Plasmid-determined AmpC-type beta-lactamases

Molecular characteristics of extended-spectrum β-lactamase/AmpC-producing Salmonella enterica serovar Virchow isolated from food-producing animals during 2010-2017 in South Korea

Global dissemination of non-typhoidal Salmonella producing extended-spectrum β-lactamase (ESBL) is a public-health concern. Recently, the prevalence of Salmonella spp. resistant to third-generation cephalosporins has been increasing in food-producing animals in Korea. In this study, we investigated resistance mechanisms and molecular characteristics of S. Virchow isolates resistant to extended-spectrum cephalosporins (ESCs). We obtained 265 S. Virchow isolates from fecal and carcasses samples of cattle (n = 2), pigs (n = 7), and chickens (n = 256) during 2010-2017, and observed high ESC-resistance (63.8%, 169/265); most of the resistant isolates (96.4%) were obtained from chickens. ESC-resistant S. Virchow isolates (n = 169) showed significantly higher resistance rates to other antimicrobials (especially aminoglycosides and tetracycline, p-value <0.0001), as well as prevalence of multidrug resistance, than did ESC-susceptible S. Virchow isolates (n = 96). All ESC-resistant S. Virchow produced CTX-M-15-type ESBL (n = 147) and/or CMY-2-type AmpC β-lactamase (n = 23). ESC-resistant S. Virchow represented seven pulsotypes, predominantly composed of type II (58.6%) and III (26.0%), detected in 69 farms in 10 provinces, and 33 farms in 7 provinces, respectively. Genes encoding ESC-resistance were horizontally transferred by conjugation to recipient E. coli J53; this was demonstrated in 28.8% (42/146) of bla_CTX-M-15-positive isolates and in 50.0% (11/22) of bla_CMY-2-positive isolates. All conjugative plasmids carrying bla_CTX-M-15 and bla_CMY-2 genes belonged to ST2-IncHI2 and ST12/CC12-IncI1, respectively. Genetic features of transferred bla genes were involved with ISEcp1 in both bla_CTX-M-15 and bla_CMY-2; ISEcp1 plays a critical role in the efficient capture, expression, and mobilization of bla genes. In addition to bla_CTX-M-15 genes, resistance markers to aminoglycosides and/or tetracycline were co-transferred to recipient E. coli J53. Our results show a high prevalence of ESBL-producing S. Virchow in chickens and chicken carcasses. Specific bla_CTX-M-15 and bla_CMY-2-carrying S. Virchow clones and plasmids were predominant in food-producing animals nationwide. Restriction of antimicrobial use and proper biosecurity practices at the farm level should be urgently implemented in the poultry industry.

A Unified Numbering Scheme for Class C β-Lactamases

A standard numbering scheme has been proposed for class C β-lactamases. This will significantly enhance comparison of biochemical and biophysical studies performed on different members of this class of enzymes and facilitate communication in the field.

Characterization of antimicrobial resistance genes in Enterobacteriaceae carried by suburban mesocarnivores and locally owned and stray dogs

The role of wildlife in the dissemination of antimicrobial-resistant bacteria and antimicrobial resistance genes (ARGs) in the environment is of increasing concern. We investigated the occurrence, richness and transmissibility potential of ARGs detected in the faeces of three mesocarnivore species: the coyote (Canis latrans), raccoon (Procyon lotor) and Virginia opossum (Didelphis virginiana), and of stray and owned dogs in suburban Chicago, IL, USA. Rectal swabs were collected from live-captured coyotes (n = 32), raccoons (n = 31) and Virginia opossums (n = 22). Fresh faecal samples were collected from locally owned (n = 13) and stray dogs (n = 18) and from the live-captured mesocarnivores, when available. Faecal samples and rectal swabs were enriched to select for Enterobacteriaceae and pooled by mesocarnivore species and dog type (owned or stray). Pooled enriched samples were then analysed for the presence of ARGs using shotgun sequencing. The three mesocarnivore and stray dog samples had twice as many unique ARGs compared to the owned dog sample, which was partly driven by a greater richness of beta-lactamase genes (genes conferring resistance to penicillins and cephalosporins). Raccoon and stray dog samples had the most ARGs in common, suggesting possible exposure to similar environmental sources of ARGs. In addition to identifying clinically relevant ARGs (e.g. bla_CMY and qnrB), some ARGs were linked to the class 1 integrase gene, intI1, which may indicate anthropogenic origin. Findings from this pilot investigation suggest that the microbial communities of suburban mesocarnivores and stray dogs can host ARGs that can confer resistance to several antimicrobials used in human and veterinary medicine.

Epidemiology of Carbapenemase-Producing Klebsiella pneumoniae in a Hospital, Portugal

We aimed to provide updated epidemiologic data on carbapenem-resistant Klebsiella pneumoniae in Portugal by characterizing all isolates (N = 46) recovered during 2013–2018 in a 123-bed hospital in Lisbon. We identified bla_KPC-3 (n = 36), bla_OXA-181 (n = 9), and bla_GES-5 (n = 8) carbapenemase genes and observed co-occurrence of bla_KPC-3 and bla_GES-5 in 7 isolates. A single GES-5–producing isolate co-produced the extended-spectrum β-lactamase BEL-1; both corresponding genes were co-located on the same ColE1-like plasmid. The bla_OXA-181 gene was always located on an IncX3 plasmid, whereas bla_KPC-3 was carried on IncN, IncFII, IncFIB, and IncFIIA plasmid types. The 46 isolates were distributed into 13 pulsotypes and 9 sequence types. All isolates remained susceptible to ceftazidime/avibactam, but some exhibited reduced antimicrobial susceptibility (MIC = 3 mg/L).

Molecular diversity of extended-spectrum β-lactamases and carbapenemases, and antimicrobial resistance

Along with the recent spread of multidrug-resistant bacteria, outbreaks of extended-spectrum β-lactamase (ESBL) and carbapenemase-producing bacteria present a serious challenge to clinicians. β-lactam antibiotics are the most frequently used antibacterial agents and ESBLs, and carbapenemases confer resistance not only to carbapenem antibiotics but also to penicillin and cephem antibiotics. The mechanism of β-lactam resistance involves an efflux pump, reduced permeability, altered transpeptidases, and inactivation by β-lactamases. Horizontal gene transfer is the most common mechanism associated with the spread of extended-spectrum β-lactam- and carbapenem resistance among pathogenic bacterial species. Along with the increase in antimicrobial resistance, many different types of ESBLs and carbapenemases have emerged with different enzymatic characteristics. For example, carbapenemases are represented across classes A to D of the Ambler classification system. Because bacteria harboring different types of ESBLs and carbapenemases require specific therapeutic strategies, it is essential for clinicians to understand the characteristics of infecting pathogens. In this review, we summarize the current knowledge on carbapenem resistance by ESBLs and carbapenemases, such as class A carbapenemases, class C extended-spectrum AmpC (ESAC), carbapenem-hydrolyzing class D β-lactamases (CHDLs), and class B metallo-β-lactamases, with the aim of aiding critical care clinicians in their therapeutic decision making.

Characterization of O25b-ST131 Escherichia coli Clone Producing CTX-M-15, DHA-4, and CMY-42 in Urinary Tract Infections in a Tunisian Island

The dissemination of extended-spectrum β-lactamases encoding genes in Escherichia coli, especially in the uropathogenic O25b-ST131 E. coli clone, constitutes a real concern. We aimed to identify the molecular mechanisms of resistance to cephalosporins among E. coli clinical isolates and to estimate the prevalence of the uropathogenic O25b-ST131 clone in our study. Forty-two cephalosporin-resistant E. coli implicated in urinary tract infections were collected from the Regional Hospital of a southeastern Tunisian Island from April 2015 to August 2016. Molecular screening of β-lactamases encoding genes by PCR and sequencing showed that the majority of our isolates harbored bla_CTX-M gene (bla_CTX-M-15 [n = 36], bla_CTX-M-14 [n = 2]). Nevertheless, the bla_SHV, bla_TEM, and bla_OXA-1 genes were not detected. Various class C β-lactamases encoding genes were observed in association or not with bla_CTX-M genes and were as follows: bla_ampC (n = 14), bla_CMY-42 (n = 7), bla_CMY-2 (n = 1), and bla_DHA-4 (n = 1). The research of O25b-ST131 clone was carried out by duplex PCR (pabB and trpA genes) and revealed that most of our isolates (n = 30) belonged to this clone. We also noted that the majority of our isolates belonged to the B2 phylogenetic group (n = 32), five isolates to the B1 phylogenetic group, three isolates to the D phylogenetic group, and only two isolates belonged to the A phylogenetic group. Our study provides new epidemiological information about E. coli clinical isolates in this area. Indeed, this is the first report of CTX-M-14 producing O25b-ST131 E. coli in our country and the first report of DHA-4 and CMY-42 producing E. coli in Tunisia.

