of the physical-chemical parameters was higher in the affected sites when compared to the unaffected sites, especially turbidity, concentration of Fe and Al. A total of 387 amplicons from 29 ARGs were detected, which confer resistance to β-lactams, quinolones, aminoglycosides, tetracyclines, sulphonamides, phenicols, macrolides, glycopeptides, and polymyxins, including extended-spectrum β-lactamases-encoding genes, and mcr-7.1. The sul1 gene had higher total concentrations than bla_TEM, tetB and qnrB in the environmental samples, and the diversity and abundance of ARGs increased at the sites affected by the Brumadinho dam disaster. Therefore, we point out that the contamination by the Brumadinho dam disaster tailings resulted in an increase in the amount and abundance of ARGs in the environment.

Identification of a multiple drug-resistance gene island in the Haemophilus parasuis chromosome

OBJECTIVES

The aim of this study was to determine the mechanisms and molecular characterisation of one strain (HPS412) of Haemophilus parasuis, which exhibited high MICs of antimicrobial susceptibility.

METHODS

A total of 113 H. parasuis strains isolated from pigs suffering from polyserositis, pneumonia or meningitis in China and screened them for antimicrobial susceptibility. Susceptibility testing of the minimal inhibitory concentrations (MIC) was determined in fastidious medium consisting of tryptone soya broth (TSB) containing 5% bovine serum and 10μg/mL NAD in 96-well microtiter plates. The genomic DNA was completely sequenced by combining PacBio RS II and Illumina HiSeq 4000 platforms. Gene prediction was performed using Glimmer v.3.02 with Hidden Markov models.

RESULTS

One strain (HPS412) exhibited high MICs of sulfamethoxazole (256μg/mL), tetracycline (128μg/mL), streptomycin (128μg/mL), gentamicin (128μg/mL), amoxicillin (128μg/mL), chloramphenicol (64μg/mL), penicillin (64μg/mL) and cefaclor (64μg/mL). Sequence analysis showed that numerous drug-resistance genes including tet(B), bla_ROB-1, sul2, catIII, aph(3″)-Ib, aph(6)-Id and aph(3')-Ia were present in a chromosomal gene island as adjacent duplicate copies and the rep-orf3-bla_ROB-1 structure most likely had a direct plasmid origin. The tet(B) and bla_ROB-1 were flanked on one or both by ISApl1 elements.

CONCLUSIONS

The acquisition of bla_ROB-1 and the other antibiotic resistance genes was related to the presence of ISApl1. ISApl1 plays important roles in the horizontal transmission of antibiotic resistance genes.

Fecal cultivable aerobic microbiota of dairy cows and calves acting as reservoir of clinically relevant antimicrobial resistance genes

Antimicrobial resistance has become a global threat to public health since multidrug-resistant (MDR) bacteria have been reported worldwide carrying different antimicrobial resistance genes (ARGs), and animals have been described as a reservoir of ARGs. The presence of antimicrobial-resistant bacteria and ARGs in the food matrix is a risk to public health. This study aimed to research the presence of clinically relevant ARGs for important antimicrobials and genetic elements in fecal samples from dairy cows and calves on a Brazilian farm. In this study, a total of 21 fecal samples were collected, and then, the DNA of cultivable aerobic bacteria was extracted. Fifty-seven ARGs and twenty-three genetic elements were researched by PCR and confirmed by sequencing. Several ARGs that confer resistance to β-lactams, tetracyclines, fluoroquinolones, sulphonamides, phenicols, aminoglycoside, glycopeptides, and macrolides were detected. A total of 200 amplicons from 23 ARGs (bla_CTX-M-Gp2, bla_CMY, bla_SHV, tetA, tetB, tetC, qepA, qnrB, qnrS, oqxA, oqxB, vanC1, vanC2/3, aadA, sul1, sul2, sul3, ermB, mefAE, floR, cmlA, aadA, aph(3')-Ia, aac(3')-Ia), and 145 amplicons from 12 genetic elements (IncF, IncFIA, IncFIB, IncI1, IncY, IncU, IncK, IncP, IncR, IncHI1, ColE-like, intI1) were detected. The results presented in this study call attention to the monitoring of antimicrobial resistance in dairy farms worldwide. MDR bacteria and ARGs can spread to different sources, including milk products, which are one of the most consumed products worldwide, representing a potential risk to human health.

