beta-Lactamases in laboratory and clinical resistance

Using Targeted Liquid Chromatography-Tandem Mass Spectrometry to Rapidly Detect β-Lactam, Aminoglycoside, and Fluoroquinolone Resistance Mechanisms in Blood Cultures Growing E. coli or K. pneumoniae

New and rapid antimicrobial susceptibility/resistance testing methods are required for bacteria from positive blood cultures. In this study, a multiplex-targeted liquid chromatography-tandem mass spectrometry (LC-MS/MS) assay was developed and validated for the detection of β-lactam, aminoglycoside, and fluoroquinolone resistance mechanisms in blood cultures growing Escherichia coli or Klebsiella pneumoniae complex. Selected targets were the β-lactamases SHV, TEM, OXA-1-like, CTX-M-1-like, CMY-2-like, chromosomal E. coli AmpC (cAmpC), OXA-48-like, NDM, VIM, and KPC; the aminoglycoside-modifying enzymes AAC(3)-Ia, AAC(3)-II, AAC(3)-IV, AAC(3)-VI, AAC(6′)-Ib, ANT(2′′)-I, and APH(3′)-VI; the 16S-RMTases ArmA, RmtB, RmtC, and RmtF; the quinolone resistance mechanisms QnrA, QnrB, AAC(6′)-Ib-cr; the wildtype quinolone resistance determining region of GyrA; and the E. coli porins OmpC and OmpF. The developed assay was evaluated using 100 prospectively collected positive blood cultures, and 148 negative blood culture samples spiked with isolates previously collected from blood cultures or isolates carrying less prevalent resistance mechanisms. The time to result was approximately 3 h. LC-MS/MS results were compared with whole-genome sequencing and antimicrobial susceptibility testing results. Overall, there was a high agreement between LC-MS/MS results and whole-genome sequencing results. In addition, the majority of susceptible and non-susceptible phenotypes were correctly predicted based on LC-MS/MS results. Exceptions were the predictions for ciprofloxacin and amoxicillin/clavulanic acid that matched with the phenotype in 85.9 and 63.7% of the isolates, respectively. Targeted LC-MS/MS based on parallel reaction monitoring can be applied for the rapid and accurate detection of various resistance mechanisms in blood cultures growing E. coli or K. pneumoniae complex.

β-Lactamase-Responsive Hydrogel Drug Delivery Platform for Bacteria-Triggered Cargo Release

Antibiotic resistance is a growing public health threat that complicates the treatment of infections. β-Lactamase enzymes, which hydrolyze the β-lactam ring present in many common antibiotics, are a major cause of this resistance and are produced by a broad range of bacterial pathogens. Here, we developed hydrogels that degrade specifically in the presence of β-lactamases and β-lactamase-producing bacteria as a platform for bacteria-triggered drug delivery. A maleimide-functionalized β-lactamase-cleavable cephalosporin was used as a crosslinker in the fabrication of hydrogels through end-crosslinked polymerization with multiarm thiol-terminated poly(ethylene glycol) macromers via Michael-type addition. We demonstrated that only hydrogels containing the responsive crosslinker were degraded by β-lactamases and β-lactamase-producing bacteria in vitro and in an ex vivo porcine skin infection model. Fluorescent polystyrene nanoparticles, encapsulated in the hydrogels as model cargo, were released at rates that closely tracked hydrogel wet mass loss, confirming β-lactamase-triggered controlled cargo release. Nonresponsive hydrogels, lacking the β-lactam crosslinker, remained stable in the presence of β-lactamases and β-lactamase-producing bacteria and exhibited no change in mass or nanoparticle release. Furthermore, the responsive hydrogels remained stable in non-β-lactamase enzymes, including collagenases and lipases. These hydrogels have the potential to be used as a bacteria-triggered drug delivery system to control unnecessary exposure to encapsulated antimicrobials, which can provide effective infection treatment without exacerbating resistance.

Express Yourself: Quantitative Real-Time PCR Assays for Rapid Chromosomal Antimicrobial Resistance Detection in Pseudomonas aeruginosa

The rise of antimicrobial-resistant (AMR) bacteria is a global health emergency. One critical facet of tackling this epidemic is more rapid AMR diagnosis in serious multidrug-resistant pathogens like Pseudomonas aeruginosa. Here, we designed and then validated two multiplex quantitative real-time PCR (qPCR) assays to simultaneously detect differential expression of the resistance-nodulation-division efflux pumps MexAB-OprM, MexCD-OprJ, MexEF-OprN, and MexXY-OprM, the AmpC β-lactamase, and the porin OprD, which are commonly associated with chromosomally encoded AMR. Next, qPCRs were tested on 15 sputa from 11 participants with P. aeruginosa respiratory infections to determine AMR profiles in vivo. We confirmed multiplex qPCR testing feasibility directly on sputa, representing a key advancement in in vivo AMR diagnosis. Notably, comparison of sputa with their derived isolates grown in Luria-Bertani broth (±2.5% NaCl) or a 5-antibiotic cocktail showed marked expression differences, illustrating the difficulty in replicating in vivo expression profiles in vitro. Cystic fibrosis sputa showed significantly reduced mexE and mexY expression compared with chronic obstructive pulmonary disease sputa, despite harboring fluoroquinolone- and aminoglycoside-resistant strains, indicating that these loci do not contribute to AMR in vivo. oprD was also significantly downregulated in cystic fibrosis sputa, even in the absence of contemporaneous carbapenem use, suggesting a common adaptive trait in chronic infections that may affect carbapenem efficacy. Sputum ampC expression was highest in participants receiving carbapenems (6.7 to 15×), some of whom were simultaneously receiving cephalosporins, the latter of which would be rendered ineffective by the upregulated ampC. Our qPCR assays provide valuable insights into the P. aeruginosa resistome, and their use on clinical specimens will permit timely treatment alterations that will improve patient outcomes and antimicrobial stewardship measures.

Liquid Chromatography-Tandem Mass Spectrometry Analysis Demonstrates a Decrease in Porins and Increase in CMY-2 β-Lactamases in Escherichia coli Exposed to Increasing Concentrations of Meropenem

While Extended-Spectrum β-Lactamases (ESBL) and AmpC β-lactamases barely degrade carbapenem antibiotics, they are able to bind carbapenems and prevent them from interacting with penicillin-binding proteins, thereby inhibiting their activity. Further, it has been shown that Enterobacterales can become resistant to carbapenems when high concentrations of ESBL and AmpC β-lactamases are present in the bacterial cell in combination with a decreased influx of antibiotics (due to a decrease in porins and outer-membrane permeability). In this study, a targeted liquid chromatography-tandem mass spectrometry (LC-MS/MS) assay was developed for the detection of the Escherichia coli porins OmpC and OmpF, its chromosomal AmpC β-lactamase, and the plasmid-mediated CMY-2 β-lactamase. BlaCMY–2–like positive E. coli isolates were cultured in the presence of increasing concentrations of meropenem, and resistant mutants were analyzed using the developed LC-MS/MS assay, Western blotting, and whole genome sequencing. In five strains that became meropenem resistant, a decrease in OmpC and/or OmpF (caused by premature stop codons or gene interruptions) was the first event toward meropenem resistance. In four of these strains, an additional increase in MICs was caused by an increase in CMY-2 production, and in one strain this was most likely caused by an increase in CTX-M-15 production. The LC-MS/MS assay developed proved to be suitable for the (semi-)quantitative analysis of CMY-2-like β-lactamases and porins within 4 h. Targeted LC-MS/MS could have additional clinical value in the early detection of non-carbapenemase-producing carbapenem-resistant E. coli.

Overcoming the rising incidence and evolving mechanisms of antibiotic resistance by novel drug delivery approaches - An overview

Antimicrobial resistance is a normal evolutionary process for microorganisms. Antibiotics exerted accelerated selective pressure that hasten bacterial resistance through mutation, and acquisition external genes. These genes often carry multiple antibiotic resistant determinants allowing the recipient microbe an instant "super-bug" status. The extent of Antimicrobial Resistance (AMR) has reached a level of global crisis, existing antimicrobials are no long effective in treating infections caused by AMR pathogens. The great majority of clinically available antimicrobial agents are administered through oral and intra-venous routes. Overcoming antibacterial resistance by novel drug delivery approach offered new hopes, particularly in the treatment of AMR pathogens in sites less assessible through systemic circulation such as the lung and skin. In the current review, we will revisit the mechanism and incidence of important AMR pathogens. Finally, we will discuss novel drug delivery approaches including novel local antibiotic delivery systems, hybrid antibiotics, and nanoparticle-based antibiotic delivery systems.