Interplay between β-lactamases and new β-lactamase inhibitors

Resistance to β-lactam antibiotics in Gram-negative bacteria is commonly associated with production of β-lactamases, including extended-spectrum β-lactamases (ESBLs) and carbapenemases belonging to different molecular classes: those with a catalytically active serine and those with at least one active-site Zn²⁺ to facilitate hydrolysis. To counteract the hydrolytic activity of these enzymes, combinations of a β-lactam with a β-lactamase inhibitor (BLI) have been clinically successful. However, some β-lactam-BLI combinations have lost their effectiveness against prevalent Gram-negative pathogens that produce ESBLs, carbapenemases or multiple β-lactamases in the same organism. In this Review, descriptions are provided for medically relevant β-lactamase families and various BLI combinations that have been developed or are under development. Recently approved inhibitor combinations include the inhibitors avibactam and vaborbactam of the diazabicyclooctanone and boronic acid inhibitor classes, respectively, as new scaffolds for future inhibitor design.

Antibiotic Susceptibility and Therapy in Central Line Infections in Pediatric Home Parenteral Nutrition Patients

BACKGROUND

Patients receiving home parenteral nutrition (HPN) are at high-risk for central line-associated bloodstream infections (CLABSI). There are no published management guidelines, however, for the antibiotic treatment of suspected CLABSI in this population. Historical microbiology data may help inform empiric antimicrobial regimens in this population.

OBJECTIVE

The aim of the study was to describe antimicrobial resistance patterns and determine the most appropriate empiric antibiotic therapy in HPN-dependent children experiencing a community-acquired CLABSI.

METHODS

Single-center retrospective cohort study evaluating potential coverage of empiric antibiotic regimens in children on HPN who developed a community-acquired CLABSI.

RESULTS

From October 1, 2011 to September 30, 2017, there were 309 CLABSI episodes among 90 HPN-dependent children with median age 3.8 years old.Fifty-nine percent of patients carried the diagnosis of surgical short bowel syndrome. Organisms isolated during these infections included 60% Gram-positive bacteria, 34% Gram-negative bacteria, and 6% fungi. Among all staphylococcal isolates, 51% were methicillin sensitive. Among enteric Gram-negative organisms, sensitivities were piperacillin-tazobactam 71%, cefepime 97%, and meropenem 99%. Organisms were sensitive to current institutional standard therapy with vancomycin and piperacillin-tazobactam in 69% of cases compared with vancomycin and cefepime or vancomycin an meropenem in 85% and 96% of cases (both P < 0.01).

CONCLUSIONS

Empiric antimicrobial therapy for suspected CLABSI in HPN-dependent children should include therapy for methicillin-resistant staphylococci as well as enteric Gram-negative organisms. Future studies are needed to evaluate clinical outcomes based upon evidence-based antimicrobial regimens.

High occurrence of CMY-2-type beta-lactamase-producing Escherichia coli among broiler flocks in Turkey

In this study, the prevalence of ESBL/pAmpC-producing Escherichia coli and their molecular characterization from cloacal swab samples were investigated. All samples were obtained from broiler flocks that are located in Hatay, Adana, and Mersin provinces of Turkey. Antimicrobial susceptibilities of the isolates were determined by disk diffusion method following the CLSI criteria. Genetic mechanisms mediating resistance in ESBL/pAmpC-producing E. coli isolates were identified by polymerase chain reaction (PCR) and followed by DNA sequencing. Phylogenetic groups and plasmid replicon types of the isolates were also investigated by PCR. The clonal relationship of selected isolates was investigated by enterobacterial repetitive intergenic consensus (ERIC)-PCR and multilocus sequence typing (MLST) method. Of 430 cloacal swab samples, 154 (35.8%) were positive for ESBL/pAmpC-producing E. coli. The ESBL/pAmpC type beta-lactamases were as follows: CMY-2 (n = 46), CMY-2 + TEM-1b (n = 63), SHV-12 (n = 5), SHV-12 + TEM-1b (n = 12), CTX-M-3 (n = 14), CTX-M-3 + TEM-1b (n = 1), CTX-M-15 (n = 4), CTX-M-15 + TEM-1b (n = 4), and CTX-M-1 (n = 3). Moreover, various rates of resistance to different antimicrobials were determined such as nalidixic acid (92.9%), ciprofloxacin (76%), sulfamethoxazole-trimethoprim (78.6%), tetracycline (73.4%), streptomycin (52.6%), chloramphenicol (44.2%), kanamycin (27.9%), tobramycin (24.7%), gentamicin (19.5%), and amikacin (0.6%). Furthermore, 148 (96.1%) isolates were found to be MDR. The ESBL/pAmpC-producing isolates were distributed into the following phylogroups: E (n = 61), B1 (n = 30), F (n = 20), A (n = 19), B2 (n = 11), D (n = 10), and C (n = 3). ERIC-PCR analysis showed 51 unrelated patterns. Out of the 28 selected isolates, the following sequence types (STs) were detected: ST354 (n = 3), ST114 (n = 3), ST5696 (n = 2), ST156 (n = 2), ST174 (n = 2), ST362 (n = 2), ST157 (n = 2), ST5114 (n = 2), ST6635, ST539, ST457, ST1640, ST95, ST5843, ST1158, ST10, ST648, and ST4248. The results of the current study revealed that broilers in Turkey are important reservoir of ESBL/pAmpC-producing E. coli, which suggest that these agents have a great potential of transmission to humans by food chain or direct contact.

Fecal Carriage and Whole-Genome Sequencing-Assisted Characterization of CMY-2 Beta-Lactamase-Producing Escherichia coli in Calves at Czech Dairy Cow Farm

The study aimed to monitor the fecal shedding of cefotaxime-resistant Escherichia coli (CREC) in a cohort of healthy calves on a dairy farm with documented antimicrobial usage and to characterize selected AmpC beta-lactamase-producing E. coli isolates. Fecal samples from 13 suckling calves (1-63 d of age; 113 samples in total) were repeatedly collected and cultivated on MacConkey agar with cefotaxime (2 mg/L). Resistant colonies were counted, and one colony obtained from the highest dilution of each fecal sample was identified by matrix-assisted laser desorption-ionization time-of-flight mass spectrometry. Susceptibility to antimicrobials and production of AmpC and extended-spectrum beta-lactamase (ESBL) were tested. No ESBL-producing E. coli was found, but representative AmpC-positive E. coli isolates were subjected to further typing and whole-genome sequencing (WGS) for the analysis of clonal relationships, resistance genes, virulence factors, and plasmid replicons. High amounts of CREC were detected in the feces of all 13 calves during the study. The number of CREC colonies varied from 1.0 log₁₀ to 8.0 log₁₀ colony-forming unit per gram. Drops in CREC density or its discontinued shedding were recorded at the end of the study period. A total of 82 (94%, n = 87) CREC isolates were confirmed as AmpC producers and all but one showed resistance to multiple antimicrobials. Twenty-nine selected AmpC-positive E. coli isolates belonged to 12 and 13 unique rep-PCR fingerprints and pulsed-field gel electrophoresis types, respectively, highlighting the variation in E. coli genotypes in individual calves. WGS of 10 selected isolates showed diverse antimicrobial resistance and virulence gene content and the presence of a bla_CMY-2 gene carried by an IncK2 plasmid. Clinically important multiresistant E. coli isolates belonging to emerging extraintestinal pathogenic E. coli ST69 and ST648 lineages were found. Our findings reinforce the urgency of efforts to prevent the spread of ESBL-/AmpC-producing bacteria in dairy cow farms.