Neonatal outcomes associated with maternal recto-vaginal colonization with extended-spectrum β-lactamase producing Enterobacteriaceae in Nigeria: a prospective, cross-sectional study

OBJECTIVES

The objective of this study was to assess the prevalence of maternal recto-vaginal extended-spectrum β-lactamase producing Enterobacteriacea (ESBL-E) colonization, identify risk factors for maternal and neonatal ESBL-E colonization, and subsequent impact on neonatal mortality.

METHODS

A prospective, cross-sectional study was conducted at the University of Abuja Teaching Hospital from April 2016 to May 2017. Maternal-neonatal pairs were screened for ESBL-E exposure at time of delivery. Neonatal mortality was assessed at 28 days.

RESULTS

A total of 1161 singleton deliveries were evaluated. In total, 9.7% (113/1161) of mothers and 4.3% (50/1161) of infants had ESBL-E-positive cultures at delivery. Maternal antibiotic exposure was associated with ESBL-E recto-vaginal colonization (18.6% (21/113) vs. 8.4% (88/1048), p < 0.001)). Maternal ESBL-E colonization (adjusted odds ratio (AOR) 14.85; 95% CI 7.83-28.15) and vaginal delivery (AOR 6.35; 95% CI 2.63-17.1) were identified as a risk factor for positive ESBL-E neonatal surface cultures. Neonatal positive ESBL-E surface cultures were a risk factor for neonatal mortality (stillbirths included, AOR 4.84; 95% CI 1.44-16.31). The finding that maternal ESBL-E recto-vaginal colonization appeared protective in regards to neonatal mortality (AOR 0.22; 95% CI .06-0.75) requires further evaluation.

CONCLUSIONS

Maternal ESBL-E recto-vaginal colonization is an independent risk factor for neonatal ESBL-E colonization and neonates with positive ESBL-E surface cultures were identified as having increased risk of neonatal mortality.

A cluster of carbapenemase-producing Enterobacter cloacae complex ST171 at a tertiary care center demonstrating an ongoing regional threat

BACKGROUND

In Minnesota and North Dakota, a clonal strain of bla_KPC-3-producing Enterobacter cloacae complex has been reported with increasing frequency.

METHODS

Between July 2015 and February 2016, 13 carbapenem-resistant E. cloacae complex isolates were identified at our institution. Five bla_KPC-positive isolates were identified by polymerase chain reaction and underwent pulsed-field gel electrophoresis and whole genome sequencing. Medical records of these patients were reviewed.

RESULTS

All 5 case-isolates belonged to sequence type 171 and were bla_KPC-3-positive. Three pulsed-field gel electrophoresis patterns with >90% similarity were identified in the 5 case-isolates. We identified overlaps in time and location between case patients. Plasmid types and resistance genes were nearly identical between the isolates. Whole genome sequencing showed isolates A, B, and D to be closely related with <10 core single-nucleotide polymorphisms differences. Isolates C and E were also closely related to each other, but more distantly to A, B, and D; all belonged to the clonal lineage of the major circulating E. cloacae complex strain in Minnesota and North Dakota. Despite having overlapping hospital stays, isolates for patients C and D were not identical.

CONCLUSIONS

Isolates A and D were nearly identical, indicating possible transmission during hospitalization. Transmission of the other isolates may have occurred elsewhere. This report highlights the importance of using both epidemiologic and molecular data to track the spread of carbapenemase-producers.

Linear gold(I) complex with tris-(2-carboxyethyl)phosphine (TCEP): Selective antitumor activity and inertness toward sulfur proteins