The Role of Bacteriophages as Important Reservoirs of Extended-Spectrum Beta-Lactamase Genes in Azerbaijan Hospitals

Aims: The aim of this study was to investigate the role of resident bacteriophages in hospital effluents, as a potential reservoir of extended-spectrum beta-lactamase (ESBL) genes. Methods: Effluent samples were collected from four major medical centers in Azerbaijan. Phage enrichments were prepared and purified using standard subculturing, amplification, and phage purification protocols. DNA materials from phage stocks and bacterial isolates were examined for the presence of ESBL genes using polymerase chain reaction. Restriction fragment length polymorphism (RFLP) profiles were used for the construction of a dendrogram and cluster analysis. Results: A total of 112 phage enrichments were obtained from 48 effluent samples against resident bacterial hosts. A total of 95 nonduplicate Gram-negative isolates were recovered from effluent samples. The most common isolate was Escherichia coli (n = 48), followed by Klebsiella pneumoniae (n = 18), Pseudomonas spp. (n = 9), and Enterobacter cloacae (n = 6). Thirty-two EcoRV-RFLP profiles consisting of ∼4 to 20 bands were obtained for the 40 E. coli phage enrichments. ESBL genes were detected in 23 of 40 (57.5%) E. coli phage enrichments, including bla_CTX-M (n = 15), bla_TEM (n = 14), and bla_SHV (n = 6). Detected genes in phage enrichments against resident hosts other than E. coli include bla_TEM (n = 4), bla_CTX-M (n = 3), and bla_SHV (n = 1). A total of 63 (66.3%) bacterial isolates were positive for tested genes, including bla_CTX-M (n = 32), bla_TEM (n = 61), and bla_SHV (n = 12). The present research provides a strong evidence for the possible role of bacteriophages in antimicrobial resistance genes circulation in Azerbaijan clinical settings through generalized transduction. Conclusions: Our results showed a remarkable occurrence of ESBL genes in bacteriophage and bacterial population of effluent discharge, which clearly indicates that bacteriophages are an important factor in ESBL genes exchange among bacterial population through generalized transduction.

Gene sharing among plasmids and chromosomes reveals barriers for antibiotic resistance gene transfer

The emergence of antibiotic resistant bacteria is a major threat to modern medicine. Rapid adaptation to antibiotics is often mediated by the acquisition of plasmids carrying antibiotic resistance (ABR) genes. Nonetheless, the determinants of plasmid-mediated ABR gene transfer remain debated. Here, we show that the propensity of ABR gene transfer via plasmids is higher for accessory chromosomal ABR genes in comparison with core chromosomal ABR genes, regardless of the resistance mechanism. Analysing the pattern of ABR gene occurrence in the genomes of 2635 Enterobacteriaceae isolates, we find that 33% of the 416 ABR genes are shared between chromosomes and plasmids. Phylogenetic reconstruction of ABR genes occurring on both plasmids and chromosomes supports their evolution by lateral gene transfer. Furthermore, accessory ABR genes (encoded in less than 10% of the chromosomes) occur more abundantly in plasmids in comparison with core ABR genes (encoded in greater than or equal to 90% of the chromosomes). The pattern of ABR gene occurrence in plasmids and chromosomes is similar to that in the total Escherichia genome. Our results thus indicate that the previously recognized barriers for gene acquisition by lateral gene transfer apply also to ABR genes. We propose that the functional complexity of the underlying ABR mechanism is an important determinant of ABR gene transferability. This article is part of the theme issue 'The secret lives of microbial mobile genetic elements'.

Membrane vesicles (MVs) from antibiotic-resistant Staphylococcus aureus transfer antibiotic-resistance to antibiotic-susceptible Escherichia coli

AIM

Bacteria naturally produce membrane vesicles (MVs), which have been shown to contribute to the spread of multi-drug resistant bacteria (MDR) by delivering antibiotic-resistant substances to antibiotic-susceptible bacteria. Here, we aim to show that MVs from Gram-positive bacteria are capable of transferring β-lactam antibiotic-resistant substances to antibiotic-sensitive Gram-negative bacteria.

MATERIALS AND METHODS

MVs were collected from a methicillin-resistant strain of Staphylococcus aureus (MRSA) and vesicle-mediated fusion with antimicrobial-sensitive Escherichia coli (RC85). It was performed by exposing the bacteria to the MVs to develop antimicrobial-resistant E. coli (RC85-T).

RESULTS

The RC85-T exhibited a higher resistance to β-lactam antibiotics compared to the parent strain. Although the secretion rates of the MVs from RC85-T and the parent strain were nearly equal, the β-lactamase activity of the MVs from RC85-T was 12-times higher than that of MVs from the parent strain, based on equivalent protein concentrations. Moreover, MVs secreted by RC85-T were able to protect β-lactam-susceptible E. coli from β-lactam antibiotic-induced growth inhibition in a dose-dependent manner.

CONCLUSION

MVs play a role in transferring substances from Gram-positive to Gram-negative bacteria, shown by the release of MVs from RC85-T that were able to protect β-lactam-susceptible bacteria from β-lactam antibiotics.

SIGNIFICANCE AND IMPACT OF STUDY

MVs are involved in the emergence of antibiotic resistant strains in a mixed bacterial culture, helping us to understand how the spread of multidrug resistant bacteria could be reduced.

Molecular detection and antibiotyping of multi-drug resistant Enterococcus faecium from healthy broiler chickens in Bangladesh

BACKGROUND

Enterococcus faecium is a ubiquitously distributed member of the intestinal microbiota of both humans and animals. Antibiotic resistant E. faecium are a major public health concern.

OBJECTIVES

This study aimed to detect multi-drug resistant (MDR) E. faecium and their antibiotic resistance genes from broiler chickens in Bangladesh.

METHODS

A total of 100 faecal samples of healthy broilers were screened by conventional methods and polymerase chain reaction (PCR) to detect E. faecium and their resistance genes. Disk diffusion test was employed to determine antibiotic profiles.

RESULTS

By PCR, among 100 samples, 45% [95% confidence interval (CI): 35.62%-54.76%] were positive for E. faecium. Based on antibiogram, all the E. faecium isolates were found resistant to ampicillin, and frequently (93.33%-55.56%) resistant to ceftriaxone, cefotaxime, streptomycin, erythromycin, and imipenem; moderate to lower (26.67%-4.44%) resistance to tetracycline, ciprofloxacin, norfloxacin, chloramphenicol, gentamicin, and vancomycin. Interestingly, 80% (95% CI: 66.18%-89.10%) E. faecium isolates were MDR in nature. In addition, the indices of multiple antibiotic resistance (MAR) ranged from 0.08 to 0.83. By bivariate analysis, high positive significant correlations were observed between resistance profiles of erythromycin and imipenem, ciprofloxacin and norfloxacin, erythromycin and streptomycin, ceftriaxone and cefotaxime, tetracycline and chloramphenicol, and streptomycin and imipenem. Furthermore, the prevalence of resistance genes of E. faecium was 58.33% (tetA), 33.33% (tetB), 35.56% (blaTEM ), 60% (CITM), 13.33% (aadA1), and 12% (SHV).

CONCLUSIONS

To the best of our knowledge, this is the first study in Bangladesh to detect MDR and MAR E. faecium and their associated resistance genes. The detection of MDR and MAR E. faecium and their corresponding resistance genes from healthy broilers is of public health concern because of their potential to enter into the food chain.

Studies on molecular epidemiology of ESβL-producing Klebsiella pneumoniae isolated from patients hospitalized in a specialist hospital in southern Poland

Introduction. Extended-spectrum β-lactamase (ESβL)-producing Klebsiella pneumoniae is currently one of the most common causes of nosocomial infections worldwide. The study aimed to characterize antibiotic resistance profile, the prevalence of selected genes encoding ESβLs, virulence, and the genetic relationship in 139 K. pneumoniae isolates identified in John Paul II Specialist Hospital in Southern Poland, collected in 2016.

Materials/Methods. Bacterial identification and the preliminary antibiotic susceptibilities was performed using the VI-TEK® 2 Compact automated system. Genes encoding ESβLs were amplified by CTX-Mplex PCR and PCR reactions. The presence of nine genes encoding virulence factors was studied by multiplex PCR. Clonality was investigated by PFGE after digestion with SpeI endonuclease.

Results. K. pneumoniae were mostly recovered from the respiratory tract (40.3%), urine (32.4%), wound swabs (19.4%) and blood (5%). In summary, 82.7% of strains were classified as multidrug resistant (MDR). All isolates were confirmed as ESβL producers and carried bla CTX-M-type (85.6%), bla SHV (82%), bla TEM (77.7%), bla CTX-M-9 (75.6%) and bla CTX-M-1 (1.4%) in various combinations. Moreover, triple bla genes were observed in 72% of isolates. The most common virulence-as-sociated genes found among the isolates were entB (91.4%), ybtS (55.4%), iutA (55.4%), magA (53.2%), kfu (14.4%), K2 (11.5%), mrkD (10.1%), rmpA (7.9%) and allS (5%). The PFGE analysis identified 4 major clusters (A–D) comprising 61% of the entire collection.

Conclusions. Our results indicate that the presence of a wide variety of MDR K. pneumoniae harbor ESβLs and virulence genes. Studies on molecular epidemiology of ESβL-producing K. pneumoniae isolates are needed, particularly for epidemiological surveillance in the hospital environment.

Characterization of a Novel Chromosome-Encoded AmpC β-Lactamase Gene, blaPRC–1, in an Isolate of a Newly Classified Pseudomonas Species, Pseudomonas wenzhouensis A20, From Animal Farm Sewage

In this work, we characterized a novel chromosome-encoded AmpC β-lactamase gene, bla_PRC–1, in an isolate of a newly classified Pseudomonas species designated Pseudomonas wenzhouensis A20, which was isolated from sewage discharged from an animal farm in Wenzhou, China. Susceptibility testing, molecular cloning, and enzyme kinetic parameter analysis were performed to determine the function and enzymatic properties of the β-lactamase. Sequencing and comparative genomic analysis were conducted to clarify the phylogenetic relationship and genetic context of the bla_PRC–1 gene. PRC-1 is a 379-amino acid AmpC β-lactamase with a molecular weight of 41.48 kDa and a predicted pI of 6.44, sharing the highest amino acid identity (57.7%) with the functionally characterized AmpC β-lactamase PDC-211 (ARX71249). bla_PRC–1 confers resistance to many β-lactam antibiotics, including penicillins (penicillin G, amoxicillin, and amoxicillin-clavulanic acid) and cephalosporins (cefazolin, ceftriaxone, and cefotaxime). The kinetic properties of PRC-1 were compatible with those of a typical class C β-lactamase showing hydrolytic activities against β-lactam antibiotics, and the hydrolytic activity was strongly inhibited by avibactam. The genetic context of bla_PRC–1 was relatively conserved, and no mobile genetic element was predicted in its surrounding region. Identification of a novel β-lactamase gene in an unusual environmental bacterium reveals that there might be numerous unknown resistance mechanisms in bacterial populations, which may pose potential risks to human health due to universal horizontal gene transfer between microorganisms. It is therefore of great value to carry out extensive research on the mechanism of antibiotic resistance.