Genetic Diversity of CMY Beta-Lactamase Genes in Clinical Isolates of Escherichia coli in Myanmar: Identification of Three Novel Types and Updated Phylogenetic Classification of blaCMY

The dissemination of CMY-type enzymes, one of the plasmid-mediated AmpC beta-lactamases, among Enterobacteriaceae has become an important public health concern. In this study, genetic diversity of CMY beta-lactamase genes was investigated for 50 bla_CMY-positive isolates detected from 426 clinical isolates of Escherichia coli in Yangon, Myanmar. CMY genes were differentiated into 9 types, with bla_CMY-42 being predominant (22 isolates, 44%), followed by bla_CMY-2, bla_CMY-6, bla_CMY-146, and included three novel types (CMY-156, CMY-158, CMY-159). Among E. coli harboring bla_CMY, phylogenetic group D-sequence type (ST)405 and A-ST410 were the most common genotypes, and bla_CTX-M-15 was detected in 72% (36/50) of isolates. bla_CMY-42 was distributed to phylogenetic groups A, B1, and D E. coli with 11 STs, which included 10 isolates harboring carbapenemase genes (bla_NDM-4, bla_NDM-5, or bla_NDM-7). Phylogenetic analysis of all the bla_CMY genes reported to date, including the three novel types in the present study, revealed the presence of at least four distinct genetic groups, that is, CMY-1, CMY-2, CMY-70, and CMY-98 group, showing less than 91% nucleotide sequence identities among different groups. CMY-2 group beta-lactamase genes, which contained by far the largest number of CMY types (89.7%) with extensive diversity, were divided into two clusters (I and II). While eight CMY types identified in the present study were classified into CMY-2 group cluster I, novel type CMY-159 was assigned into CMY-98 group with a Citrobacter freundii strain in Thailand.

High Levels of Resistance to Cephalosporins Associated with the Presence of Extended-Spectrum and AmpC β-Lactamases in Escherichia coli from Broilers in Southern Brazil

The clinical importance of extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli has increased steadily over the years. The presence of the bla_TEM, bla_SHV, and bla_CTX-M genes in the environment has been recently recognized as an important issue in the dissemination of resistance to cephalosporins. Food animals are considered important vectors for transfer of ESBL genes from the environment to humans. The objective of this study was to characterize the ESBL genes (bla_TEM, bla_SHV, and bla_CTX-M types) that were most prevalent among 343 ceftazidime-resistant E. coli isolates (17 batches from 12 different farms) obtained from cloacal swabs of broiler chicken in southern Brazil. The bla_SHV, bla_CTX-M, bla_TEM, bla_IMP-type, bla_VIM-type, bla_NDM-1, bla_KPC-type, bla_GES-type, bla_OXA-48, and mcr-1 genes were evaluated by polymerase chain reaction. A total of 27 (7.9%) E. coli isolates were positive for ESBL genes as follows: 24 for bla_CTX-M (23 bla_CTX-M-2 Group and 1 bla_CTX-M-8) and 3 for bla_SHV (2 bla_SHV-2a and 1 bla_SHV-18). A random sample of 32 ceftazidime/cefotaxime-resistant isolates that were negative for ESBL genes were evaluated for the presence of bla_CMY-2 and 24 (75%) tested positive. We detected the bla_CMY-2 gene in isolates from all farms. All isolates positive for ESBL or bla_CMY-2 are considered multidrug resistant (resistant to at least three antibiotic classes). Our results suggest that broiler chickens are an important reservoir of bla_CMY-2 and ESBL genes, including bla_SHV-2a, described for the first time in animals originating from Brazil in this study, and bla_SHV-18, which has never been described in Brazil before. This fact highlights the importance of controlling the use of antibiotics in animal production to reduce environmental sources of resistance genes.

Structural Insights into Catalytic Relevances of Substrate Poses in ACC-1

ACC-1 is a plasmid-encoded class C β-lactamase identified in clinical isolates of Klebsiella pneumoniae, Proteus mirabilis, Salmonella enterica, and Escherichia coli ACC-1-producing bacteria are susceptible to cefoxitin, whereas they are resistant to oxyimino cephalosporins. Here, we depict crystal structures of apo ACC-1, adenylylated ACC-1, and acylated ACC-1 complexed with cefotaxime and cefoxitin. ACC-1 has noteworthy structural alterations in the R2 loop, the Ω loop, and the Phe119 loop located along the active-site rim. The adenylate covalently bonded to the nucleophilic serine reveals a tetrahedral phosphorus mimicking the deacylation transition state. Cefotaxime in ACC-1 has a proper conformation for the substrate-assisted catalysis in that its C-4 carboxylate and N-5 nitrogen are adequately located to facilitate the deacylation reaction. In contrast, cefoxitin in ACC-1 has a distinct conformation, in which those functional groups cannot contribute to catalysis. Furthermore, the orientation of the deacylating water relative to the acyl carbonyl group in ACC-1 is unfavorable for nucleophilic attack.

The mobile FOX AmpC beta-lactamases originated in Aeromonas allosaccharophila

OBJECTIVE

It is important to understand the origins of antibiotic resistance genes so that risks associated with the emergence of novel resistance genes can be assessed and managed. The chromosomal ampC gene (CAV-1) of Aeromonas caviae (A. caviae) has been reported as the origin of mobile FOX cephalosporinases. The recent identification of A. caviae as the origin of MOX-2 cephalosporinases and the comparably great sequence divergence between FOX and MOX genes makes it unlikely that both genes arose from the same species. Therefore, this study investigated the origin of FOX cephalosporinases using large-scale genomics.

METHODS

Publicly available genomes and plasmids were searched for FOX-like genes. Synteny and nucleotide identities of the identified FOX-like genes and their genetic environments were compared and a phylogenetic tree was generated.

RESULTS

FOX-like genes were identified in > 230 Aeromonas genomes and in 46 Enterobacteriaceae isolates. Analysis of the genomic context of CAV-1 revealed a truncated insertion sequence directly upstream of the ampC gene. The chromosomal ampCs of A. caviae (n = 31) were 75-78% identical to CAV-1. In contrast, CAV-1, mobile FOX genes and their context were 95-98% similar to the chromosomal ampC-locus of Aeromonas allosaccharophila (A. allosaccharophila) (n = 6). The A. allosaccharophila ampCs formed a monophyletic branch with mobile FOX genes, whereas the A. caviae ampCs clustered with mobile MOX genes.

CONCLUSIONS

These findings show that FOX cephalosporinases originate not in A. caviae, as previously reported, but in A. allosaccharophila, which is a fish pathogen. This finding agrees with the hypothesis that antibiotic use in aquaculture could have contributed to the emergence of FOX genes in human pathogens.

Acquisition of class C β-lactamase PAC-1 by ST664 strains of Pseudomonas aeruginosa

Four ST664 (serotype O:5) strains of Pseudomonas aeruginosa highly resistant to antibiotics including ceftolozane/tazobactam and ceftazidime/avibactam but susceptible to colistin, were found to harbor the rare class C β-lactamase PAC-1 encoding gene on a chromosomally-located Tn1721-like transposon. Gene bla _PAC-1 was associated with the 16S rRNA methylase determinant rmtF2, that confers pan-aminoglycoside resistance. These genotypically-related strains were isolated in repatriated patients from Mauricius and Afghanistan and close to a lineage reported in Nepal, Pakistan and India.

Species-specific mutation rates for ampC derepression in Enterobacterales with chromosomally encoded inducible AmpC β-lactamase

Background

AmpC β-lactamases are encoded on the chromosomes of certain Enterobacterales and lead to clinical resistance to various β-lactams in case of high-level expression. In WT bacteria with inducible AmpC, the expression is low, but selection of stably ampC-derepressed mutants may occur during β-lactam therapy. Thus, for Enterobacter spp., Citrobacter freundii complex, Serratia spp. and Morganella morganii that test susceptible in vitro to oxyimino-cephalosporins, the EUCAST expert rules recommend suppressing susceptibility testing results for these agents or noting that their use in monotherapy should be discouraged, owing to the risk of selecting resistance. However, clinical observations suggest that emergence of resistance is not equally common in all species with inducible AmpC.

Objectives

To determine species-specific mutation rates, which are more accurate and reproducible than previously described mutant frequencies, for ampC derepression in Enterobacterales with inducible AmpC.

Methods

Mutation rates were determined using a protocol based on Luria-Delbrück fluctuation analyses. Overall, 237 isolates were analysed.

Results

Mutation rates were high in Enterobacter cloacae complex, Enterobacter aerogenes, C. freundii complex and Hafnia alvei isolates, with a mean mutation rate of 3 × 10-8. In contrast, mean mutation rates were considerably lower in Providencia spp., Serratia spp. and especially M. morganii isolates. Furthermore, we observed species-specific variations in the resistance patterns of ampC-derepressed mutants.

Conclusions

Our data might help to predict the risk of treatment failure with oxyimino-cephalosporins in infections by different Enterobacterales with inducible AmpC. Moreover, we make a proposal for optimization of the current EUCAST expert rule.

Prevalence of resistance to some beta-lactams among commensal canine E. coli isolates

The sensitivity of 80 E. coli strains isolated from canine rectal swabs to antimicrobial drugs was tested in this study. The results showed 47.5% resistance to ampicillin, 18.7% to the combination amoxicillin/clavulanic acid and 6.2% to cephalothin. The percentage of E. coli isolates resistant to tetracycline was 26.2%, to ciprofloxacin 12.5%, and to gentamicin 10%. The resistance to cefotaxime and ceftazidime was the lowest (1.2% and 2.5% respectively). Determined MIC90 of ampicillin were 16 μg/mL, and of amoxicillin/clavulanic acid and cephalothin 8 μg/mL. The main resistance genotype of isolates to tested beta-lactams was associated with presence of blaTEM.