The search for modulating ligand substitution reaction in gold complexes is essential to find new active metallo compounds for medical applications. In this work, a new linear and hydrosoluble gold^I complex with tris-(2-carboxyethylphosphine) (AuTCEP). The two phosphines coordinate linearly to the metal as solved by single crystal X-ray diffraction. Complete spectroscopic characterization is also reported. In vitro growth inhibition (GI₅₀) in a panel of nine tumorigenic and one non-tumorigenic cell lines demonstrated the complex is highly selective to ovarium adenocarcinoma (OVCAR-03) with GI₅₀ of 3.04 nmol mL^-1. Moreover, non-differential uptake of AuTCEP was observed between OVCAR-03 (tumor) and HaCaT (non-tumor) two cell lines. Biophysical evaluation with the sulfur-rich biomolecules showed the compound does not interact with two types of zinc fingers, bovine serum albumin, N-acetyl-l-cysteine and also l-histidine, revealing to be inert to ligand substitution reactions with these molecules. However, AuTCEP demonstrated to cleave plasmidial DNA, suggesting DNA as a possible target. No antibacterial activity was observed in the strains evaluated. Besides, it inhibits 15% of the activity of a mixture of serine-β-lactamase and metallo-β-lactamase from Bacillus cereus in the enzymatic activity assay, similarly to EDTA. These results suggest AuTCEP is selective to metallo-β-lactamase but the cell uptake is hindered, and the compound does not reach the periplasmic space of Gram-positive bacteria. The unique inert behavior of AuTCEP is interesting and represent the modulation of the reactivity through coordination chemistry to decrease the toxicity associated with Au^I complexes and its lack of specificity, generating very selective compounds with unexpected targets.

The Growing Threat of Antibiotic Resistance in Children

Antimicrobial resistance is a global public health threat and a danger that continues to escalate. These menacing bacteria are having an impact on all populations; however, until recently, the increasing trend in drug-resistant infections in infants and children has gone relatively unrecognized. This article highlights the current clinical and molecular data regarding infection with antibiotic-resistant bacteria in children, with an emphasis on transmissible resistance and spread via horizontal gene transfer.

Optimization of novel monobactams with activity against carbapenem-resistant Enterobacteriaceae - Identification of LYS228

Metallo-β-lactamases (MBLs), such as New Delhi metallo-β-lactamase (NDM-1) have spread world-wide and present a serious threat. Expression of MBLs confers resistance in Gram-negative bacteria to all classes of β-lactam antibiotics, with the exception of monobactams, which are intrinsically stable to MBLs. However, existing first generation monobactam drugs like aztreonam have limited clinical utility against MBL-expressing strains because they are impacted by serine β-lactamases (SBLs), which are often co-expressed in clinical isolates. Here, we optimized novel monobactams for stability against SBLs, which led to the identification of LYS228 (compound 31). LYS228 is potent in the presence of all classes of β-lactamases and shows potent activity against carbapenem-resistant isolates of Enterobacteriaceae (CRE).

Extended Spectrum Beta-Lactamase (ESBL)-producing bacteria isolated from hospital wastewaters, rivers and aquaculture sources in Nigeria

Untreated wastewater is a risk factor for the spread of antibiotic resistance in the environment. However, little is known about the contribution of untreated wastewater to the burden of antibiotic resistance in the Nigerian environment. In this study, a total of 143 ceftazidime-/cefpodoxime-resistant bacteria isolated from untreated wastewater and untreated wastewater-contaminated surface and groundwater in Nigeria were screened for extended-spectrum β-lactamase (ESBL) genes, integrons and integron gene cassettes by PCR. The genetic environment of bla _CTX-M-15 was mapped by PCR and potentially conjugative plasmids were detected among the isolates by degenerate primer MOB typing (DPMT). ESBL production was confirmed in 114 (79.7%) isolates and ESBL genes (bla _SHV, bla _CTX-M-15 and bla _TEM) were detected in 85 (74.6%) ESBL-producing isolates. bla _CTX-M-15 was associated with ISEcp1 and with orf477 in 12 isolates and with ISEcp1, IS26 and orf477 in six others. To the best of our knowledge, this is the first report of bla _CTX-M-15 in hand-dug wells and borehole serving as sources of drinking water and a first report of the genetic environment of bla _CTX-M-15 in environmental bacteria from Nigeria. The results of this study confirm untreated wastewater as an important medium for the spread of ESBL-producing bacteria within the Nigerian environment. Hence, the widespread practice of discharging untreated wastewater into the aquatic ecosystem in Nigeria is a serious risk to public health.