Unveiling the evolution routes of TEM-type extended-spectrum β-lactamases

The TEM-1 β-lactamase can only cleave penicillin and the first-generation cephalosporins but it has evolved to become active against second-, third- and fourth-generation drugs. Through sequence analysis of natural TEM variants and those created by mutagenesis experiments, we described two distinct evolution routes of TEM-1 that has generated over 220 enzyme variants. One began with the Gly²³⁸Ser alteration and the other originated with the Arg¹⁶⁴Ser substitution. Further acquisition of mutations in the background of each of these two first-step mutants led to stepwise alteration in enzyme structure and hence activity, eventually producing a wide range of enzyme variants whose substrate specificities cover cephalosporins of all generations. Dissemination of strains producing TEM-1 variants generated from these two evolution routes underlies the markedly increased prevalence of bacterial resistance to β-lactams in the past few decades. This study provides insights into the evolution of hydrolysing enzymes, in particular β-lactamases.

Antibiotic resistance modifying ability of phytoextracts in anthrax biological agent Bacillus anthracis and emerging superbugs: a review of synergistic mechanisms

Background and objectives

The chemotherapeutic management of infections has become challenging due to the global emergence of antibiotic resistant pathogenic bacteria. The recent expansion of studies on plant-derived natural products has lead to the discovery of a plethora of phytochemicals with the potential to combat bacterial drug resistance via various mechanisms of action. This review paper summarizes the primary antibiotic resistance mechanisms of bacteria and also discusses the antibiotic-potentiating ability of phytoextracts and various classes of isolated phytochemicals in reversing antibiotic resistance in anthrax agent Bacillus anthracis and emerging superbug bacteria.

Methods

Growth inhibitory indices and fractional inhibitory concentration index were applied to evaluate the in vitro synergistic activity of phytoextract-antibiotic combinations in general.

Findings

A number of studies have indicated that plant-derived natural compounds are capable of significantly reducing the minimum inhibitory concentration of standard antibiotics by altering drug-resistance mechanisms of B. anthracis and other superbug infection causing bacteria. Phytochemical compounds allicin, oleanolic acid, epigallocatechin gallate and curcumin and Jatropha curcas extracts were exceptional synergistic potentiators of various standard antibiotics.

Conclusion

Considering these facts, phytochemicals represents a valuable and novel source of bioactive compounds with potent antibiotic synergism to modulate bacterial drug-resistance.

Klebsiella oxytoca Complex: Update on Taxonomy, Antimicrobial Resistance, and Virulence

Klebsiella oxytoca is actually a complex of nine species-Klebsiella grimontii, Klebsiella huaxiensis, Klebsiella michiganensis, K. oxytoca, Klebsiella pasteurii, Klebsiella spallanzanii, and three unnamed novel species. Phenotypic tests can assign isolates to the complex, but precise species identification requires genome-based analysis. The K. oxytoca complex is a human commensal but also an opportunistic pathogen causing various infections, such as antibiotic-associated hemorrhagic colitis (AAHC), urinary tract infection, and bacteremia, and has caused outbreaks. Production of the cytotoxins tilivalline and tilimycin lead to AAHC, while many virulence factors seen in Klebsiella pneumoniae, such as capsular polysaccharides and fimbriae, have been found in the complex; however, their association with pathogenicity remains unclear. Among the 5,724 K. oxytoca clinical isolates in the SENTRY surveillance system, the rates of nonsusceptibility to carbapenems, ceftriaxone, ciprofloxacin, colistin, and tigecycline were 1.8%, 12.5%, 7.1%, 0.8%, and 0.1%, respectively. Resistance to carbapenems is increasing alarmingly. In addition to the intrinsic bla_OXY, many genes encoding β-lactamases with varying spectra of hydrolysis, including extended-spectrum β-lactamases, such as a few CTX-M variants and several TEM and SHV variants, have been found. bla_KPC-2 is the most common carbapenemase gene found in the complex and is mainly seen on IncN or IncF plasmids. Due to the ability to acquire antimicrobial resistance and the carriage of multiple virulence genes, the K. oxytoca complex has the potential to become a major threat to human health.

Antibiotic resistance genes in an urban stream before and after a state fair

The global spread of antibiotic resistance genes (ARGs) concomitant with a decrease in antibiotic effectiveness is a major public health issue. While research has demonstrated the impact of various urban sources, such as wastewater treatment plant (WWTP) effluent, stormwater runoff, and industrial discharge on ARG abundance in receiving waters, the impact of short-term gatherings such as state fairs is not comprehensively understood. The objective of this research was to explore the impact of a 2-week Wisconsin State Fair gathering - over 1.1 million visitors and 7,100 farm animals - on the abundance of the ARG bla_TEM, the integrase of the class 1 integron (intI1), a marker for horizontal gene transfer, and the 16S rRNA gene, a marker for total biomass, in an urban stream receiving runoff from the state fair. Stream samples downstream of the state fair were taken before and after the event and quantified via a droplet digital polymerase chain reaction. The absolute abundance of all genes was significantly higher (p<0.05) following the event. This research showcases the prevalence and persistence of ARG contamination in an urban stream before and after a state fair gathering, suggesting that short-term events can be a significant source of ARGs into the environment.

Evaluating the antibacterial effect of cobalt nanoparticles against multi-drug resistant pathogens

This study aimed to estimate the effect of cobalt nanoparticles (Co NPs) with different concentrations against multidrug-resistant (MDR) pathogenic bacteria. Three isolates of Staphylococcus aureus (gram-positive), Proteus spp. (gram-negative), and Escherichia coli (gram-negative) bacteria were extracted from various clinical examples utilizing routine methods on bacteriological culture media. The antibacterial sensitivity of commercial antibiotics such as Ciprofloxacin, Cefotaxime, Gentamycin, and Amoxicillin was broken down on a Muller Hinton agar plate and evaluated using the disk diffusion method. The study results demonstrated the antibacterial effect of the Co NPs against the bacterial isolates with three different concentrations utilized in the study. The results indicated that the Co NPs showed the highest antibacterial activity when utilizing 100 μg/ml against Escherichia coli followed by Proteus spp and Staphylococcus aureus with zones of inhibition measured as 22.2±0.1 mm, 20.3±0.15 mm, and 15.8±0.1 mm; respectively. Co NPs at a 100 μg/mL concentration showed higher inhibition zones than several common antibiotics except for Ciprofloxacin, which demonstrated better antibacterial activity against the bacterial isolates employed in this study. Scanning Electron Microscope (SEM)and X-Ray diffraction (XRD)studies confirmed that Cobalt nanoparticles (Co NPs) were synthesized from cobalt sulphate solution with a size ranging from 40 nm to 60 nm. The nanoparticles showed a crystalline structure with a round shape and smooth surface. The antibacterial resistance of Co NPs against three common bacteria such as Staphylococcus aureus, Proteus spp, and Escherichia coli was assessed in this study. The optimum concentration of the Co NPs was identified as 100 μg/ml, which could provide a similar or higher antibacterial effect.

Molecular Characterization of Antibiotic Resistance Associated with TEM and CTX-M ESBL in Uropathogenic E. coli Strains Isolated from Outpatients

Background & Objective

Escherichia coli (E. coli) is a leading cause of urinary tract infections becoming resistant against beta-lactams and cephalosporins through different mechanisms, including ESBL production due to the presence of ESBL specific genes, including blaCTX-M and blaTEM. The purpose of the present study was to detect the uropathogenic E. coli strains producing the ESBL.

Methods

A total of 100 isolates of uropathogenic E. coli were randomly selected in a period of 6 months and their resistances to a number of antibiotics including amoxicillin, amikacin, gentamicin, ciprofloxacin, ceftazidime, cefotaxime, ceftriaxone, ceftizoxime, nalidixic acid, and nitrofurantoin were determined. Then, DDT test was used to detect the presence of ESBL. Finally, the presence of blaCTX-M and blaTEM resistance genes was analyzed by PCR method.

Results

The resistance profile of bacterial isolates to the antibiotics was as follows: amoxicillin: 16.7%, amikacin: 7.8%, gentamicin: 20.3%, ciprofloxacin: 35.5/%, ceftazidime: 35.0%, cefotaxime: 40.0%, ceftriaxone: 41.3%, nalidixic acid: 64.0%, nitrofurantoin: 9.7%, and ceftizoxime: 100%. Of these, 28 isolates (28%) were reported to be resistant to cefotaxime, ceftazidime, and ceftriaxone. In DDT test, 21 ESBL positive cases (21%) were detected. PCR results showed that the presence of blaCTX-M and blaTEM genes in the isolates were 21% and 20%, respectively.

Conclusion

Regarding the production of ESBL by some E. coli isolates, phenotypic detection of ESBL-producing isolates is routinely suggested in the laboratories. Likewise, the treatment regimen should be selected regarding the ESBL production to avoid treatment failure.