Present and Future of Carbapenem-resistant Enterobacteriaceae (CRE) Infections

Carbapenem-resistant Enterobacteriaceae (CRE) have become a public health threat worldwide. There are three major mechanisms by which Enterobacteriaceae become resistant to carbapenems: enzyme production, efflux pumps and porin mutations. Of these, enzyme production is the main resistance mechanism. There are three main groups of enzymes responsible for most of the carbapenem resistance: KPC (Klebsiella pneumoniae carbapenemase) (Ambler class A), MBLs (Metallo-ß-Lactamases) (Ambler class B) and OXA-48-like (Ambler class D). KPC-producing Enterobacteriaceae are endemic in the United States, Colombia, Argentina, Greece and Italy. On the other hand, the MBL NDM-1 is the main carbapenemase-producing resistance in India, Pakistan and Sri Lanka, while OXA-48-like enzyme-producers are endemic in Turkey, Malta, the Middle-East and North Africa. All three groups of enzymes are plasmid-mediated, which implies an easier horizontal transfer and, thus, faster spread of carbapenem resistance worldwide. As a result, there is an urgent need to develop new therapeutic guidelines to treat CRE infections. Bearing in mind the different mechanisms by which Enterobacteriaceae can become resistant to carbapenems, there are different approaches to treat infections caused by these bacteria, which include the repurposing of already existing antibiotics, dual therapies with these antibiotics, and the development of new ß-lactamase inhibitors and antibiotics.

Molecular Epidemiology of Ceftriaxone Non-Susceptible Enterobacterales Isolates in an Academic Medical Center in the United States

Background

Knowledge of whether Enterobacterales are not susceptible to ceftriaxone without understanding the underlying resistance mechanisms may not be sufficient to direct appropriate treatment decisions. As an example, extended-spectrum β-lactamase (ESBL)–producing organisms almost uniformly display nonsusceptibility to ceftriaxone. Regardless of susceptibility to piperacillin-tazobactam or cefepime, carbapenem antibiotics are the treatment of choice for invasive infections. No such guidance exists for ceftriaxone-nonsusceptible organisms with mechanisms other than ESBL production. We sought to investigate the molecular epidemiology of ceftriaxone-nonsusceptible Enterobacterales.

Methods

All consecutive Escherichia coli, Klebsiella pneumoniae, Klebsiella oxytoca, or Proteus mirabilis clinical isolates with ceftriaxone minimum inhibitory concentrations (MICs) of ≥2 mcg/mL from unique patients at a United States hospital over an 8-month period were evaluated for β-lactamase genes using a DNA microarray–based assay.

Results

Of 1929 isolates, 482 (25%) had ceftriaxone MICs of ≥2 mcg/mL and were not resistant to any carbapenem antibiotics. Of the 482 isolates, ESBL (bla_CTX-M, bla_SHV, bla_TEM) and/or plasmid-mediated ampC (p-ampC) genes were identified in 376 (78%). ESBL genes were identified in 310 (82.4%), p-ampC genes in 2 (0.5%), and both ESBL and p-ampC genes in 64 (17.0%) of the 376 organisms. There were 211 (56%), 120 (32%), 41 (11%), and 4 (1%) isolates with 1, 2, 3, or ≥4 ESBL or p-ampC genes. The most common ESBL genes were of the bla_CTX-M-1 group (includes bla_CTX-M-15), and the most common p-ampC gene was bla_CMY-2.

Conclusions

There is considerable diversity in the molecular epidemiology of ceftriaxone-nonsusceptible Enterobacterales. An understanding of this diversity can improve antibiotic decision-making.

Plasmid Replicons and β-Lactamase-Encoding Genes of Multidrug-Resistant Escherichia coli Isolated from Humans and Food Animals in Lagos, Southwest Nigeria

As resistance to the β-lactam class of antibiotics has become a worldwide problem, multidrug-resistant (MDR) human (n = 243) and food animal (n = 211) isolates from Lagos, Nigeria were further tested to characterize β-lactamase-encoding genes and plasmid replicons. Four β-lactamase-encoding genes (bla_CMY, bla_CTX-M, bla_OXA, and bla_TEM) were detected using PCR-based replicon typing, 13 and 17 different replicons were identified using a subset of MDR E. coli from humans (n = 48) and animals (n = 96), respectively. Replicon types FIB and X2 were detected in equal numbers (2/48; 4.2% each) from human isolates, while type Y (16/96; 16.7%) was the most common type from animals. Only two replicon types, FIB and Y, were detected in both groups; all other types were confined to one group or the other, but not both. Using conjugation, replicon type Y, present in three donors, transferred in all three instances, whereas FIA transferred in 75% (3/4) of the matings. This study showed that β-lactamase genes were prevalent in MDR E. coli from both humans and animals in Nigeria and also contained diverse plasmid replicons. As the replicon-associated genes were mobile, they are likely to continue disseminating among E. coli and facilitating transfer of associated β-lactamase genes in this region.

Antimicrobial Susceptibility and Molecular Epidemiology of Proteus mirabilis Isolates from Three Hospitals in Northern Taiwan

Of all the Proteus spp., Proteus mirabilis is the most common species identified in clinical specimens and is a leading agent of complicated urinary tract infection. This study was undertaken to understand the antimicrobial susceptibility, prevalence of antibiotic resistance genes, and molecular typing of P. mirabilis isolates collected from three hospitals in northern Taiwan. The results showed that the collected isolates of P. mirabilis were susceptible to most antibiotics except cefazolin and tigecycline. Many resistance genes were detected in the collected isolates, of which TEM genes were the most common. Resistance to third- or fourth-generation cephalosporins was related to the presence of at least one of the tested extended-spectrum β-lactamase (ESBL) or AmpC genes. The presence of the VEB-1 gene seemed to be a good predictor for both cefepime and ceftazidime resistance, which was further supported by quantitative polymerase chain reaction results. Of the four imipenem-resistant P. mirabilis isolates, three isolates could hydrolyze imipenem by mass spectrometry analysis. Molecular typing by pulsed-field gel electrophoresis showed that the pulsotyping of the selected P. mirabilis isolates was heterogeneous. By analyzing the relationship of antimicrobial resistance and the presence of resistance genes, revision of the Clinical and Laboratory Standards Institute cefepime and ceftazidime MIC breakpoints for Enterobacteriaceae to predict ESBL producers might possibly be needed.

Induction of plasmid-mediated AmpC β-lactamase DHA-1 by piperacillin/tazobactam and other β-lactams in Enterobacteriaceae

Chromosomal AmpC β-lactamase induction by several types of β-lactams has been reported, but not enough data are available on DHA-1 β-lactamase, a plasmid-mediated AmpC β-lactamase. Therefore, we evaluated the DHA-1 β-lactamase induction by various antibiotics including piperacillin/tazobactam (PIP/TZB) in this study. Six strains (Enterobacter cloacae 2 strains, Citrobacter freundii 1 strain, Serratia marcescens 2 strain, and Morganella morganii 1 strain) possessing chromosomal inducible AmpC β-lactamase were used as controls. Four strains (Escherichia coli 2 strains, Klebsiella pneumoniae 1 strain, and C. koseri 1 strain) possessing DHA-1 β-lactamase were used. The β-lactamase activities were determined by a spectrophotometer using nitrocefin. β-lactamase induction by PIP, PIP/TZB was not observed in any strains and β-lactamase induction by third- and fourth-generation cephems was not observed in most strains. The induction ratios of the chromosomal AmpC β-lactamase in the reference group by PIP/TZB were <1.51, and those of the DHA-1 β-lactamase were <1.36, except for K. pneumoniae Rkp2004 (2.22). The β-lactamase induction by first- and second-generation cephems, flomoxef, and carbapenem differed in each strain. Cefmetazole (CMZ) strongly induced β-lactamase. This study demonstrated that the induction of DHA-1 β-lactamase was similar to that of chromosomal AmpC using various Enterobacteriaceae, although the induction of β-lactamase in both groups by PIP/TZB was low. We also reported that the induction of PIP/TZB, a β-lactamase inhibitor combination antibiotic, against various AmpC-producing Enterobacteriaceae, including DHA-1 producers, was low.