Occurrence of Enterobacter hormaechei carrying blaNDM-1 and blaKPC-2 in China

Three carbapenem-resistant clinical isolates of the Enterobacter cloacae complex (ECC) were recovered from different patients in a hospital. All 3 isolates carried 2 carbapenemase genes bla_KPC-2 and bla_NDM-1. A study was performed to characterize their relatedness and to investigate possible links among the patients. Whole genome sequencing revealed that the isolates were Enterobacter hormaechei and belonged to ST177 of the ECC. There were 19-142 single nucleotide polymorphisms (SNPs) between the isolates, suggesting that the isolates were likely from a central reservoir, which might have existed for some time. bla_KPC-2 and bla_NDM-1 were carried on 2 different IncF-type plasmids in the isolates. The 3 bla_NDM-1-carrying plasmids were almost identical and were self-transmissible, while the bla_KPC-2-carrying plasmids were only transmissible in the presence of the bla_NDM-1-carrying plasmid. The source of and direct links among them were not identified, suggesting a hospital transmission of a common multidrug resistant strain.

Spread of multidrug-resistant high-risk Klebsiella pneumoniae clones in a tertiary hospital from southern Brazil

Klebsiella pneumoniae is among the most important pathogens found in hospitals. The emergence of multiple antibiotic resistant K. pneumoniae associated with its virulence factors is a worldwide concern and its early identification is crucial, especially for controlling the spread of emerging clones. This article reports a high prevalence of multiresistant K. pneumoniae in a university hospital in southern Brazil, harboring several virulence and β-lactamase encoding genes, including pandrug-resistant high-risk international clones belonging to the clonal group 258 (ST11, ST15, ST101, ST258, ST340 and ST874).

New β-Lactamase Inhibitors in the Clinic

Given the serious medical burden of β-lactamases, many approaches are being used identify candidate agents for β-lactamase inhibition. Here, we review two β-lactam-β-lactamase inhibitor (BL-BLI) combinations, ceftolozane-tazobactam and ceftazidime-avibactam that recently entered the clinic. In addition, we focus on BL-BLI combinations in preclinical development that have demonstrated activity in clinical isolates via susceptibility testing and/or in in vivo models of infection. We highlight only the BLIs that are able to reduce the Clinical Laboratory Standards Institute (CLSI) breakpoints for the BL partner into the susceptible range. Our analysis includes the primary literature, meeting abstracts, as well as the patent literature.

Structure and Functional Characterisation of a Distinctive β-Lactamase from an Environmental Strain EMB20 of Bacillus cereus

The rampant use and misuse of antibiotics in human medicine, agriculture and veterinary have become the key contributors to global antimicrobial resistance. One of the significant resistance mechanisms that inactivates antibiotics and impedes treatment of bacterial infections is the expression of β-lactamases. Rising evidence of newer variants of β-lactamases in the environment is therefore a serious threat to the presently available antibiotic armoury. The present work describes the purification of a variant β-lactamase isolated from a soil strain EMB20 of Bacillus cereus. The lactamase was purified using three-phase partitioning and gel filtration chromatography to a 30-fold purification and 15% recovery yield. Contrary to the general trend, the lactamase was not a metalloenzyme, but its activity was enhanced in the presence of Mg²⁺ and Mn²⁺. The EMB20 lactamase exhibited improved stability against inhibitors and denaturing agents such as urea and GdmCl as compared to its commercial analogue. The improved stability of EMB20 lactamase was further validated by circular dichroism and fluorescence spectroscopy. This study reemphasizes the rising prevalence of environmental lactamase variants. Decoding the structure-function correlation of such lactamases in the presence of inhibitors will provide insights into the response of this enzyme towards inhibitors as well as its substrates.

Enhanced identification of β-lactamases and its classes using sequence, physicochemical and evolutionary information with sequence feature characterization of the classes

β-lactamases provides one of the most successful means of evading the therapeutic effects of β lactam class of antibiotics by many gram positive and gram negative bacteria. On the basis of sequence identity, β-lactamases have been identified into four distinct classes- A, B, C and D. The classes A, C and D are the serine β-lactamases and class B is the metallo-lactamse. In the present study, we developed a two stage cascade classification system. The first-stage performs the classification of β-lactamases from non-β-lactamases and the second-stage performs the further classification of β-lactamases into four different β-lactamase classes. In the first-stage binary classification, we obtained an accuracy of 97.3% with a sensitivity of 89.1% and specificity of 98.0% and for the second stage multi-class classification, we obtained an accuracy of 87.3% for the class A, 91.0% for the class B, 96.3% for the class C and 96.4% for class D. A systematic statistical analysis is carried out on the sieved-out, correctly-predicted instances from the second stage classifier, which revealed some interesting patterns. We analyzed different classes of β-lactamases on the basis of sequence and physicochemical property differences between them. Among amino acid composition, H, W, Y and V showed significant differences between the different β-lactamases classes. Differences in average physicochemical properties are observed for isoelectric point, volume, flexibility, hydrophobicity, bulkiness and charge in one or more β-lactamase classes. The key differences in physicochemical property groups can be observed in small and aromatic groups. Among amino acid property group n-grams except charged n-grams, all other property group n-grams are significant in one or more classes. Statistically significant differences in dipeptide counts among different β-lactamase classes are also reported.