Selection and characterization of mutational resistance to aztreonam/avibactam in β-lactamase-producing Enterobacterales

BACKGROUND

Aztreonam/avibactam is being developed for its broad activity against carbapenemase-producing Enterobacterales, including those with metallo-β-lactamases (MBLs). Its potential to select resistance in target pathogens was explored. Findings are compared with previous data for ceftazidime/avibactam and ceftaroline/avibactam.

METHODS

Single-step mutants were sought from 52 Enterobacterales with AmpC, ESBL, KPC, MBL and OXA-48-like enzymes. Mutation frequencies were calculated. MICs were determined by CLSI agar dilution. Genomes were sequenced using Illumina methodology.

RESULTS

Irrespective of β-lactamase type and of whether avibactam was used at 1 or 4 mg/L, mutants could rarely be obtained at >4× the starting MIC, and most MIC rises were correspondingly small. Putative resistance (MIC >8 + 4 mg/L) associated with changes to β-lactamases was seen only for mutants of AmpC, where it was associated with Asn346Tyr and Tyr150Cys substitutions. Asn346Tyr led to broad resistance to avibactam combinations; Tyr150Cys significantly affected only aztreonam/avibactam. MIC rises up to 4 + 4 mg/L were seen for producers of mutant KPC-2 or -3 enzymes, and were associated with Trp105Arg, Ser106Pro and Ser109Pro substitutions, which all reduced the MICs of other β-lactams. For producers of other β-lactamase types, we largely found mutants with lesions in baeRS or envZ, putatively affecting drug accumulation. Single mutants had lesions in ampD, affecting AmpC expression or ftsI, encoding PBP3.

CONCLUSIONS

The risk of mutational resistance to aztreonam/avibactam appears smaller than for ceftazidime/avibactam, where Asp179Tyr arises readily in KPC enzymes, conferring frank resistance. Asn346 substitutions in AmpC enzymes may remain a risk, having been repeatedly selected with multiple avibactam combinations in vitro.

Prevalence of non-extended spectrum β-lactamases SHV-1 and TEM-1 or -2 types in multidrug-resistant Enterobacteriaceae in northern Iran

The present study aimed to evaluate TEM-1 or -2 and SHV-1 β-lactamases frequency in multidrug-resistant (MDR) Enterobacteriaceae isolated from patients' urine in northern Iran. The resistance pattern to 20 antibiotics and ESBL production in 200 MDR Enterobacteriaceae was detected using the disk diffusion test and double-disk synergy test (DDST), respectively. Multiplex PCR was applied to detect bla_{TEM-1 or -2} and bla_SHV genes in isolates. DDST findings were inconsistent with multiplex PCR results. The distribution of each of bla_{TEM-1 or -2} and bla_SHV genes, either alone or in combination, in the ESBL-producing isolates was higher than the non-ESBL-producing isolates. There was a significant effect of the presence of bla_{TEM-1 or -2} gene on resistance to cephalotin at the p < 0.01 level and cefepime, tetracycline, and streptomycin at the P < 0.05 level, and the presence of bla_SHV-1 gene on resistance to fosfomycin at the P < 0.05 level as well as the presence both bla_{TEM-1 or -2} and bla_SHV-1 genes on resistance to cephalotin and fosfomycin at the P < 0.01 level. In all isolates, ESBL production, except for cephalotin resistance, did not improve resistance to other antibiotics used and even non-ESBL-producing isolates showed higher resistance to antibiotics compared to ESBL-producing isolates. It seems that mechanisms other than production of ESBL to be involved as part of the resistance mechanisms of the studied isolates against the used antibiotics. For epidemiological studies, both phenotypic and molecular tests must be included to identify the bla_{TEM-1 or -2} and bla_SHV-1 genotypes to ensure infection prevention and control.

Helicobacter pylori infection and antibiotic resistance - from biology to clinical implications

Helicobacter pylori is a major human pathogen for which increasing antibiotic resistance constitutes a serious threat to human health. Molecular mechanisms underlying this resistance have been intensively studied and are discussed in this Review. Three profiles of resistance - single drug resistance, multidrug resistance and heteroresistance - seem to occur, probably with overlapping fundamental mechanisms and clinical implications. The mechanisms that have been most studied are related to mutational changes encoded chromosomally and disrupt the cellular activity of antibiotics through target-mediated mechanisms. Other biological attributes driving drug resistance in H. pylori have been less explored and this could imply more complex physiological changes (such as impaired regulation of drug uptake and/or efflux, or biofilm and coccoid formation) that remain largely elusive. Resistance-related attributes deployed by the pathogen cause treatment failures, diagnostic difficulties and ambiguity in clinical interpretation of therapeutic outcomes. Subsequent to the increasing antibiotic resistance, a substantial drop in H. pylori treatment efficacy has been noted globally. In the absence of an efficient vaccine, enhanced efforts are needed for setting new treatment strategies and for a better understanding of the emergence and spread of drug-resistant bacteria, as well as for improving diagnostic tools that can help optimize current antimicrobial regimens.

Genomic Investigation of Antimicrobial-Resistant Salmonella enterica Isolates From Dead Chick Embryos in China

Salmonella spp. is recognized as an important zoonotic pathogen. The emergence of antimicrobial resistance in Salmonella enterica poses a great public health concern worldwide. While the knowledge on the incidence and the characterization of different S. enterica serovars causing chick embryo death remains obscure in China. In this study, we obtained 45 S. enterica isolates from 2,139 dead chick embryo samples collected from 28 breeding chicken hatcheries in Henan province. The antimicrobial susceptibility assay was performed by the broth microdilution method and the results showed that 31/45 (68.8%) isolates were multidrug-resistant (≥3 antimicrobial classes). Besides the highest resistance rate was observed in the aminoglycoside class, all the isolates were susceptible to chloramphenicol, azithromycin, and imipenem. Furthermore, genomic characterization revealed that S. Enteritidis (33.33%; 15/45) was a frequent serovar that harbored a higher number of virulence factors compared to other serovars. Importantly, genes encoding β-lactamases were identified in three serovars (Thompson, Enteritidis, and Kottbus), whereas plasmid-mediated quinolone resistance genes (qnrB4) were detected in certain isolates of S. Thompson and the two S. Kottbus isolates. All the examined isolates harbored the typical virulence factors from Salmonella pathogenicity islands 1 and 2 (SPI-1 and SPI-2). Additionally, a correlation analysis between the antimicrobial resistance genes, phenotype, and plasmids was conducted among Salmonella isolates. It showed strong positive correlations (r < 0.6) between the different antimicrobial-resistant genes belonging to certain antimicrobial classes. Besides, IncF plasmid showed a strong negative correlation (r > −0.6) with IncHI2 and IncHI2A plasmids. Together, our study demonstrated antimicrobial-resistant S. enterica circulating in breeding chicken hatcheries in Henan province, highlighting the advanced approach, by using genomic characterization and statistical analysis, in conducting the routine monitoring of the emerging antimicrobial-resistant pathogens. Our findings also proposed that the day-old breeder chicks trading could be one of the potential pathways for the dissemination of multidrug-resistant S. enterica serovars.

Catestatin in innate immunity and Cateslytin-derived peptides against superbugs

Chromogranin A (CgA) is the precursor of several antimicrobial peptides, such as Catestatin (Cts, bovine CgA344-364), initially described as a potent inhibitor of catecholamines. This peptide displays direct antimicrobial activities and contributes to immune system regulation. The aim of the present study is to investigate a designed peptide based on Cts to fight infections against superbugs and more particularly Staphylococcus aureus. In addition to Cateslytin (Ctl, bovine CgA344-358), the active domain of Catestatin, several peptides including dimers, D-isomer and the new designed peptide DOPA-K-DOPA-K-DOPA-TLRGGE-RSMRLSFRARGYGFR (Dopa5T-Ctl) were prepared and tested. Cateslytin is resistant to bacterial degradation and does not induce bacterial resistance. The interaction of Catestatin with immune dermal cells (dendritic cells DC1a, dermal macrophages CD14 and macrophages) was analyzed by using confocal microscopy and cytokine release assay. The dimers and D-isomer of Ctl were tested against a large variety of bacteria showing the potent antibacterial activity of the D-isomer. The peptide Dopa5T-Ctl is able to induce the self-killing of S. aureus after release of Ctl by the endoprotease Glu-C produced by this pathogen. It permits localized on-demand delivery of the antimicrobial drug directly at the infectious site.

Detection of β-Lactamase-Producing Proteus mirabilis Strains of Animal Origin in Andhra Pradesh, India and Their Genetic Diversity

ABSTRACT

Proteus mirabilis is abundant in soil and water. Although this bacterium is part of the normal human intestinal flora, it can cause serious infections in humans, including complicated urinary tract infections. This pathogen is also commonly associated with multidrug resistance. In the present study, analysis of 1,093 samples from foods of animal origin and animal intestinal samples recovered 232 P. mirabilis isolates identified by PCR assay. Of these 232 isolates, 72 produced β-lactamase (determined by both phenotypic and genotypic methods), with the highest prevalence in poultry cloacal swabs (11.82%) followed by mutton (9.18%), khoa (6.32%), pork (5.63%), pig rectal swabs (5.52%), beef (5.45%), and chicken (5.13%) but none from sheep rectal swabs and bovine rectal swabs. Among β-lactamase genes, blaTEM was the predominant gene detected (59 isolates) followed by blaOXA (11 isolates), blaSHV (5 isolates), blaFOX (5 isolates), blaCIT (4 isolates), blaCTX-M1 and blaCTX-M9 (2 isolates each) and blaCTX-M2, blaDHA, and blaEBC (1 isolate each). None of the isolates carried blaACC, blaMOX, or carbapenemase genes (blaVIM, blaIMP, blaKPC, and blaNDM-1). Dendrogram analysis of enterobacterial repetitive intergenic consensus sequences and repetitive extragenic palindromic sequences obtained with PCR analysis of β-lactamase-producing isolates revealed 63 isolates, but 9 isolates did not yield bands. The analysis revealed that 6.58% of the samples had β-lactamase-producing P. mirabilis isolates that may affect food safety and contaminate the environment. Further genotyping revealed the genetic relationships between isolates of different origin. These findings emphasize the need for careful use of antibiotics to control the spread of β-lactamase-producing bacteria.