Molecular Characterization of Multidrug-Resistant Escherichia coli Isolates in Azerbaijan Hospitals

Aims: The emergence and clonal occurrence of multidrug-resistant (MDR) Escherichia coli isolates are increasing worldwide. In this study, phenotypic and genotypic characteristics of MDR E. coli isolates overexpressing efflux pump were investigated in medical centers of Azerbaijan. Two hundred nineteen consecutive and nonduplicated isolates of E. coli were collected and screened, and confirmed for extended-spectrum β-lactamase, AmpC, and carbapenemase activities and respective genes. MDR isolates were selected and subjected to efflux pump overexpression assay. Cefoxitin-nonsusceptible isolates were subjected to mutational analysis of promoter region of chromosomal ampC gene. MDR isolates with overexpressed efflux were analyzed for acrR and marR mutations and assigned to multilocus sequence typing. Results: Eighty (36.5%) isolates had MDR pattern, among which 16 (20%) isolates were positive for overexpressed efflux. Ninety-eight of 99 suspected isolates were positive for any β-lactamase genes, particularly CTX-M groups 1 and 9. Ten out of 33 cefoxitin-nonsusceptible isolates had mutations in promoter region of chromosomal AmpC gene, including -32T→A (n = 5), -42C→T, and -18G→A (n = 3) and -13TT and GT insertion (n = 2). Detected mutations in efflux regulatory genes include G103S and Y137H (n = 15), K62R (n = 8), S3N (n = 3), and A53E (n = 1) in marR and L109 (n = 2) and L190 (n = 1) frameshift mutations and T12M, T213I, N214T, I113V, and H115Y point mutations (n = 5) in acrR. Conclusions: Overexpressing efflux pump isolates belonging to sequence type (ST)131 and ST73 clones are emerging in Azerbaijan hospitals. Clonal occurrence of MDR E. coli is an alarming situation in Azerbaijan hospitals.

Gradual in vitro Evolution of Cefepime Resistance in an ST131 Escherichia coli Strain Expressing a Plasmid-Encoded CMY-2 β-Lactamase

Background

In a previous report, a clinical ST131 Escherichia coli isolate (Ec-1),producing a plasmid-encoded AmpC β-lactamase CMY-2, evolved in vivo under cefepime (FEP) treatment to the FEP-resistant Ec-2 strain expressing an extended-spectrum β-lactamase CMY-33. To compare factors responsible for in vitro and in vivo FEP resistance, we reproduced in vitro FEP resistance evolution in Ec-1.

Methods

FEP-resistant mutants were generated by subjecting Ec-1 (FEP MIC = 0.125 mg/L) to sub-inhibitory concentrations of FEP. MICs were obtained by broth microdilution or Etest. Strains were sequenced on an Illumina HiSeq platform. Transcriptional levels and plasmid copy numbers were determined by real-time PCR. Outer membrane proteins (OMPs) were extracted and separated by SDS-PAGE. Growth kinetics was evaluated by measuring OD₄₅₀.

Results

The CMY-2 expressed by Ec-1 evolved to a CMY-69 (strain EC-4) by an Ala294Pro substitution after 24 passages. After 30 passages, the FEP MIC increased to 256 mg/L (strain EC-32). SDS PAGE did not reveal any lack of OMPs in the mutant strains. However, bla_CMY transcription levels were up to 14-times higher than in Ec-1, which was partially explained by mutations in the upstream region of repA resulting in a higher copy number of the bla_CMY-harboring IncI1 plasmid. All mutants showed a slight growth defect but no significant difference in relative growth rates compared to Ec-1.

Conclusion

In vitro sub-inhibitory concentrations of FEP resulted in the selection of resistance mutations altering the H-10 helix of the CMY-2 and increasing the plasmid copy number. Appropriate dosing strategies may help preventing resistance evolution during treatments.

Antibiotic Adjuvants: Make Antibiotics Great Again!

Multiple approaches have been developed to combat bacterial resistance. However, the combination of antibiotic resistance mechanisms by bacteria and the limited number of effective antibiotics available decreases the effective interventions for the treatment of current bacterial infections. This review covers the many ways that bacteria resist antibiotics including antibiotic target modification, the use of efflux pumps, and antibiotic inactivation. As a pertinent example, the use of beta lactamase inhibitors in combination with β-lactam containing antibiotics is discussed in detail. The solution to emerging antibiotic resistance may involve combination therapies of existing antibiotics and potentiating adjuvants, which re-empower the antibiotic agent to become efficacious against the resistant strain of interest. We report herein that a reasoned adjuvant design permits one to perform polypharmacy on bacteria by not only providing greater internal access to the codosed antibiotics but also by de-energizing the efflux pumps used by the bacteria to escape antibiotic action.

False-Positive Carbapenem-Hydrolyzing Confirmatory Tests Due to ACT-28, a Chromosomally Encoded AmpC with Weak Carbapenemase Activity from Enterobacter kobei

In Enterobacter cloacae complex (ECC), the overproduction of the chromosome-encoded cephalosporinase (cAmpC) associated with decreased outer membrane permeability may result in carbapenem resistance. In this study, we have characterized ACT-28, a cAmpC with weak carbapenemase activity, from a single Enterobacter kobei lineage. ECC clinical isolates were characterized by whole-genome sequencing (WGS), susceptibility testing, and MIC, and carbapenemase activity was monitored using diverse carbapenem hydrolysis methods. ACT-28 steady-state kinetic parameters were determined. Among 1,039 non-carbapenemase-producing ECC isolates with decreased susceptibility to carbapenems received in 2016-2017 at the French National Reference Center for antibiotic resistance, only 8 had a positive carbapenemase detection test (Carba NP). These eight ECC isolates were resistant to broad-spectrum cephalosporins due to AmpC derepression, showed decreased susceptibility to carbapenems, and were categorized as carbapenemase-producing Enterobacteriaceae (CPE) according to several carbapenemase detection assays. WGS identified a single clone of E. kobei ST125 expressing only its cAmpC, ACT-28. The bla _ACT-28 gene was expressed in a wild-type and in a porin-deficient Escherichia coli background and compared to the bla _ACT-1 gene. Detection of carbapenemase activity was positive only for E. coli expressing the bla _ACT-28 gene. Kinetic parameters of purified ACT-28 revealed a slightly increased imipenem hydrolysis compared to that of ACT-1. In silico porin analysis revealed the presence of a peculiar OmpC-like protein specific to E. kobei ST125 that could impair carbapenem influx into the periplasm and thus enhance carbapenem-resistance caused by ACT-28. We described a widespread lineage of E. kobei ST125 producing ACT-28, with weak carbapenemase activity that can lead to false-positive detection by several biochemical and phenotypic diagnostic tests.

An ancient family of mobile genomic islands introducing cephalosporinase and carbapenemase genes in Enterobacteriaceae

The exchange of mobile genomic islands (MGIs) between microorganisms is often mediated by phages, which may provide benefits to the phage’s host. The present study started with the identification of Enterobacter cloacae, Klebsiella pneumoniae and Escherichia coli isolates with exceptional cephalosporin and carbapenem resistance phenotypes from patients in a neonatal ward. To identify possible molecular connections between these isolates and their β-lactam resistance phenotypes, the respective bacterial genome sequences were compared. This unveiled the existence of a family of ancient MGIs that were probably exchanged before the species E. cloacae, K. pneumoniae and E. coli emerged from their common ancestry. A representative MGI from E. cloacae was named MIR17-GI, because it harbors the novel β-lactamase gene variant bla_MIR17. Importantly, our observations show that the MIR17-GI-like MGIs harbor genes associated with high-level resistance to cephalosporins. Among them, MIR17-GI stands out because MIR17 also displays carbapenemase activity. As shown by mass spectrometry, the MIR17 carbapenemase is among the most abundantly expressed proteins of the respective E. cloacae isolate. Further, we show that MIR17-GI-like islands are associated with integrated P4-like prophages. This implicates phages in the spread of cephalosporin and carbapenem resistance amongst Enterobacteriaceae. The discovery of an ancient family of MGIs, mediating the spread of cephalosporinase and carbapenemase genes, is of high clinical relevance, because high-level cephalosporin and carbapenem resistance have serious implications for the treatment of patients with enterobacteriaceal infections.