Enhancement of antibiotic-activity through complexation with metal ions - Combined ITC, NMR, enzymatic and biological studies

Alternative solutions need to be developed to overcome the growing problem of multi-drug resistant bacteria. This study explored the possibility of creating complexes of antibiotics with metal ions, thereby increasing their activity. Analytical techniques such as isothermal titration calorimetry and nuclear magnetic resonance were used to examine the structure and interactions between Cu(II), Ag(I) or Zn(II) and β-lactam antibiotics. The metal-β-lactam complexes were also tested for antimicrobial activity, by micro-broth dilution and disk diffusion methods, showing a synergistic increase in the activity of the drugs, and enzymatic inhibition assays confirming inhibition of β-lactamases responsible for resistance. The metal-antibiotic complex concept was proven to be successful with the activity of the drugs enhanced against β-lactamase-producing bacteria. The highest synergistic effects were observed for complexes formed with Ag(I).

Rapid screening for antibiotic resistance elements on the RNA transcript, protein and enzymatic activity level

Background

The emerging threat posed by antibiotic resistance has affected public health systems all over the world. Surveillance of resistant bacteria in clinical settings and identifying them in mixed cultures is of paramount importance and can contribute to the control of their spreading. Culture-independent monitoring approaches are highly desirable, since they yield results much faster than traditional susceptibility testing. However, many rapid molecular methods like PCR only detect the sole presence of a potential resistance gene, do not provide information regarding efficient transcription, expression and functionality and, in addition, cannot assign resistance genes to species level in mixed cultures.

Methods

By using plasmid-encoded TEM β-lactamase mediated ampicillin resistances as a proof of principle system, we (1) developed a fluorescence in situ hybridization-test (FISH) capable to detect the respective mRNAs, (2) implemented an immunofluorescence test to identify the corresponding proteins and (3) compared these two microscopic tests with an established colorimetric nitrocefin assay to assess the enzymatic activity.

Results

All three methods proved to be suitable for the testing of antibiotic resistance, but only FISH and immunofluorescence were able to differentiate between susceptible and resistant bacteria on the single cell level and can be combined with simultaneous species identification.

Conclusions

Fluorescence in situ hybridization and immunofluorescence tests are promising techniques in susceptibility testing since they bridge the gap between the slow, but accurate and sound cultural methods and molecular detection methods like PCR with much less functional relevance.

Electronic supplementary material

The online version of this article (doi:10.1186/s12941-016-0167-8) contains supplementary material, which is available to authorized users.

[Prevalence and risk factors for extended-spectrum β-lactamase-producing Escherichia coli causing community-onset urinary tract infections in Colombia]

INTRODUCTION

Urinary tract infections (UTI) are common in the community. However, information of resistant isolates in this context is limited in Latin America. This study aims to determine the prevalence and risk factors associated with community-onset UTI (CO-UTI) caused by extended-spectrum β-lactamase (ESBL)-Producing Escherichia coli in Colombia.

MATERIALS AND METHODS

A case-control study was conducted between August and December of 2011 in three Colombian tertiary-care institutions. All patients who were admitted to the Emergency Department with a probable diagnosis of CO-UTI were invited to participate. All participating patients were asked for a urine sample. ESBL confirmatory test, antibiotic susceptibility, and molecular epidemiology were performed in these E.coli isolates (Real Time-PCR for bla genes, repetitive element palindromic PCR [rep-PCR], multilocus sequence typing [MLST] and virulence factors by PCR). Clinical and epidemiological information was recorded, and a statistical analysis was performed.