HIGHLIGHTS

High potency of sequential therapy with only β-lactam antibiotics

Evolutionary adaptation is a major source of antibiotic resistance in bacterial pathogens. Evolution-informed therapy aims to constrain resistance by accounting for bacterial evolvability. Sequential treatments with antibiotics that target different bacterial processes were previously shown to limit adaptation through genetic resistance trade-offs and negative hysteresis. Treatment with homogeneous sets of antibiotics is generally viewed to be disadvantageous as it should rapidly lead to cross-resistance. We here challenged this assumption by determining the evolutionary response of Pseudomonas aeruginosa to experimental sequential treatments involving both heterogenous and homogeneous antibiotic sets. To our surprise, we found that fast switching between only β-lactam antibiotics resulted in increased extinction of bacterial populations. We demonstrate that extinction is favored by low rates of spontaneous resistance emergence and low levels of spontaneous cross-resistance among the antibiotics in sequence. The uncovered principles may help to guide the optimized use of available antibiotics in highly potent, evolution-informed treatment designs.

Overuse of antibiotic drugs is leading to the appearance of antibiotic-resistant bacteria; this is, bacteria with mutations that allow them to survive treatment with specific antibiotics. This has made some bacterial infections difficult or impossible to treat. Learning more about how bacteria evolve resistance to antibiotics could help scientists find ways to prevent it and develop more effective treatments.

Changing antibiotics frequently may be one way to prevent bacteria from evolving resistance. That way if a bacterium acquires mutations that allow it to escape one antibiotic, another antibiotic will kill it, stopping it from dividing and preventing the appearance of descendants with resistance to several antibiotics. In order to use this approach, testing is needed to find the best sequences of antibiotics to apply and the optimal timings of treatment.

To find out more, Batra, Roemhild et al. grew bacteria in the laboratory and exposed them to different sequences of antibiotics, switching antibiotics at different time intervals. This showed that sequential treatments with different antibiotics can limit bacterial evolution, especially when antibiotics are switched quickly. Unexpectedly, one of the most effective sequences used very similar antibiotics. This was surprising because using similar antibiotics should lead to the evolution of cross-resistance, which is when a drug causes changes that make the bacterium less sensitive to other treatments. However, in the tested case, cross-resistance did not evolve when antibiotics were switched quickly, thereby ensuring efficiency of treatment.

Batra et al. show that alternating sequences of antibiotics may be an effective strategy to prevent drug resistance. Because the experiments were done in a laboratory setting it will be important to verify the results in studies in animals and humans before the approach can be used in medical or veterinary settings. If the results are confirmed, it could reduce the need to develop new antibiotics, which is expensive and time consuming.

High Prevalence of ESBL and Plasmid-Mediated Quinolone Resistance Genes in Salmonella enterica Isolated from Retail Meats and Slaughterhouses in Egypt

The emergence and spread of multidrug-resistant Salmonella enterica (S. enterica) to humans through food of animal origin are considered a major global public health concern. Currently, little is known about the prevalence of important antimicrobial resistance genes in S. enterica from retail food in Africa. Therefore, the screening and characterization of the extended-spectrum β-lactamase (ESBL) and plasmid-mediated quinolone resistance (PMQR) genes in S. enterica isolated from retail meats and slaughterhouses in Egypt were done by using PCR and DNA sequencing techniques. Twenty-eight out of thirty-four (82.4%) non-duplicate S. enterica isolates showed multidrug-resistance phenotypes to at least three classes of antimicrobials, and fourteen (41.2%) exhibited an ESBL-resistance phenotype and harbored at least one ESBL-encoding gene. The identified β-lactamase-encoding genes included bla_CTX-M-1, bla_CTX-M-3, bla_CTX-M-13, bla_CTX-M-14, bla_CTX-M-15, and bla_SHV-12 (ESBL types); bla_CMY-2 (AmpC type); and bla_TEM-1 and bla_OXA-1 (narrow-spectrum types). PMQR genes (included qnrA, qnrB, qnrS, and aac(6′)-Ib-cr) were identified in 23 (67.6%) isolates. The presence of ESBL- and PMQR-producing S. enterica with a high prevalence rate in retail meats and slaughterhouses is considered a major threat to public health as these strains with resistance genes could be transmitted to humans through the food chain.

Extended-spectrum β-lactamases: an update on their characteristics, epidemiology and detection

Extended-spectrum β-lactamase (ESBL)-producing Gram-negative pathogens are a major cause of resistance to expanded-spectrum β-lactam antibiotics. Since their discovery in the early 1980s, they have spread worldwide and an are now endemic in Enterobacterales isolated from both hospital-associated and community-acquired infections. As a result, they are a global public health concern. In the past, TEM- and SHV-type ESBLs were the predominant families of ESBLs. Today CTX-M-type enzymes are the most commonly found ESBL type with the CTX-M-15 variant dominating worldwide, followed in prevalence by CTX-M-14, and CTX-M-27 is emerging in certain parts of the world. The genes encoding ESBLs are often found on plasmids and harboured within transposons or insertion sequences, which has enabled their spread. In addition, the population of ESBL-producing Escherichia coli is dominated globally by a highly virulent and successful clone belonging to ST131. Today, there are many diagnostic tools available to the clinical microbiology laboratory and include both phenotypic and genotypic tests to detect β-lactamases. Unfortunately, when ESBLs are not identified in a timely manner, appropriate antimicrobial therapy is frequently delayed, resulting in poor clinical outcomes. Several analyses of clinical trials have shown mixed results with regards to whether a carbapenem must be used to treat serious infections caused by ESBLs or whether some of the older β-lactam-β-lactamase combinations such as piperacillin/tazobactam are appropriate. Some of the newer combinations such as ceftazidime/avibactam have demonstrated efficacy in patients. ESBL-producing Gram-negative pathogens will continue to be major contributor to antimicrobial resistance worldwide. It is essential that we remain vigilant about identifying them both in patient isolates and through surveillance studies.

Cefazolin versus ceftriaxone as definitive treatment for Klebsiella pneumoniae bacteraemia: a retrospective multicentre study in Singapore

BACKGROUND

Ceftriaxone is the preferred treatment for bacteraemia caused by non-MDR (antibiotic-susceptible) Klebsiella pneumoniae. Excessive and widespread ceftriaxone use creates selection pressure for ESBLs. Cefazolin is an alternative, although there are theoretical concerns that SHV-1 β-lactamase in K. pneumoniae may inactivate cefazolin in an inoculum-dependent manner.

OBJECTIVES

In this retrospective study, we investigated the outcomes in K. pneumoniae bacteraemia patients treated with IV cefazolin versus IV ceftriaxone as definitive therapy.

METHODS

A total of 917 patients infected with K. pneumoniae from 1 January to 31 December 2016 in three public acute care hospitals in Singapore were screened for study eligibility. Consecutive unique episodes of monomicrobial bacteraemia caused by cefazolin- and/or ceftriaxone-susceptible K. pneumoniae were analysed (n = 284).

RESULTS

There were 143 patients (50.4%) in the cefazolin group and 141 patients (49.6%) in the ceftriaxone group. Demographics, baseline illness severity and risk factors for healthcare-associated bacteraemia were comparable in the two treatment groups. The primary outcome of 28 day all-cause mortality was not significantly different between the cefazolin and ceftriaxone groups (10.5% versus 7.1%, P = 0.403). Both in the crude analysis and using a multivariable logistic regression model with inverse probability weighting based on propensity score, cefazolin treatment was not associated with increased risk of 28 day mortality (OR 1.51 with ceftriaxone as the reference group, 95% CI 0.67-3.53; adjusted OR 1.55, 95% CI 0.33-7.40).

CONCLUSIONS

Cefazolin may be a ceftriaxone-sparing alternative treatment for antibiotic-susceptible K. pneumoniae bacteraemia. This observation may provide sufficient clinical equipoise for a randomized controlled trial.

GPC-1, a novel class A carbapenemase detected in a clinical Pseudomonas aeruginosa isolate

OBJECTIVES

To investigate the carbapenem resistance mechanism of a carbapenem-resistant clinical Pseudomonas aeruginosa isolate.

METHODS

A carbapenem-resistant P. aeruginosa isolate was recovered from a tracheal swab from a patient of a general ward in central Germany. Various phenotypic tests confirmed production of a carbapenemase that could not be identified further by PCR. A novel bla gene was identified by WGS and its carbapenemase activity was verified by heterologous expression in an Escherichia coli cloning strain. Kinetic parameters of the novel β-lactamase were determined by spectrophotometric measurements using purified enzyme.

RESULTS

WGS confirmed the presence of a novel class A carbapenemase. The novel bla gene was named GPC-1 (GPC standing for German Pseudomonas Carbapenemase) and exhibited 77% amino acid identity to BKC-1. WGS also showed that blaGPC-1 was located on the chromosome surrounded by multiple ISs as part of a 26 kb genetic island. Heterologous expression of GPC-1 in E. coli TOP10 led to increased MICs of penicillins, oxyimino-cephalosporins, aztreonam and imipenem, but not of meropenem or ertapenem. Spectrophotometric measurements supported the MIC studies, but detected a slight hydrolysis of ertapenem and meropenem when using high concentrations of purified enzyme.