A survey of antimicrobial resistance in Enterobacteriaceae isolated from the Chesapeake Bay and adjacent upper tributaries

In recent years, the rise in antimicrobial resistance (AR) in the healthcare setting as well as the environment has been recognized as a growing public health problem. The Chesapeake Bay (CB) and its upper tributaries (UT) is a large and biologically diverse estuary. This pilot study evaluated the presence of AR of gram‐negative bacteria isolated from water samples collected at various sites of the Chesapeake Bay. Bacterial organisms were identified and antimicrobial susceptibility testing was performed by phenotypic and genotypic methods. Ninety‐two distinctly different gram‐negative bacteria were identified; Klebsiella pneumoniae, Enterobacter cloacae, Enterobacter aerogenes, Serratia marcescens, and Escherichia coli were most often isolated. Serratia marcescens was more frequently isolated in samples from the UT compared to the CB. Antimicrobial resistance was more frequently detected in organisms from the CB by phenotypic and genotypic methods. Antimicrobial resistance to ampicillin, imipenem, tetracycline, and chloramphenicol were the most frequently observed resistance patterns. ACT‐1, CMY, and SHV genes were the most frequently detected resistance genes, with predominance in organism isolated from the CB. The results from this study emphasize the importance for further developing comprehensive surveillance programs of AR in bacterial isolates in the various environments, such as recreational and other water systems.

Transcriptome analysis of beta-lactamase genes in diarrheagenic Escherichia coli

Beta (β)-lactamases are the most important agents that confer drug resistance among gram-negative bacteria. Continuous mutations in β-lactamases make them remarkably diverse. We carried out the transcriptome analysis of 10 β-lactamase genes of Extended-Spectrum β-lactamases (ESBL), Metallo β-lactamases (MBL), and AmpC β-lactamases (ABL) in drug-resistant and sensitive diarrheagenic E. coli (DEC) isolates obtained from children up to 5 years of age. Out of the 10 β-lactamase genes, four belonged to ESBL (TEM, SHV, CTX, and OXA); three to MBL (NDM-1, IMP, and VIM); and three to ABL (ACT, DHA and CMY) class of genes. The different categories of DEC were estimated for β-lactamases production using a set of conventional phenotypic tests, followed by detection of their messenger RNA (mRNA) expression. The study revealed a direct correlation between mRNA expression of these genes and the presence of antibiotic resistance; also corroborated by mutation analysis of the AmpC promoter region. All the 10 β-lactamase genes showed a significant increase in their expression levels in resistant isolates, compared to those of the sensitive isolates, indicating their possible role in the disease pathogenesis. Increase in mRNA expression of β-lactamase genes, and thereby virulence, may be due to multifactorial parameters causing phenotypic as well as genotypic changes. Our study highlights the necessity of instantaneous detection of β-lactamase gene expression to curb the overwhelming threat posed by emergence of drug resistance amongst the commensal E. coli strains in children from developing countries for larger public health interest.

Prevalence of plasmid-mediated AmpC in Enterobacteriaceae isolated from humans and from retail meat in Zagazig, Egypt

Background

The objective of this study was to determine the prevalence of plasmid-mediated AmpC (pAmpC) among Enterobacteriaceae isolated from humans and from retail meat in Egypt.

Methods

Enterobacteriaceae were isolated from patients with suspected bloodstream infection, human fecal samples, retail chicken meat samples and retail sheep meat samples. All group I Enterobacteriaceae were analyzed for presence of pAmpC genes by PCR. Antibiotic susceptibility testing was performed in all pAmpC positive isolates, followed by phenotypic and genotypic ESBL and carbapenemase testing on indication.

Results

The prevalence of pAmpC among group I Enterobacteriaceae isolated from 225 patients with bloodstream infection was 5.6% [95%CI 2.2–13.4]. Among 100 patients with community-onset gastroenteritis the prevalence in fecal samples was 4.8% [95%CI 2.1–10.7]. The prevalence among 112 chicken carcasses and 100 sheep meat samples was 2.4% [95%CI 0.7–8.4] and 1.1% [95%CI 0.2–5.7], respectively. In half of the AmpC positive isolates we detected an ESBL gene and 2 isolates harbored a carbapenemase gene. In five isolates there was resistance to at least three important alternative antibiotic drugs.

Conclusions

We consider the prevalence of pAmpC in Egypt, as found in our study, moderately low. To follow future trends in prevalence of pAmpC worldwide, a standardized screening algorithm for the detection of pAmpC is needed.

Investigating colistin drug resistance: The role of high-throughput sequencing and bioinformatics

Bacterial infections involving antibiotic-resistant gram-negative bacteria continue to increase and represent a major global public health concern. Resistance to antibiotics in these bacteria is mediated by chromosomal and/or acquired resistance mechanisms, these give rise to multi-drug resistant (MDR), extensive-drug resistant (XDR) or pan-drug resistant (PDR) bacterial strains. Most recently, plasmid-mediated resistance to colistin, an antibiotic that had been set apart as the last resort antibiotic in the treatment of infections involving MDR, XDR and PDR gram-negative bacteria has been reported. Plasmid-mediated colistin resistant gram-negative bacteria have been described to be PDR, implying a state devoid of alternative antibiotic therapeutic options. This review concisely describes the evolution of antibiotic resistance to plasmid-mediated colistin resistance and discusses the potential role of high-throughput sequencing technologies, genomics, and bioinformatics towards improving antibiotic resistance surveillance, the search for novel drug targets and precision antibiotic therapy focused at combating colistin resistance, and antibiotic resistance as a whole.

Investigating colistin drug resistance: The role of high-throughput sequencing and bioinformatics

Bacterial infections involving antibiotic resistant gram-negative bacteria continue to increase and represent a major global public health concern. Resistance to antibiotics in these bacteria is mediated by chromosomal and/or acquired resistance mechanisms, these give rise to multi-drug resistant (MDR) or extensive drug resistant (XDR) bacterial strains. Most recently, a novel acquired plasmid mediated resistance mechanism to colistin, an antibiotic that had been set apart as the last resort antibiotic in the treatment of infections involving MDR and XDR gram-negative bacteria, has been reported. Plasmid mediated colistin resistant gram-negative bacteria have been described to be pan-drug resistant, implying a state devoid of alternative antibiotic therapeutic options. This review describes the evolution of antibiotic resistance to plasmid mediated colistin resistance, and discusses the potential role of high-throughput sequencing technologies, genomics and bioinformatics towards improving antibiotic resistance surveillance, the search for novel drug targets and precision antibiotic therapy focused at combating colistin resistance, and antimicrobial resistance as a whole.

Genotypes and Antimicrobial Susceptibility Profiles of Hemolytic Escherichia coli from Diarrheic Piglets

Hemolytic Escherichia coli are important pathogens in neonatal and weaned pigs. In this study, we analyzed 95 hemolytic E. coli isolated from intestinal contents or fecal samples of diarrheic piglets in 15 states of the United States between November 2013 and December 2014. Phenotypic antimicrobial susceptibility was determined through Sensititre BOFO6F plates for all the strains. They were all resistant to clindamycin, penicillin, tiamulin, tilmicosin, and highly resistant to oxytetracycline (91.6%), chlortetracycline (78.9%), ampicillin (75.8%), and sulfadimethoxine (68.4%). 86.2% of them were multidrug resistant. Whole genome sequencing (WGS) showed that 55 strains were enterotoxigenic E. coli (ETEC) and 40 strains were non-ETEC, and the strains belonged to 22 known and 2 novel sequence types (STs). ST100 and ST10 were the main and predominant STs in ETEC strains, whereas the non-ETEC strains were diverse with ST23 and ST761 as the main STs. Antibiotic resistance gene/mutation profiling of the genomes confirmed the results of antimicrobial susceptibility test. Notably, significant differences were found in the susceptibility to enrofloxacin between ETEC and non-ETEC (58.2% vs. 5.0%) and gentamicin (32.7% vs. 7.5%). ampH, ampC2, and ampC1 were the most common beta-lactamase genes in all E. coli strains, and extended-spectrum beta-lactamase (ESBL) genes were rare in these isolates. This study provides new insights into antibiotic resistance and genotypes of intestinal pathogenic E. coli associated with swine disease in the United States, and support the utility of WGS in accurate prediction of resistance to most antibiotics.