RESULTS

Of the 2124 recruited patients, 629 had a positive urine culture, 431 of which grew E.coli; 54 were positive for ESBL, of which 29 were CTX-M-15. The majority of ESBL isolates were susceptible to ertapenem, phosphomycin and amikacin. Complicated UTI was strongly associated with ESBL-producing E.coli infections (OR=3.89; 95%CI: 1.10-13.89; P=.03). CTX-M-15-producing E.coli showed 10 different pulsotypes, 65% were PT1 or PT4, and corresponded to ST131. Most of these isolates had 8 out of the 9 analysed virulence factors.

DISCUSSION

E.coli harbouring bla_CTX-M-15 associated with ST131 is still frequent in Colombia. The presence of complicated CO-UTI increases the risk of ESBL-producing E.coli, and must be taken into account in order to provide an adequate empirical therapy.

Carbapenem-resistant Klebsiella pneumoniae isolates from Egypt containing blaNDM-1 on IncR plasmids and its association with rmtF

OBJECTIVES

The aim of this study was to characterize carbapenem-resistant Klebsiella pneumoniae (CRKP) isolates recovered from clinical specimens at a tertiary care hospital in Egypt over a period of 15 months.

METHODS

Eight CRKP isolates were included in this study. The minimum inhibitory concentrations of different antibiotics were determined by broth microdilution and Etest methods. Multilocus sequence typing was performed. Antibiotic resistance genes were assessed by PCR and DNA sequencing. Plasmid analysis was done by S1 nuclease digestion of whole genomic DNA followed by pulsed-field gel electrophoresis (S1-PFGE).

RESULT

Eight carbapenem-resistant NDM-1-producing K. pneumoniae isolates of three different sequence types (ST) were identified (ST147, ST11, and ST17), in which blaNDM-1 was carried by either IncR or untypeable plasmids. Seven out of the eight isolates also contained the rmtF methylase gene.

CONCLUSION

This study describes the occurrence of IncR plasmids carrying blaNDM-1 and rmtF in Egypt, raising concerns regarding this type of replicon and its role in the transmission of these resistance determinants.

Detection and Genetic Characterization of Metallo-β-Lactamase IMP-1 and VIM-2 in Pseudomonas aeruginosa Strains From Different Hospitals in Kermanshah, Iran

Background:

Pseudomonas aeruginosais a frequent nosocomial pathogen that causes severe diseases in many settings. Carbapenems, including meropenem and imipenem, are effective antibiotics against this organism. However, the use of carbapenems has been hampered by the emergence of strains resistant to carbapenemsvia different mechanisms such as the production of metallo-β-lactamases (MBLs), which hydrolyze all carbapenems. Several kinds of MBLs have been reported, among them VIM and IMP types being the most clinically significant carbapenemases.

Objectives:

We aimed to determine the distribution of bla_VIM-2 and bla_IMP-1 transferable genes encoding MBLs in P. aeruginosa isolated from three academic hospitals in Kermanshah.

Patients and Methods:

From 22nd June to 22nd September 2012, 225 isolates of P. aeruginosa were collected. These isolates were tested for antibiotic susceptibility with the Kirby-Bauer disk-diffusion method, and the MBLs were assessed using the imipenem-EDTA double-disk synergy test. The isolates were investigated for bla_VIM-2 and bla_IMP-1 genes using polymerase chain reaction.

Results:

Among the 225 isolates, 33.7% (76/225) and 18.1% (41/225) were resistant to imipenem and meropenem, respectively. Of the 76 imipenem-resistant P. aeruginosa strains, 45 (59.2%) were positive for MBLs, 34 (75%) strains carried the bla_IMP-1 gene, and 1 (2.2%) strain carried the bla_VIM-2 gene.

Conclusions:

Our results showed that there was a high frequency of IMP-1 positive P. aeruginosa in the different wards of the hospitals.

Isolation and in silico characterization of novel esterase gene with β-lactamase fold isolated from metagenome of north western Himalayas

An esterase-producing clone Aph2 was isolated from the Apharwat soil metagenomic library, a mountain peak in NW Himalayas. ORF 2 (Est Ac) of clone Aph2 corresponds to 271 aa protein and showed 26 % sequence similarity to carboxylesterase gene of Synechococcus sp. JA-2-3B. Est Ac contains nucleophilic Ser in S68-X-X-K71 motif of β-lactamases with Tyr Y103. The conserved sequences are common with family VIII carboxylesterase and class C β-lactamase sequences. Phylogenetic analysis revealed that Est Ac sequence is closely related to esterase than to β-lactamases. In silico 3D protein structure of Est Ac was generated using MODELLER software (9.10 version). Model was generated on the basis of carboxylesterase template (PDB:1CI8) of Est B (Burkholderia gladioli) and the stereochemical parameters of the model generated were satisfactory. Docking with diisopropyl-fluorophosphate confirmed catalytic activity of Ser68 present in S-X-X-K motif.