CONCLUSIONS

The biochemical characterization of GPC-1 emphasizes the ongoing emergence of novel carbapenemases. Strains expressing a weak carbapenemase like GPC-1 might go unrecognized by routine diagnostics due to low MICs for the bacterial strains producing such enzymes.

Role of AmpG in the resistance to β-lactam agents, including cephalosporins and carbapenems: candidate for a novel antimicrobial target

BACKGROUND

A complex cascade of genes, enzymes, and transcription factors regulates AmpC β-lactamase overexpression. We investigated the network of AmpC β-lactamase overexpression in Klebsiella aerogenes and identified the role of AmpG in resistance to β-lactam agents, including cephalosporins and carbapenems.

METHODS

A transposon mutant library was created for carbapenem-resistant K. aerogenes YMC2008-M09-943034 (KE-Y1) to screen for candidates with increased susceptibility to carbapenems, which identified the susceptible mutant derivatives KE-Y3 and KE-Y6. All the strains were subjected to highly contiguous de novo assemblies using PacBio sequencing to investigate the loss of resistance due to transposon insertion. Complementation and knock-out experiments using lambda Red-mediated homologous recombinase and CRISPR-Cas9 were performed to confirm the role of gene of interest.

RESULTS

In-depth analysis of KE-Y3 and KE-Y6 revealed the insertion of a transposon at six positions in each strain, at which truncation of the AmpG permease gene was common in both. The disruption of the AmpG permease leads to carbapenem susceptibility, which was further confirmed by complementation. We generated an AmpG permease gene knockout using lambda Red-mediated recombineering in K. aerogenes KE-Y1 and a CRISPR-Cas9-mediated gene knockout in multidrug-resistant Klebsiella pneumoniae-YMC/2013/D to confer carbapenem susceptibility.

CONCLUSIONS

These findings suggest that inhibition of the AmpG is a potential strategy to increase the efficacy of β-lactam agents against Klebsiella aerogenes.

Exploring antimicrobial resistance to beta-lactams, aminoglycosides and fluoroquinolones in E. coli and K. pneumoniae using proteogenomics

Antimicrobial resistance is mostly studied by means of phenotypic growth inhibition determinations, in combination with PCR confirmations or further characterization by means of whole genome sequencing (WGS). However, the actual proteins that cause resistance such as enzymes and a lack of porins cannot be detected by these methods. Improvements in liquid chromatography (LC) and mass spectrometry (MS) enabled easier and more comprehensive proteome analysis. In the current study, susceptibility testing, WGS and MS are combined into a multi-omics approach to analyze resistance against frequently used antibiotics within the beta-lactam, aminoglycoside and fluoroquinolone group in E. coli and K. pneumoniae. Our aim was to study which currently known mechanisms of resistance can be detected at the protein level using liquid chromatography-mass spectrometry (LC-MS/MS) and to assess whether these could explain beta-lactam, aminoglycoside, and fluoroquinolone resistance in the studied isolates. Furthermore, we aimed to identify significant protein to resistance correlations which have not yet been described before and to correlate the abundance of different porins in relation to resistance to different classes of antibiotics. Whole genome sequencing, high-resolution LC-MS/MS and antimicrobial susceptibility testing by broth microdilution were performed for 187 clinical E. coli and K. pneumoniae isolates. Resistance genes and proteins were identified using the Comprehensive Antibiotic Resistance Database (CARD). All proteins were annotated using the NCBI RefSeq database and Prokka. Proteins of small spectrum beta-lactamases, extended spectrum beta-lactamases, AmpC beta-lactamases, carbapenemases, and proteins of 16S ribosomal RNA methyltransferases and aminoglycoside acetyltransferases can be detected in E. coli and K. pneumoniae by LC-MS/MS. The detected mechanisms matched with the phenotype in the majority of isolates. Differences in the abundance and the primary structure of other proteins such as porins also correlated with resistance. LC-MS/MS is a different and complementary method which can be used to characterize antimicrobial resistance in detail as not only the primary resistance causing mechanisms are detected, but also secondary enhancing resistance mechanisms.

Prevalence of extended-spectrum β-lactamase (ESBL)-producing Salmonella enterica from retail fishes in Egypt: A major threat to public health

The increase in multidrug-resistant Salmonella enterica and its spread from food to humans are considered a serious public health concern worldwide. Little is currently known about the prevalence of extended-spectrum β-lactamase (ESBL)-producing S. enterica in fish in Africa. Therefore, this study aimed to investigate the existence of ESBL-producing S. enterica in retail fish in Egypt. In total, 200 fish samples were collected randomly from various retail fish markets in Egypt. S. enterica were detected in 19 (9.5%; 95% CI: 5.8-14.4) of the fish samples analyzed. Of the 19 non-repetitive S. enterica isolates, 18 were serologically categorized into eight S. enterica serovars and a non-typable serovar. All 19 S. enterica isolates (100%) showed multidrug-resistant phenotypes to at least three classes of antimicrobials, and 11 (57.9%) exhibited an ESBL-resistant phenotype and harbored at least one ESBL-encoding gene. The ESBL-producing S. enterica serovars were as follows: Kentucky (3 isolates; 15.8%), Enteritidis (2 isolates; 10.5%), Typhimurium (2 isolates; 10.5%), and 1 isolate (5.3%) each of Infantis, Virchow, Paratyphi B, and Senftenberg. The identified β-lactamase-encoding genes included ESBL-encoding genes bla_CTX-M-3, bla_CTX-M-14, bla_CTX-M-15, bla_SHV-1, bla_SHV-2 and bla_SHV-12; the AmpC β-lactamase-encoding gene bla_CMY-2; and the narrow-spectrum β-lactamase-encoding genes bla_TEM-1 and bla_OXA-1. All S. enterica isolates were negative for carbapenemase-encoding genes. Molecular analysis of plasmid transferability and replicon typing revealed that most plasmids (with β-lactamase-encoding genes) were transferrable, and the most common incompatibility groups were IncI1, IncA/C, IncHI1, and IncN. To the best of our knowledge, this is the first report for molecular characterization of ESBL-producing S. enterica in fish in Egypt. The occurrence of ESBL-producing S. enterica in retail fish constitutes a potential public health threat with the possibility of transmission of these strains with resistance genes to humans. Such transmission would exacerbate the resistance to an important class of antibiotics commonly used in hospitals to treat typhoid and non-typhoidal Salmonella infections.

Faecal concentrations of ceftiofur metabolites in finisher pigs administered intramuscularly with ceftiofur

The objective of this study was to determine the effects of dietary fibre level and source on faecal ceftiofur metabolites concentrations after intramuscular administration of therapeutic ceftiofur hydrochloride in finisher pigs. Pens of finisher pigs (n = 36), with an equal number of barrows and gilts, were randomly assigned to 1 of 3 dietary treatment groups: basal diet composed of corn grain and soy bean meal with no supplement and formulated to contain 8.7% neutral detergent fibre (NDF), supplemented with 20% distillers dried grains with solubles (a byproduct of the ethanol production from corn grain) formulated to contain 13.6% NDF, primarily insoluble fibre or supplemented with 14.5% sugar beet pulp formulated to contain 13.6% NDF. Faecal samples were collected 6–8 hr after ceftiofur injection from treated and untreated pen‐mate pigs on days 1 and 3 of the 3‐day treatment regimen. Faecal concentrations of ceftiofur metabolites, including the major metabolite, desfuroylceftiofur, were analysed by reverse‐phase high pressure liquid chromatography with ultraviolet detection. Overall, the faecal concentrations of ceftiofur metabolites did not differ significantly between the dietary treatments. The mean concentrations of metabolites tended to be lower (p = .1) on day 3 compared to day 1 of the 3‐day treatment regimen. Faecal concentrations of metabolites were not affected by the gender of the finisher pigs. The concentrations of ceftiofur metabolites in the faeces are likely reflective of the microbial activity in the hindgut. Our data suggest that the fibre level and source used in the study did not affect the faecal concentrations of ceftiofur metabolites.

Genetic Characterization of CTX-M-2-Producing Klebsiella pneumoniae and Klebsiella oxytoca Associated With Bovine Mastitis in Japan

CTX-M-2-producing Klebsiella oxytoca (K. oxytoca) has not received much attention in animal husbandry compared with Klebsiella pneumoniae (K. pneumoniae), a major reservoir of extended-spectrum β-lactamase (ESBL) genes. Bacteriological examinations of 1,466 mastitic milk samples between October 2012 and December 2014 were conducted. Ninety-five K. pneumoniae isolates (total prevalence: 6.5%) and 81 K. oxytoca isolates (total prevalence: 5.5%) were obtained. Seventeen K. pneumoniae isolates obtained from 15 animals reared on 11 farms and 9 K. oxytoca isolates obtained from 9 animals reared on the same farm were phenotypically confirmed to be ESBL producers. All nine ESBL-producing K. oxytoca isolates were obtained from one farm between June and November 2013 and related to a significantly (p < 0.05) higher monthly prevalence of mild mastitis (in June, August, September, October, and November 2013). Pulsed-field gel electrophoresis (PFGE) patterns of ESBL-producing K. pneumoniae isolates were distinguished from each other by more than 6-band differences except for two isolates from two animals, whereas all nine K. oxytoca isolates showed an identical PFGE pattern. Transferability of the bla _CTX-M-2 gene was found in 14 K. pneumoniae and 9 K. oxytoca isolates by conjugation analysis. Of these isolates, the bla _CTX-M-2 gene was detected on plasmids belonging to the incompatibility (Inc) groups P and N derived from five K. pneumoniae and nine K. oxytoca isolates, respectively, although the plasmids from the remaining nine K. pneumoniae were untypeable. All the transconjugants exhibited elevated minimum inhibitory concentrations of ampicillin, cefotaxime, and ceftiofur compared with those in the wild-type, recipient strain. Restriction fragment length polymorphism analysis demonstrated that the IncN plasmids extracted from eight of nine transconjugants, which received resistance against β-lactams from K. oxytoca, showed an identical DraI digestion pattern. These results suggest that the CTX-M-2-producing K. oxytoca strain with the above-mentioned characteristics may have clonally spread within a farm, whereas the bla _CTX-M-2 gene in K. pneumoniae possibly disseminated among the farms through different plasmids. Thus, monitoring of ESBL genes, including the bla _CTX-M-2 gene, among causative agents of bacterial mastitis in cows can help to develop relevant treatments and control practices.