Rapid Detection of Extended-Spectrum β-Lactamases (ESBL) and AmpC β-Lactamases in Enterobacterales: Development of a Screening Panel Using the MALDI-TOF MS-Based Direct-on-Target Microdroplet Growth Assay

Introduction: Antibiotic resistant bacteria are a growing concern worldwide. Extended-spectrum β-lactamases (ESBL) represent the most common resistance mechanism of Gram-negative bacteria against β-lactams, underlining the need for adequate diagnostic methods that provide reliable information in the shortest time possible. AmpC, a less prevalent but increasingly relevant class of β-lactamases, pose an additional challenge as their detection is complex. Here, we present an ESBL and AmpC screening panel employing the MALDI-TOF MS-based direct-on-target microdroplet growth assay (DOT-MGA). Materials and Methods: Four reference strains recommended by the European Committee on Antimicrobial Susceptibility Testing (EUCAST) were used to develop the panel, which was further validated on 50 clinical Enterobacterales isolates resistant to third generation cephalosporins. The panel relies on the synergistic effect between ESBL and/or AmpC β-lactamase inhibitors and cephalosporins, which indicates β-lactamase production. Microdroplets containing the tested microorganism, cephalosporins in different concentrations and inhibitors were pipetted onto an MBT Biotarget and incubated for 3 or 4 h at 35 ± 1°C. Afterward, the liquid medium was removed and the material adhered to the spots was analyzed by MALDI-TOF MS. Synergy was detected by determining and comparing the minimum inhibitory concentrations of the tested cephalosporins with and without β-lactamase inhibitors. Data were interpreted following a diagnostic algorithm proposed by EUCAST in order to establish a final diagnosis. In comparison, PCR, broth microdilution (BMD) and combination disk tests (CDT) were performed. Results: Compared to the PCR results, the following positive and negative percent agreement values (PPA/NPA) were obtained for each resistance mechanism: ESBL, 94.44/100%; AmpC, 94.44/93.75% and ESBL+AmpC, 100/100%. These results, obtained after 4 h of incubation, were comparable with those of BMD and showed a higher accuracy than CDT. Discussion: We propose a novel phenotypic method for detection of ESBL and AmpC β-lactamases in Enterobacterales that provides reliable results in a short time, representing a promising alternative to the diagnostic techniques currently available. This easy-to-perform approach has potential for being implemented in routine laboratories, contributing to the further diversification of mass spectrometry technology into other fields such as antibiotic resistance testing.

Antimicrobial Resistance in Escherichia coli

Multidrug resistance in Escherichia coli has become a worrying issue that is increasingly observed in human but also in veterinary medicine worldwide. E. coli is intrinsically susceptible to almost all clinically relevant antimicrobial agents, but this bacterial species has a great capacity to accumulate resistance genes, mostly through horizontal gene transfer. The most problematic mechanisms in E. coli correspond to the acquisition of genes coding for extended-spectrum β-lactamases (conferring resistance to broad-spectrum cephalosporins), carbapenemases (conferring resistance to carbapenems), 16S rRNA methylases (conferring pan-resistance to aminoglycosides), plasmid-mediated quinolone resistance (PMQR) genes (conferring resistance to [fluoro]quinolones), and mcr genes (conferring resistance to polymyxins). Although the spread of carbapenemase genes has been mainly recognized in the human sector but poorly recognized in animals, colistin resistance in E. coli seems rather to be related to the use of colistin in veterinary medicine on a global scale. For the other resistance traits, their cross-transfer between the human and animal sectors still remains controversial even though genomic investigations indicate that extended-spectrum β-lactamase producers encountered in animals are distinct from those affecting humans. In addition, E. coli of animal origin often also show resistances to other-mostly older-antimicrobial agents, including tetracyclines, phenicols, sulfonamides, trimethoprim, and fosfomycin. Plasmids, especially multiresistance plasmids, but also other mobile genetic elements, such as transposons and gene cassettes in class 1 and class 2 integrons, seem to play a major role in the dissemination of resistance genes. Of note, coselection and persistence of resistances to critically important antimicrobial agents in human medicine also occurs through the massive use of antimicrobial agents in veterinary medicine, such as tetracyclines or sulfonamides, as long as all those determinants are located on the same genetic elements.

[Sensitivity and resistance to antimicrobial agents ESBL-producing and not producing ESBL strains of E. coli in patients with urinary tract infection.]

As a result of the conducted researches it is shown that 44.1% of urinary tract infections (UTIS) caused by E. coli are accounted for by producers of beta-lactamase of the extended spectrum of action (ESBL). Associated resistance to fluoroquinolones and co-trimoxazole was found in 93.3% of BLRS-producing E. coli strains. All studied strains regardless of ESBL production were sensitive to imipenem, the majority showed sensitivity to ertapenem, gentamicin and resistance to doxycycline. Not producing ESBL strains of E. coli were sensitive to fosfomycin. Comparison of data obtained during testing of isolated cultures on ESBL, study of their sensitivity and resistance to beta-lactams (amoxicillin/clavulanate, ceftazidime, ceftriaxone, cefotaxime, imipenem) indicates the need to test isolates for AmpC products. To this end, during the screening test for ESBL and the method of «double disks», along with cephalosporins of III generation, it is necessary to use a phenotypic test for sensitivity to cefepime. The use of test results of E. coli isolates isolated from patients with UTIS for the production of ESBL, ampC enzymes, carbapenemase and sensitivity to AMP will improve the effectiveness of antimicrobial therapy and will help to curb the formation and spread of antimicrobial-resistan strains.

Acquisition of plasmid-mediated cephalosporinase producing Enterobacteriaceae after a travel to the tropics

Travelers are at high risk of acquiring multi-drug resistant Enterobacteriaceae (MRE) while traveling abroad. Acquisition of extended spectrum beta-lactamase producing Enterobacteriaceae (ESBL-E) while traveling has been extensively described, but not that of plasmid-mediated cephalosporinase producing Enterobacteriaceae (pAmpC-E). Here, we characterized the pAmpC-E acquired in 574 French travelers to tropical areas enrolled in the VOYAG-R study. Among the 526 MRE isolated at return, 57 (10.8%) from 49 travelers were pAmpC-E. The acquisition rate of pAmpC-E was 8.5% (49/574) ranging from 12.8% (25/195) in Asia, 7.6% (14/184) in Latin America to 5.1% (10/195) in Africa. The highest acquisition rates were observed in Peru (21.9%), India (21.4%) and Vietnam (20%). The carriage of pAmpC-E decreased quickly after return with 92.5% of colonized travelers being negative at one month. Most enzymes were CMY types (96.5%, n = 55, only met in Escherichia coli), including 40 CMY-2 (70.2%), 12 CMY-42 (21.1%), 1 CMY-6 and two new CMY-2 variants. The remaining were two DHA observed in Klebsiella pneumoniae. CMY-2 producing strains were acquired worldwide whereas CMY-42, except for one, were all acquired in Asia. Bla_CMY-2 genes were associated with different plasmid types, including IncI1 (45. 2%), IncF (10%), IncF-IncI (7.5%), IncA/C (5%) and IncR (2.5%) whereas bla_CMY-42 were all associated with IncI1 plasmids. Even though the pAmpC-E acquisition rate was much lower than that of ESBL-E, it was significant, especially in Asia, showing that pAmpC-E, especially CMY-type producing E. coli have spread in the community settings of tropical regions.

Contemporary IncI1 plasmids involved in the transmission and spread of antimicrobial resistance in Enterobacteriaceae

IncI1 has become one of the most common plasmid families in contemporary Enterobacteriaceae from both human and animal sources. In clinical epidemiology, this plasmid type ranks first as the confirmed vehicle of transmission of extended spectrum beta-lactamase and plasmid AmpC genes in isolates from food-producing animals. In this review, we describe the epidemiology and evolution of IncI1 plasmids and closely related IncIγ plasmids. We highlight the emergence of epidemic plasmids circulating among different bacterial hosts in geographically distant countries, and we address the phylogeny of the IncI1 and IncIγ family based on plasmid Multilocus Sequence Typing.

Characterization of Gene Families Encoding Beta-Lactamases of Gram-Negative Rods Isolated from Ready-to-Eat Vegetables in Mexico City

Beta-lactam resistant bacteria, which are commonly resident in tertiary hospitals, have emerged as a worldwide health problem because of ready-to-eat vegetable intake. We aimed to characterize the genes that provide resistance to beta-lactam antibiotics in Enterobacteriaceae, isolated from five commercial salad brands for human consumption in Mexico City. In total, twenty-five samples were collected, grown in blood agar plates, and the bacteria were biochemistry identified and antimicrobial susceptibility testing was done. The carried family genes were identified by endpoint PCR and the specific genes were confirmed with whole genome sequencing (WGS) by Next Generation Sequencing (NGS). Twelve positive cultures were identified and their microbiological distribution was as follows: 8.3% for Enterobacter aerogene (n = 1), 8.3% for Serratia fonticola (n = 1), 16.7% for Serratia marcesens (n = 2), 16.7% for Klebsiella pneumoniae (n = 2), and 50% (n = 6) for Enterobacter cloacae. The endpoint PCR results showed 11 colonies positive for blaBIL (91.7%), 11 for blaSHV (91.7%), 11 for blaCTX (97.7%), 12 for blaDHA (100%), four for blaVIM (33.3%), two for blaOXA (16.7%), two for blaIMP (16.7%), one for blaKPC (8.3%), and one for blaTEM (8.3%) gen; all samples were negative for blaROB, blaCMY, blaP, blaCFX and blaLAP gene. The sequencing analysis revealed a specific genotype for Enterobacter cloacae (blaSHV-12, blaCTX-M-15, blaDHA-1, blaKPC-2); Serratia marcescens (blaSHV-1, blaCTX-M-3, blaDHA-1, blaVIM-2); Klebsiella pneumoniae (blaSHV-12, blaCTX-M-15, blaDHA-1); Serratia fonticola (blaSHV-12, blaVIM-1, blaDHA-1); and, Enterobacter aerogene (blaSHV-1, blaCTX-M-1, blaDHA-1, blaVIM-2, blaOXA-9). Our results indicate that beta-lactam-resistant bacteria have acquired integrons with a different number of genes that provide pan-resistance to beta-lactam antibiotics, including penicillins, oxacillins, cefalosporins, monobactams, carbapenems, and imipenems.