Molecular characterization of quinolone resistance mechanisms and extended-spectrum β-lactamase production in Escherichia coli isolated from dogs

The increasing prevalence of antimicrobial resistances is now a worldwide problem. Investigating the mechanisms by which pets harboring resistant strains may receive and/or transfer resistance determinants is essential to better understanding how owners and pets can interact safely. Here, we characterized the genetic determinants conferring resistance to β-lactams and quinolones in 38 multidrug-resistant Escherichia coli isolated from fecal samples of dogs, through PCR and sequencing. The most frequent genotype included the β-lactamase groups TEM (n=5), and both TEM+CTX-M-1 (n=5). Within the CTX-M group, we identified the genes CTX-M-32, CTX-M-1, CTX-M-15, CTX-M-55/79, CTX-M-14 and CTX-M-2/44. Thirty isolates resistant to ciprofloxacin presented two mutations in the gyrA gene and one or two mutations in the parC gene. A mutation in gyrA (reported here for the first time), due to a transversion and transition (TCG→GTG) originating a substitution of a serine by a valine in position 83 was also detected. The plasmid-encoded quinolone resistance gene, qnrs1, was detected in three isolates. Dogs can be a reservoir of genetic determinants conferring antimicrobial resistance and thus may play an important role in the spread of antimicrobial resistance to humans and other co-habitant animals.

Acquisition of extended-spectrum cephalosporin- and colistin-resistant Salmonella enterica subsp. enterica serotype Newport by pilgrims during Hajj

Gatherings like the Hajj involving many people who travel from different parts of the world represent a risk for the acquisition and dissemination of infectious diseases. In this study, acquisition of multidrug-resistant (MDR) Salmonella spp. in 2013 Hajj pilgrims from Marseille, France, was investigated. In total, 267 rectal swabs were collected from 129 participants before their departure and after their return from the pilgrimage as well as during the pilgrimage from patients with diarrhoea. Samples were screened for the presence of Salmonella using quantitative real-time PCR and culture. Whole-genome sequencing was performed to characterise one of the isolates, and the mechanism leading to colistin resistance was investigated. Six post-Hajj samples and one sample collected during a diarrhoea episode in Hajj were positive for Salmonella by real-time PCR, with five Salmonella enterica belonging to several serotypes recovered by culture, whereas no pre-Hajj sample was positive. Two of the isolates belonged to the epidemic Newport serotype, were resistant to cephalosporins, gentamicin and colistin, and harboured the bla(CTX-M-2) gene and a 12-nucleotide deletion in the pmrB gene leading to colistin resistance. This study shows that pilgrims acquired Salmonella bacteria, including a novel MDR clone, during the Hajj pilgrimage. This calls for more improved public health surveillance during Hajj because Salmonella is one of the most common diarrhoea-causing bacteria worldwide. Therefore, returning pilgrims could disseminate MDR bacteria worldwide upon returning to their home countries.

Extended-Spectrum β-Lactamase-Producing and Third-Generation Cephalosporin-Resistant Enterobacteriaceae in Children: Trends in the United States, 1999-2011

BACKGROUND

Enterobacteriaceae infections resistant to extended-spectrum β-lactams are an emerging problem in children. We used a large database of clinical isolates to describe the national epidemiology of extended-spectrum β-lactamase (ESBL)-producing and third-generation cephalosporin-resistant (G3CR) Enterobacteriaceae.

METHODS

Antimicrobial susceptibilities of Klebsiella pneumoniae, Escherichia coli, and Proteus mirabilis reported to ∼300 laboratories participating in The Surveillance Network (TSN) between January 1999 and December 2011 were used to phenotypically identify G3CR and ESBL isolates cultured from patients <18 years. Bi-annual trends in the prevalence of each phenotype were stratified by species, patient location, culture site, age, and region. Children of age 0-1 years were excluded from analysis as data were only available from 2010 onwards.