Prevalence and Characterization of Extended-Spectrum Beta-Lactamase-Producing Enterobacteriaceae in Major Hospitals in Gabon

In Gabon, few data exist on extended-spectrum beta-lactamases-producing Enterobacteriaceae (ESBL-PE). This study investigated ESBL-PE prevalence and the associated resistance genes in clinical samples (n = 5,956) and anal swabs (n = 78) analyzed in eight hospitals and a medical analysis laboratory in Gabon from January 2016 to March 2018. Matrix-Assisted Laser Desorption Ionization-Time Of Flight (MALDI-TOF) mass spectrometry analysis identified 790 Enterobacteriaceae isolates (n = 712 clinical samples and n = 78 fecal samples). ESBL-PE prevalence (Müller-Hinton agar disk diffusion method and double-disk synergy test) was 11.8% (84/712) in clinical samples (15.5% from inpatients and 7.1% from outpatients; p < 0.05) and 16.7% (13/78) in carriage isolates. Most ESBL-PE were isolated from urine samples (46/84). In clinical and carriage ESBL-PE isolates, Escherichia coli was predominant (42.8% and 61.5%; phylogroups A, B1, B2, and D), followed by Klebsiella pneumoniae (41.7% and 23.1%). Multiplex PCR and bi-directional sequencing showed that CTX-M group 1 (blaCTX-M-15) was predominant in clinical and carriage ESBL-PE (94% and 92.3%) among which 85.7% and 92.3% also harbored one to three β-lactamase-encoding genes (blaTEM-1, blaOXA-1, or blaSHV-1). Resistance genes were detected in all hospitals in Gabon. ESBL-PE prevalence in Gabon has not reached alarming levels yet, but corrective and monitoring measures are needed to curb their emergence.

Identification of β-Lactamase-Encoding (bla) Genes in Phenotypically β-Lactam-Resistant Escherichia coli Isolated from Young Calves in Belgium

The bla genes identification present in 94 phenotypically resistant Escherichia coli isolated from feces or intestinal contents of young calves with diarrhea or enteritis in Belgium was performed by microarrays (MA) and whole genome sequencing (WGS). According to their resistance phenotypes to 8 β-lactams at the disk diffusion assay these 94 E. coli produced a narrow-spectrum-β-lactamase (NSBL), an extended-spectrum-β-lactamase (ESBL) or a cephalosporinase (AmpC). All ESBL-encoding genes identified by MA and WGS belonged to the bla_CTX-M family, with a majority to the bla_CTX-M-1 subfamily. Two different genes encoding an AmpC, bla_CMY-2, and bla_DHA-1 were detected in isolates with an AmpC phenotype. The bla_TEM-1 and the bla_OXA-1 were detected alone in isolates with a NSBL phenotype or in combination with ESBL-/AmpC-encoding bla genes. Furthermore, the WGS identified mutations in the ampC gene promoter at nucleotides -42 (C>T) and/or -18 (G>A) that could not be identified by MA, in several isolates with an AmpC-like resistance phenotype. No carbapenemase-encoding gene was detected. To our knowledge this is the first survey on the identification of bla genes in E. coli isolated from young diarrheic or septicemic calves in Belgium.

A Novel Marine Pathogen Isolated from Wild Cunners (Tautogolabrus adspersus): Comparative Genomics and Transcriptome Profiling of Pseudomonas sp. Strain J380

Cunner (Tautogolabrus adspersus) is a cleaner fish being considered for utilized in the North Atlantic salmon (Salmo salar) aquaculture industry to biocontrol sea lice infestations. However, bacterial diseases due to natural infections in wild cunners have yet to be described. This study reports the isolation of Pseudomonas sp. J380 from infected wild cunners and its phenotypic, genomic, and transcriptomic characterization. This Gram-negative motile rod-shaped bacterium showed a mesophilic (4-28 °C) and halotolerant growth. Under iron-limited conditions, Pseudomonas sp. J380 produced pyoverdine-type fluorescent siderophore. Koch's postulates were verified in wild cunners by intraperitoneally (i.p.) injecting Pseudomonas sp. J380 at 4 × 103, 4 × 105, and 4 × 107 colony forming units (CFU)/dose. Host-range and comparative virulence were also investigated in lumpfish and Atlantic salmon i.p. injected with ~106 CFU/dose. Lumpfish were more susceptible compared to cunners, and Atlantic salmon was resistant to Pseudomonas sp. J380 infection. Cunner tissues were heavily colonized by Pseudomonas sp. J380 compared to lumpfish and Atlantic salmon suggesting that it might be an opportunistic pathogen in cunners. The genome of Pseudomonas sp. J380 was 6.26 megabases (Mb) with a guanine-cytosine (GC) content of 59.7%. Biochemical profiles, as well as comparative and phylogenomic analyses, suggested that Pseudomonas sp. J380 belongs to the P. fluorescens species complex. Transcriptome profiling under iron-limited vs. iron-enriched conditions identified 1159 differentially expressed genes (DEGs). Cellular metabolic processes, such as ribosomal and energy production, and protein synthesis, were impeded by iron limitation. In contrast, genes involved in environmental adaptation mechanisms including two-component systems, histidine catabolism, and redox balance were transcriptionally up-regulated. Furthermore, iron limitation triggered the differential expression of genes encoding proteins associated with iron homeostasis. As the first report on a bacterial infection in cunners, the current study provides an overview of a new marine pathogen, Pseudomonas sp. J380.

Brief survey on organometalated antibacterial drugs and metal-based materials with antibacterial activity

Rising bacterial antibiotic resistance is a global threat. To deal with it, new antibacterial agents and antiseptic materials need to be developed. One alternative in this quest is the organometallic derivatization of well-established antibacterial drugs and also the fabrication of advanced metal-based materials having antibacterial properties. Metal-based agents and materials often show new modes of antimicrobial action which enable them to overcome drug resistance in pathogenic bacterial strains. This review summarizes recent (2017-2020) progress in the field of organometallic-derived antibacterial drugs and metal-based materials having antibacterial activity. Specifically, it covers organometallic derivatives of antibacterial drugs including β-lactams, ciprofloxacin, isoniazid, trimethoprim, sulfadoxine, sulfamethoxazole, and ethambutol as well as non-antibacterial drugs like metformin, phenformin and aspirin. Recent advances and reported clinical trials in the use of metal-based nanomaterials as antibiofouling coatings on medical devices, as photocatalytic agents in indoor air pollutant control, and also as photodynamic/photothermal antimicrobial agents are also summarized.

Antimicrobial Potential of Naturally Occurring Bioactive Secondary Metabolites

The use of traditional medicines of natural origin has been prevalent since ancient times globally as the plants produce a great diversity in their secondary metabolites. The naturally occurring bioactive constituents in food and other plant materials have shown widespread attention for their use as alternative medicine to prevent and cure microbial growth with the least toxic manifestations. The inclusion of these contents revealed their crucial role to improve the therapeutic efficacy of the classical drugs against various pathogenic microorganisms. Furthermore, several metabolites have also been explored in combination with antimicrobial agents to overcome the problems associated with drug resistance. This current review discusses the antimicrobial activities of secondary metabolites as well as their role in drug sensitivity against multiple-drug resistant pathogenic microbes.

Evaluation of Asymptomatic Bacteriuria and Urinary Tract Infection in Patients With Primary Sjögren's Syndrome

Objectives

This study aims to determine the frequency and risk factors of bacteriuria and urinary tract infection (UTI) in patients with primary Sjögren's syndrome (SS) and their differences from healthy individuals and rheumatoid arthritis (RA) patients.

Patients and methods

The study included 107 female primary SS patients (mean age 50.7±11.6 years; range, 23 to 76 years), 53 healthy female control subjects (mean age 46.8±15.5 years; range 21 to 80 years), and 40 females with RA (mean age 51.7±14.2 years; range, 25 to 79 years). Participants were questioned for UTI risk factors and symptoms. Middle stream urine samples were taken and cultured. All participants were examined with urinary symptom questioning survey of American Urological Association (AUA-7).

Results

The urine cultures were positive in 18 primary SS patients (16.8%), eight RA patients (20%), and two healthy controls (3.7%). Escherichia coli, enterococci, Klebsiella, streptococci, and candida were detected in SS patients' cultures. Extended-spectrum beta-lactamase was positive in three cultures. Asymptomatic bacteriuria was not detected in any SS patient. The highest AUA-7 score was determined in SS group (p=0.031). Nineteen SS patients had vaginal dryness symptom and their AUA-7 scores were higher than the rest of the SS group. The risk of UTI development was not different between those who had or did not have vaginal dryness.

