Characterization of Inhibitor-Resistant TEM β-Lactamases and Mechanisms of Fluoroquinolone Resistance in Escherichia coli Isolates

Prevalence of poultry Escherichia coli isolates producing extended-spectrum beta-lactamases and their public health importance

Recently, different reports highlighted the problem with dissemination of Escherichia coli producing extended spectrum beta-lactamases (ESBL) in poultry farms in Europe. The high incidence of Escherichia coli among poultry in Europe harbouring blaCTX-M-1 and the occurrence of ESBL and AmpC-producing Escherichia coli in raw meat samples collected from slaughterhouses in Europe have been discussed. ESBL-producing Enterobacteriaceae can be transmitted along the broiler production chain. Plasmids responsible for ESBL production frequently carry genes coding resistance to other antimicrobial classes, such as fluoroquinolones, aminoglycosides, sulphonamides. Resistance to cephalosporins in Enterobacteriaceae is of special concern for public health, because these anti­microbial agents are critically important. The aim of this mini review was to describe the mechanisms of resistance and prevalence of ESBL-producing E. coli. It is important to investigate the spread of these bacteria among poultry, the role of farm birds as reservoir of E. coli and the risk for people.

Fecal Carriage and Genetic Characterization of CTX-M-1/9/1-Producing Escherichia coli From Healthy Humans in Hangzhou, China

CTX-M-199, a novel chimeric β-lactamase which mediated resistance to sulbactam and tazobactam, was recently identified in Hangzhou, China. This study investigated the prevalence of fecal carriage of bacteria producing CTX-M-199 and other CTX-M-1/9/1-type enzymes among healthy individuals and characterized the genetic features of bla_{CTX–M–1/9/1}-bearing mobile elements. A total of 74 Enterobacterales strains carrying various bla_{CTX–M–1/9/1} genes, including bla_CTX–M–64 (n = 40, carriage rate of 0.74%), bla_{CTX–M–199} (n = 23, 0.40%), bla_{CTX–M–123} (n = 5, 0.10%), novel bla_{CTX–M–153} (n = 5, 0.10%), and bla_{CTX–M–132} (n = 2, 0.04%), were isolated from 68 out of 5,000 (1.36%) fecal samples of healthy adults in Hangzhou City. Phylogenetic analysis based on whole-genome sequencing data showed that 72 bla_{CTX–M–1/9/1}-bearing Escherichia coli isolates were clustered into four major clades, three of which included CTX-M-199 producers. Sixty out of 75 bla_{CTX–M–1/9/1} genes were located on plasmids belonging to four Inc types: IncI2, IncI1, IncFIB, and IncHI2. The bla_{CTX–M–199} genes were harbored by three of the four types of plasmids except for IncHI2. All these bla_{CTX–M–1/9/1} genes were carried on an ISEcp1-mediated transposition unit. In conclusion, human fecal carriage of bla_{CTX–M–1/9/1} was low in healthy populations of China. The ISEcp1 was commonly associated with bla_{CTX–M–1/9/1} and may mediate its transmission on various mobile elements. Our findings provide insights into the dissemination and the development of further measures for the control of pathogens producing CTX-M-1/9/1-type enzymes.

Genomic analysis of phylogenetic group B2 extraintestinal pathogenic E. coli causing infections in dogs in Australia

This study investigated the prevalence of extraintestinal pathogenic E. coli (ExPEC)-associated sequence types (STs) from phylogenetic group B2 among 449 fluoroquinolone-susceptible dog clinical isolates from Australia. Isolates underwent PCR-based phylotyping and random amplified polymorphic DNA analysis to determine clonal relatedness. Of the 317 so-identified group B2 isolates, 77 underwent whole genome sequencing (WGS), whereas the remainder underwent PCR-based screening for ST complexes (STc) STc12, STc73, STc372, and ST131. The predominant ST was ST372 according to both WGS (31 % of 77) and ST-specific PCR (22 % of 240), followed by (per WGS) ST73 (17 %), ST12 (7 %), and ST80 (7 %). A WGS-based phylogenetic comparison of ST73 isolates from dogs, cats, and humans showed considerable overall phylogenetic diversity. Although most clusters were species-specific, some contained closely related human and animal (dog > cat) isolates. For dogs in Australia these findings both confirm ST372 as the predominant E. coli clonal lineage causing extraintestinal infections and clarify the importance of human-associated group B2 lineage ST73 as a cause of UTI, with some strains possibly being capable of bi-directional (i.e., dog-human and human-dog) transmission.