RESULTS

Out of 368,398 pediatric isolates, 1.97% (7255) were identified as G3CR, and 0.47% (1734) as ESBL producers. The prevalence of both phenotypes increased, respectively, from 1.39% and 0.28% in 1999-2001 to 3% and 0.92% in 2010-2011. Trends were significant across all demographic and age groups, including outpatients, with the highest proportion of isolates in the 1-5-year-old age group. The majority of G3CR and ESBL isolates were E. coli (67.8% and 65.2%, respectively). Among ESBLs, resistance to ≥3 antibiotic classes was 74%. The lower regional prevalence of ESBL-producing bacteria in the upper Midwest relative to the rest of the country is consistent with recent local data.

CONCLUSIONS

Rates of G3CR and ESBL infections in children are increasing in both inpatient and ambulatory settings nationally. The identification of host factors and exposures leading to infection in children is essential.

Mechanisms of β-lactam antimicrobial resistance and epidemiology of major community- and healthcare-associated multidrug-resistant bacteria

Alexander Fleming's discovery of penicillin heralded an age of antibiotic development and healthcare advances that are premised on the ability to prevent and treat bacterial infections both safely and effectively. The resultant evolution of antimicrobial resistant mechanisms and spread of bacteria bearing these genetic determinants of resistance are acknowledged to be one of the major public health challenges globally, and threatens to unravel the gains of the past decades. We describe the major mechanisms of resistance to β-lactam antibiotics - the most widely used and effective antibiotics currently - in both Gram-positive and Gram-negative bacteria, and also briefly detail the existing and emergent pharmacological strategies to overcome such resistance. The global epidemiology of the four major types of bacteria that are responsible for the bulk of antimicrobial-resistant infections in the healthcare setting - methicillin-resistant Staphylococcus aureus, vancomycin-resistant enterococci, Enterobactericeae, and Acinetobacter baumannii - are also briefly described.

Bacterial vaccines and antibiotic resistance

Spread of antibiotic resistance is mediated by clonal lineages of bacteria that besides being resistant also possess other properties promoting their success. Some vaccines already in use, such as the pneumococcal conjugate vaccines, have had an effect on these successful clones, but at the same time have allowed for the expansion and resistance evolution of previously minor clones not covered by the vaccine. Since resistance frequently is horizontally transferred it will be difficult to generate a vaccine that covers all possible genetic lineages prone to develop resistance unless the vaccine target(s) is absolutely necessary for spread and/or disease development. Targeting the resistance mechanism itself by a vaccine is an interesting but hitherto unexplored approach.

Detection of OqxAB efflux pumps, OmpK35 and OmpK36 porins in extended-spectrum-β-lactamase-producing Klebsiella pneumoniae isolates from Iran

BACKGROUND & AIM

The aim of this study was the detection of OqxAB efflux pumps, OmpK35 and OmpK36 porins among extended-spectrum-β-lactamase-producing Klebsiella pneumoniae isolates from Iran.

MATERIALS AND METHODS

This study was conducted with 83 K. pneumoniae isolates from two hospitals in Tehran, Iran. Antibiotic susceptibility tests were performed by Kirby-Bauer disc diffusion and Broth Microdilution methods according to CLSI guidelines. The OqxAB , blaTEM, blaSHV and blaCTX-M genes were detected by PCR and sequencing methods.The outer membrane porins OmpK35 and OmpK36 were analyzed by SDS-PAGE, PCR and sequencing methods.

RESULTS

Among the 83 K. pneumoniae strains, 48 (57.5%) were ESBL positive. The existence of blaTEM, blaSHV and blaCTX-M was detected in 24 (50%), 30 (62.5%) and 28 (58.33%) ESBL-producing isolates respectively. The prevalence of both oqxA and oqxB detected in K. pneumoniae was high: 50 (60.2%) and 50 (60.2%), respectively. OmpK35 was detected in 30 (62.5%) while OmpK36 was found in 35 (72.91%) out of 48 ESBL-producing isolates. In this study, fosfomycin and tigecycline were more active than other antibiotics.

CONCLUSIONS

The prevalence of beta-lactamase-producing K. pneumoniae detected in this study is of great concern and highlights the need of infection control measures including antibacterial management and prompt identification of beta-lactamase-producing isolates.