Conclusion

Urinary tract infections are seen more often in SS patients rather than normal population, which may be caused by SS' urinary system effects. It is difficult to distinguish between asymptomatic bacteriuria and infection because of the underlying urinary symptoms. Clinicians must be careful in patients receiving immunosuppressive therapy due to the high frequency of UTIs.

Hinge-shift mechanism as a protein design principle for the evolution of β-lactamases from substrate promiscuity to specificity

TEM-1 β-lactamase degrades β-lactam antibiotics with a strong preference for penicillins. Sequence reconstruction studies indicate that it evolved from ancestral enzymes that degraded a variety of β-lactam antibiotics with moderate efficiency. This generalist to specialist conversion involved more than 100 mutational changes, but conserved fold and catalytic residues, suggesting a role for dynamics in enzyme evolution. Here, we develop a conformational dynamics computational approach to rationally mold a protein flexibility profile on the basis of a hinge-shift mechanism. By deliberately weighting and altering the conformational dynamics of a putative Precambrian β-lactamase, we engineer enzyme specificity that mimics the modern TEM-1 β-lactamase with only 21 amino acid replacements. Our conformational dynamics design thus re-enacts the evolutionary process and provides a rational allosteric approach for manipulating function while conserving the enzyme active site.

Genomic characterisation and epidemiology of nosocomial Serratia marcescens isolates resistant to ceftazidime and their plasmids mediating rare blaTEM-61

OBJECTIVES

We determined the whole DNA sequences of plasmids carrying a rare extended-spectrum β-lactamase gene (bla_TEM-61) to precisely understand the spread of resistance among nosocomial Serratia marcescens populations.

METHODS

Twenty non-duplicate ceftazidime-resistant S. marcescens nosocomial isolates (ceftazidime MICs, 32 to >128 mg/L) collected over 1 year were pulsotyped and nucleotide sequences of the bla_TEM-61 gene and its promoter region were determined. Twelve representative isolates were analysed by whole-genome sequencing.

RESULTS

The 20 isolates comprised two distinct pulsotypes: I (14 isolates) and II (6 isolates). They all contained the bla_TEM-61 gene. A polymorphism in the repeat number of a 15-nucleotide sequence (5'-ATGTCATGATAATAA-3') was found in the promoter region of bla_TEM-61; two, three and four repeat units were found in 6, 12 and 2 isolates, respectively. Single nucleotide polymorphism (SNP)-based phylogenetic analysis of 12 isolates revealed that 7 isolates of pulsotype I (12-44 SNP differences) and 5 isolates of pulsotype II (15-55 SNP differences) formed two distinct clusters of genotypes 1 and 2, respectively. All 12 isolates harboured a plasmid carrying the Tn1-bla_TEM-61 element, although they were slightly different in size (78 883 bp, 78 898 bp and 78 913 bp) owing to differences in the number of 15-bp repetitive sequences. A 42 542-bp broad-host-range plasmid carrying the Tn1-bla_TEM-61 element was also found in one of the isolates.

CONCLUSIONS

We characterised a plasmid-encoded novel Tn1-bla_TEM-61 element and transposon-dependent mechanisms underlying the propagation of antibiotic resistance, together with repeated new polymorphic 15-bp units in the promoter of bla_TEM-61.

A Test for the Rapid Detection of the Cefazolin Inoculum Effect in Methicillin-Susceptible Staphylococcus aureus

The cefazolin inoculum effect (CzIE) has been associated with therapeutic failures and mortality in invasive methicillin-susceptible Staphylococcus aureus (MSSA) infections. A diagnostic test to detect the CzIE is not currently available. We developed a rapid (∼3 h) CzIE colorimetric test to detect staphylococcal-β-lactamase (BlaZ) activity in supernatants after ampicillin induction. The test was validated using 689 bloodstream MSSA isolates recovered from Latin America and the United States. The cefazolin MIC determination at a high inoculum (10⁷ CFU/ml) was used as a reference standard (cutoff ≥16 μg/ml). All isolates underwent genome sequencing. A total of 257 (37.3%) of MSSA isolates exhibited the CzIE by the reference standard method. The overall sensitivity and specificity of the colorimetric test was 82.5% and 88.9%, respectively. Sensitivity in MSSA isolates harboring type A BlaZ (the most efficient enzyme against cefazolin) was 92.7% with a specificity of 87.8%. The performance of the test was lower against type B and C enzymes (sensitivities of 53.3% and 72.3%, respectively). When the reference value was set to ≥32 μg/ml, the sensitivity for isolates carrying type A enzymes was 98.2%. Specificity was 100% for MSSA lacking blaZ The overall negative predictive value ranged from 81.4% to 95.6% in Latin American countries using published prevalence rates of the CzIE. MSSA isolates from the United States were genetically diverse, with no distinguishing genomic differences from Latin American MSSA, distributed among 18 sequence types. A novel test can readily identify most MSSA isolates exhibiting the CzIE, particularly those carrying type A BlaZ. In contrast to the MIC determination using high inoculum, the rapid test is inexpensive, feasible, and easy to perform. After minor validation steps, it could be incorporated into the routine clinical laboratory workflow.

A proposed scheme for the monitoring of antibiotic resistance in veterinary pathogens of food animals in the UK

BACKGROUND

Antibiotic resistance in bacteria is a global threat to both animal and public health, and detecting its occurrence is an important component of control strategies. Monitoring programmes for antibiotic resistance are currently in place in food-producing animals in the European Union covering the zoonotic bacteria Salmonella enterica, Campylobacter coli and Campylobacter jejuni and the indicator bacteria Escherichia coli, Enterococcus faecalis and Enterococcus faecium. However, there is no equivalent pan-European statutory monitoring programme covering the antibiotic susceptibility of veterinary bacterial pathogens in food animals. This paper considers that issue and aims to facilitate and stimulate further discussion.

METHODS

Recommendations, proposed by the authors from the scientific literature and following expert discussion at international meetings, are presented for monitoring the susceptibility of key veterinary pathogens.

RESULTS

The selected veterinary pathogens comprise Actinobacillus pleuropneumoniae, Bordetella bronchiseptica, E. coli, Histophilus somni, Mannheimia haemolytica, Pasteurella multocida, Staphylococcus aureus and Streptococcus spp. from the major food animal species cattle, pigs and poultry. The organisms are tested using harmonised panels of antibiotics over specified dilution ranges in a broth microdilution method.

CONCLUSION

The selected antibiotics and their respective dilution ranges are presented together with the underlying rationale for inclusion; the ranges chosen are suitable for incorporation into three microtitre plates, with each organism tested using a single plate. The recommendations are being implemented in 2020 in the UK for monitoring of the susceptibility of veterinary bacterial pathogens.

Benzimidazole and Benzoxazole Zinc Chelators as Inhibitors of Metallo-β-Lactamase NDM-1

Bacterial expression of β-lactamases, which hydrolyze β-lactam antibiotics, contributes to the growing threat of antibacterial drug resistance. Metallo-β-lactamases, such as NDM-1, use catalytic zinc ions in their active sites and hydrolyze nearly all clinically available β-lactam antibiotics. Inhibitors of metallo-β-lactamases are urgently needed to overcome this resistance mechanism. Zinc-binding compounds are promising leads for inhibitor development, as many NDM-1 inhibitors contain zinc-binding pharmacophores. Here, we evaluated 13 chelating agents containing benzimidazole and benzoxazole scaffolds as NDM-1 inhibitors. Six of the compounds showed potent inhibitory activity with IC50 values as low as 0.38 μM, and several compounds restored the meropenem susceptibility of NDM-1-expressing E. coli. Spectroscopic and docking studies suggest ternary complex formation as the mechanism of inhibition, making these compounds promising for development as NDM-1 inhibitors.

Risk factor analysis for piperacillin-tazobactam-resistant Enterobacter spp. bacteremia at a tertiary hospital

This study aimed to analyze the risk factors for piperacillin-tazobactam (TZP¹)-resistant Enterobacter spp. bacteremia. The medical records of 111 patients with Enterobacter spp. bacteremia divided into a TZP-susceptible group (minimum inhibitory concentrations [MICs²] ≤16 μg/mL) and TZP-resistant group (MICs >16 μg/mL) were retrospectively reviewed. The male-to-female ratio, age, underlying disease, and infection site did not differ between the 2 groups. Multivariate analysis revealed that the independent predictor associated with TZP-resistant Enterobacter spp. bacteremia was the previous usage of third-generation cephalosporins (P = 0.036). In conclusion, TZP administration in cases of suspected Enterobacter spp. bacteremia previously treated with third-generation cephalosporin should be cautiously considered.

ModFlex: Towards Function Focused Protein Modeling

There is a wide, and continuously widening, gap between the number of proteins known only by their amino acid sequence versus those structurally characterized by direct experiment. To close this gap, we mostly rely on homology-based inference and modeling to reason about the structures of the uncharacterized proteins by using structures of homologous proteins as templates. With the rapidly growing size of the Protein Data Bank, there are often multiple choices of templates, including multiple sets of coordinates from the same protein. The substantial conformational differences observed between different experimental structures of the same protein often reflect function related structural flexibility. Thus, depending on the questions being asked, using distant homologs, or coordinate sets with lower resolution but solved in the appropriate functional form, as templates may be more informative. The ModFlex server (https://modflex.org/) addresses this seldom mentioned gap in the standard homology modeling approach by providing the user with an interface with multiple options and tools to select the most relevant template and explore the range of structural diversity in the available templates. ModFlex is closely integrated with a range of other programs and servers developed in our group for the analysis and visualization of protein structural flexibility and divergence.