The impact of long-distance mutations on the Ω-loop conformation in TEM type β-lactamases

β-lactamases are hydrolytic enzymes primarily responsible for occurrence and abundance of bacteria resistant to β-lactam antibiotics. TEM type β-lactamases are formed by the parent enzyme TEM-1 and more than two hundred of its mutants. Positions for the known amino acid substitutions cover ∼30% of TEM type enzyme's sequence. These substitutions are divided into the key mutations that lead to changes in catalytic properties of β-lactamases, and the secondary ones, which role is poorly understood. In this study, Residue Interaction Networks were constructed from molecular dynamic trajectories of β-lactamase TEM-1 and its variants with two key substitutions, G238S and E240K, and their combinations with secondary ones (M182T and Q39K). Particular attention was paid to a detailed analysis of the interactions that affect conformation and mobility of the Ω-loop, representing a part of the β-lactamase active site. It was shown that key mutations weakened the stability of contact inside the Ω-loop thus increasing its mobility. Combination of three amino acid substitutions, including the 182 residue, leads to the release of R65 promoting its new contacts with N175 and D176. As a result, Ω-loop is fixed on the protein globule. The second distal mutation Q39K prevents changes in spatial position of R65, which lead to the weakening of the effect of M182T substitution and the recovery of the Ω-loop mobility. Thus, the distal secondary mutations are directed for recovering the mobility of enzyme disturbed by the key mutations responsible for expansion of substrate specificity. AbbreviationsESBLextended spectrum beta-lactamasesIRinhibitor resistant beta-lactamasesMDmolecular dynamicsRINresidue interaction networksRMSDroot mean square deviationRMSFroot mean square fluctuations.Communicated by Ramaswamy H. Sarma.

Past and Present Perspectives on β-Lactamases

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

Mutual influence of secondary and key drug-resistance mutations on catalytic properties and thermal stability of TEM-type β-lactamases

Highly mutable β-lactamases are responsible for the ability of Gram-negative bacteria to resist β-lactam antibiotics. Using site-directed mutagenesis technique, we have produced in vitro a number of recombinant analogs of naturally occurring TEM-type β-lactamases, bearing the secondary substitution Q39K and key mutations related to the extended-spectrum (E104K, R164S) and inhibitor-resistant (M69V) β-lactamases. The mutation Q39K alone was found to be neutral and hardly affected the catalytic properties of β-lactamases. However, in combination with the key mutations, this substitution resulted in decreased KM values towards hydrolysis of a chromogenic substrate, CENTA. The ability of enzymes to restore catalytic activity after exposure to elevated temperature has been examined. All double and triple mutants of β-lactamase TEM-1 bearing the Q39K substitution showed lower thermal stability compared with the enzyme with Q39 intact. A sharp decrease in the stability was observed when Q39K was combined with E104K and M69V. The key R164S substitution demonstrated unusual ability to resist thermal inactivation. Computer analysis of the structure and molecular dynamics of β-lactamase TEM-1 revealed a network of hydrogen bonds from the residues Q39 and K32, related to the N-terminal α-helix, towards the residues R244 and G236, located in the vicinity of the enzyme's catalytic site. Replacement of Q39 by lysine in combination with the key drug resistance mutations may be responsible for loss of protein thermal stability and elevated mobility of its secondary structure elements. This effect on the activity of β-lactamases can be used as a new potential target for inhibiting the enzyme.

Isolation, Antimicrobial Susceptibility Profile and Detection of Sul1, blaTEM, and blaSHV in Amoxicillin-Clavulanate-Resistant Bacteria Isolated From Retail Sausages in Kampar, Malaysia

Background

Due to the overuse of antibiotics in livestock as a growth-promoting agent, the emergence of multi-antibiotic resistant bacteria is becoming a concern.

Objectives

In this study, we aimed to detect the presence and discover the molecular determinants of foodborne bacteria in retail sausages resistant towards the antibacterial agent amoxicillin-clavulanate.

Methods

Two grams of sausages were chopped into small pieces and transferred into sterile Luria-Bertani (LB) enrichment broths overnight before they were plated on MacConkey agar petri dishes. The bacteria isolated were then screened for amoxicillin-clavulanate resistance, and an antimicrobial susceptibility test of each isolate was performed by using the disc diffusion method. Double synergy and phenotypic tests were carried out to detect the presence of extended spectrum β-lactamase (ESBL). API 20E kit was used to identify the Enterobacteriaceae. All isolates were further examined by polymerase chain reaction (PCR) for resistant genes blaOXA-1, blaOXA-10, plasmid-mediated AmpC (blaCMY and blaDHA), and the chromosome-mediated AmpC, Sul1, blaTEM, and blaSHV genes.

Results

A total of 18 amoxicillin-clavulanate resistant isolates were obtained from seven different types of retail sausages. Only half of them were identified as Enterobacteriaceae, but none were ESBL-producers. All the 18 isolated strains demonstrated resistance towards amoxicillin-clavulanate, penicillin and oxacillin (100%), cefotaxime (71.4%), cefpodoxime (66.7%), and ampicillin (83.3%). blaTEM was the most frequently detected β-lactamase gene. Both plasmid- and chromosomal-bound blaTEM genes were detected in all of the isolated Enterobacteriaceae. blaSHV and Sul1 accounted for 22.2% and 11.1% of the amoxicillin-clavulanate resistant isolates, respectively, whereas blaAMPC, blaCMY, blaDHA, blaOXA-1, and blaOXA-10 were not found in any of the isolates. The only one ESBL-producing bacteria detected in this study was Chryseobacterium meningosepticum, which harbored the blaTEM gene.

Conclusions

The multidrug resistant bacteria that carry antibiotic resistant genes from retail sausages may increase the risk of transmission to humans via the consumption of contaminated sausages. Stricter measures must be taken to address the use of antibiotics in animal agriculture and to consider their potential impact on human health.