Bacterial Enzymes and Antibiotic Resistance

The resistance of microorganisms to antibiotics has been developing for more than 2 billion years and is widely distributed among various representatives of the microbiological world. Bacterial enzymes play a key role in the emergence of resistance. Classification of these enzymes is based on their participation in various biochemical mechanisms: modification of the enzymes that act as antibiotic targets, enzymatic modification of intracellular targets, enzymatic transformation of antibiotics, and the implementation of cellular metabolism reactions. The main mechanisms of resistance development are associated with the evolution of superfamilies of bacterial enzymes due to the variability of the genes encoding them. The collection of all antibiotic resistance genes is known as the resistome. Tens of thousands of enzymes and their mutants that implement various mechanisms of resistance form a new community that is called "the enzystome." Analysis of the structure and functional characteristics of enzymes, which are the targets for different classes of antibiotics, will allow us to develop new strategies for overcoming the resistance.

Impact of Inducible blaDHA-1 on Susceptibility of Klebsiella pneumoniae Clinical Isolates to LYS228 and Identification of Chromosomal mpl and ampD Mutations Mediating Upregulation of Plasmid-Borne blaDHA-1 Expression

Twenty-three Klebsiella pneumoniae (blaDHA-1) clinical isolates exhibited a range of susceptibilities to LYS228, with MICs of ≥8 μg/ml for 9 of these. Mutants with decreased susceptibility to LYS228 and upregulated expression of blaDHA-1 were selected from representative isolates. These had mutations in the chromosomal peptidoglycan recycling gene mpl or ampD Preexisting mpl mutations were also found in some of the clinical isolates examined, and these had strongly upregulated expression of blaDHA-1.

Decline in AmpC β-lactamase-producing Escherichia coli in a Dutch teaching hospital (2013-2016)

OBJECTIVE

The objective of this study is to determine the prevalence of rectal carriage of plasmid- and chromosome-encoded AmpC β-lactamase-producing Escherichia coli and Klebsiella spp. in patients in a Dutch teaching hospital between 2013 and 2016.

METHODS

Between 2013 and 2016, hospital-wide yearly prevalence surveys were performed to determine the prevalence of AmpC β-lactamase-producing E. coli and Klebsiella spp. rectal carriage. Rectal swabs were taken and cultured using an enrichment broth and selective agar plates. All E. coli and Klebsiella spp. isolates were screened for production of AmpC β-lactamase using phenotypic confirmation tests and for the presence of plasmid-encoded AmpC (pAmpC) genes. E. coli isolates were screened for chromosome-encoded AmpC (cAmpC) promoter/attenuator alterations.

RESULTS

Fifty (2.4%) of 2,126 evaluable patients were identified as rectal carrier of AmpC β-lactamase-producing E. coli. No carriage of AmpC β-lactamase producing Klebsiella spp. was found. Nineteen (0.9%) patients harboured isolates with pAmpC genes and 30 (1,4%) patients harboured isolates with cAmpC promoter/attenuator alterations associated with AmpC β-lactamase overproduction. For one isolate, no pAmpC genes or cAmpC promotor/attenuator alterations could be identified. During the study period, a statistically significant decline in the prevalence of rectal carriage with E. coli with cAmpC promotor/attenuator alterations was found (p = 0.012). The prevalence of pAmpC remained stable over the years.

CONCLUSIONS

The prevalence of rectal carriage of AmpC-producing E. coli and Klebsiella spp. in patients in Dutch hospitals is low and a declining trend was observed for E. coli with cAmpC promotor/attenuator alterations.

Community-Acquired Urinary Tract Infection by Escherichia coli in the Era of Antibiotic Resistance

Urinary tract infections (UTIs) caused by Escherichia coli (E. coli) are the most common types of infections in women. The antibiotic resistance of E. coli is increasing rapidly, causing physicians to hesitate when selecting oral antibiotics. In this review, our objective is to ensure that clinicians understand the current seriousness of antibiotic-resistant E. coli, the mechanisms by which resistance is selected for, and methods that can be used to prevent antibiotic resistance.

Emergence of CMY-2-Producing Salmonella Heidelberg Associated with IncI1 Plasmids Isolated from Poultry in Brazil

In this study we report the characterization of plasmid-mediated CMY-2-producing Salmonella Heidelberg recovered from food, poultry, and poultry environment in Brazil, between 2014 and 2016. The bla_CMY-2 resistance gene was allocated in large (90-148 kb) IncI1 type transferable plasmids. Salmonella Heidelberg isolates were genetically related, indicating the dissemination of closely related isolates among food, poultry, and its environment. This is the first report of IncI1 replicon-types of plasmids encoding the bla_CMY-2 resistance gene in Salmonella Heidelberg isolates in Brazil, the world's biggest exporter of chickens.

The association between extended spectrum beta-lactamase (ESBL) and ampicillin C (AmpC) beta-lactamase genes with multidrug resistance in Escherichia coli isolates recovered from turkeys in Brazil

1. The aim of this study was to analyse the association between Escherichia coli isolates recovered from turkeys and the expression of beta-lactamase genes, such as extended spectrum beta-lactamase (ESBL) and ampicillin class C (AmpC). The phenotype of the resistance profile was examined using the association between amoxicillin and ceftiofur resistance. 2. Results showed that 84% from the turkey isolates harboured 4 or 5 genes associated with the CoIV plasmid. In an antibiogram test, 82% of the isolates were multidrug-resistant, the highest levels of resistance being against erythromycin (99%) and amoxicillin (76.1%). ESBL-positive groups were 31% positive for the ctx-m-2 gene, 6.8% were positive for ctx-m-8 and 70% harboured the tem wild gene. 3. All positive isolates from the AmpC beta-lactamase-positive group harboured the cmy-2 gene. The presence of the cmy-2 gene was associated with both the CTX-group genes and resistance to ceftiofur. 4. There was a high prevalence of avian pathogenic E. coli in suspected cases of colibacillosis in turkeys and a high antimicrobial resistance index. The results highlighted the risk of ceftiofur resistance and the presence of both ESBL and AmpC beta-lactamase E. coli in the turkey production chain.

Tackling the Antibiotic Resistance Caused by Class A β-Lactamases through the Use of β-Lactamase Inhibitory Protein

β-Lactams are the most widely used and effective antibiotics for the treatment of infectious diseases. Unfortunately, bacteria have developed several mechanisms to combat these therapeutic agents. One of the major resistance mechanisms involves the production of β-lactamase that hydrolyzes the β-lactam ring thereby inactivating the drug. To overcome this threat, the small molecule β-lactamase inhibitors (e.g., clavulanic acid, sulbactam and tazobactam) have been used in combination with β-lactams for treatment. However, the bacterial resistance to this kind of combination therapy has evolved recently. Therefore, multiple attempts have been made to discover and develop novel broad-spectrum β-lactamase inhibitors that sufficiently work against β-lactamase producing bacteria. β-lactamase inhibitory proteins (BLIPs) (e.g., BLIP, BLIP-I and BLIP-II) are potential inhibitors that have been found from soil bacterium Streptomyces spp. BLIPs bind and inhibit a wide range of class A β-lactamases from a diverse set of Gram-positive and Gram-negative bacteria, including TEM-1, PC1, SME-1, SHV-1 and KPC-2. To the best of our knowledge, this article represents the first systematic review on β-lactamase inhibitors with a particular focus on BLIPs and their inherent properties that favorably position them as a source of biologically-inspired drugs to combat antimicrobial resistance. Furthermore, an extensive compilation of binding data from β-lactamase–BLIP interaction studies is presented herein. Such information help to provide key insights into the origin of interaction that may be useful for rationally guiding future drug design efforts.