Molecular distribution of ROB-1 beta-lactamase in Actinobacillus pleuropneumoniae

Genomic epidemiology of third-generation cephalosporin-resistant Escherichia coli from Argentinian pig and dairy farms reveals animal-specific patterns of co-resistance and resistance mechanisms

Control measures are being introduced globally to reduce the prevalence of antibiotic resistance (ABR) in bacteria on farms. However, little is known about the current prevalence and molecular ecology of ABR in bacterial species with the potential to be key opportunistic human pathogens, such as Escherichia coli, on South American farms. Working with 30 dairy cattle farms and 40 pig farms across two provinces in central-eastern Argentina, we report a comprehensive genomic analysis of third-generation cephalosporin-resistant (3GC-R) E. coli, which were recovered from 34.8% (cattle) and 47.8% (pigs) of samples from fecally contaminated sites. Phylogenetic analysis revealed substantial diversity suggestive of long-term horizontal and vertical transmission of 3GC-R mechanisms. CTX-M-15 and CTX-M-2 were more often produced by isolates from dairy farms, while CTX-M-8 and CMY-2 and co-carriage of amoxicillin/clavulanate resistance and florfenicol resistance were more common in isolates from pig farms. This suggests different selective pressures for antibiotic use in these two animal types. We identified the β-lactamase gene blaROB, which has previously only been reported in the family Pasteurellaceae, in 3GC-R E. coli. blaROB was found alongside a novel florfenicol resistance gene, ydhC, also mobilized from a pig pathogen as part of a new composite transposon. As the first comprehensive genomic survey of 3GC-R E. coli in Argentina, these data set a baseline from which to measure the effects of interventions aimed at reducing on-farm ABR and provide an opportunity to investigate the zoonotic transmission of resistant bacteria in this region.

IMPORTANCE

Little is known about the ecology of critically important antibiotic resistance among bacteria with the potential to be opportunistic human pathogens (e.g., Escherichia coli) on South American farms. By studying 70 pig and dairy cattle farms in central-eastern Argentina, we identified that third-generation cephalosporin resistance (3GC-R) in E. coli was mediated by mechanisms seen more often in certain species and that 3GC-R pig E. coli were more likely to be co-resistant to florfenicol and amoxicillin/clavulanate. This suggests that on-farm antibiotic usage is key to selecting the types of E. coli present on these farms. 3GC-R E. coli and 3GC-R plasmids were diverse, suggestive of long-term circulation in this region. We identified the de novo mobilization of the resistance gene blaROB from pig pathogens into E. coli on a novel mobile genetic element, which shows the importance of surveying poorly studied regions for antibiotic resistance that might impact human health.

WGS analysis of a penicillin-resistant Neisseria meningitidis strain containing a chromosomal ROB-1 β-lactamase gene

Objectives

Neisseria meningitidis is rarely penicillin resistant. We describe WGS analysis of a penicillin-resistant N. meningitidis collected from a case of invasive meningococcal disease.

Methods

Serogrouping, serotyping and serosubtyping were performed with specific antibodies. β-Lactamase was detected by nitrocefin. MICs were determined by Etest and agar dilution. Sequencing of N. meningitidis genomes was done on the Illumina MiSeq platform and genome data were analysed using the Bacterial Isolate Genome Sequence Database (BIGSdb) on the PubMLST Neisseria website (https://pubmlst.org/neisseria/). Transformation was used to confirm the genetic basis of the penicillin resistance.

Results

An N. meningitidis blood isolate from a female patient in her mid-50s with a painful and septic left shoulder was found to have penicillin MIC values of 3–12 mg/L. The isolate was typed as Y: 14, 19: P1.– and ST3587, and was weakly β-lactamase positive. WGS analysis identified a full-length copy of the β-lactamase gene bla_ROB-1, which was contained on a 1719 bp insert with a G + C content of 41.7% (versus a G + C content of N. meningitidis of 51.7%), suggesting that the bla_ROB-1 gene came from a different bacterial species. A GenBank analysis of the bla_ROB-1 gene insert found 99.77% identity with a DNA segment found in plasmid pB1000′ from Haemophilus influenzae. Transformation of a penicillin-susceptible strain with the bla_ROB-1 gene conferred β-lactamase activity and penicillin resistance.

Conclusions

N. meningitidis serogroup Y, ST3587 can carry and express the bla_ROB-1 gene, leading to penicillin resistance. It is highly likely that the N. meningitidis isolate acquired the bla_ROB-1 gene from H. influenzae.

Antimicrobial Resistance in Pasteurellaceae of Veterinary Origin

Members of the highly heterogeneous family Pasteurellaceae cause a wide variety of diseases in humans and animals. Antimicrobial agents are the most powerful tools to control such infections. However, the acquisition of resistance genes, as well as the development of resistance-mediating mutations, significantly reduces the efficacy of the antimicrobial agents. This article gives a brief description of the role of selected members of the family Pasteurellaceae in animal infections and of the most recent data on the susceptibility status of such members. Moreover, a review of the current knowledge of the genetic basis of resistance to antimicrobial agents is included, with particular reference to resistance to tetracyclines, β-lactam antibiotics, aminoglycosides/aminocyclitols, folate pathway inhibitors, macrolides, lincosamides, phenicols, and quinolones. This article focusses on the genera of veterinary importance for which sufficient data on antimicrobial susceptibility and the detection of resistance genes are currently available (Pasteurella, Mannheimia, Actinobacillus, Haemophilus, and Histophilus). Additionally, the role of plasmids, transposons, and integrative and conjugative elements in the spread of the resistance genes within and beyond the aforementioned genera is highlighted to provide insight into horizontal dissemination, coselection, and persistence of antimicrobial resistance genes. The article discusses the acquisition of diverse resistance genes by the selected Pasteurellaceae members from other Gram-negative or maybe even Gram-positive bacteria. Although the susceptibility status of these members still looks rather favorable, monitoring of their antimicrobial susceptibility is required for early detection of changes in the susceptibility status and the newly acquired/developed resistance mechanisms.

Pasteurellaceae bacteria from the oral cavity of Tasmanian devils (Sarcophilus Harrisii) show high minimum inhibitory concentration values towards aminoglycosides and clindamycin

Threatened by Devil Facial Tumor Disease, the Tasmanian devil populations are vulnerable and decreasing. Additionally, the devils' biting behaviour elevates their risk of acquiring bite wound infections caused by members of the bacterial Pasteurellaceae family that are natural inhabitants of the oral microbiota. In medical management of such bite wounds, antimicrobial susceptibility profiles are crucial. Prior to this investigation, no available data on minimal inhibitory concentration (MIC) values existed. A total of 26 isolates obtained from the oral cavity of 26 healthy Tasmanian devils were tested for their antimicrobial susceptibility by broth micro dilution. Most prominently, high MIC values for clindamycin (≥4 μg ml(-1) ), gentamicin (≥8 μg ml(-1) ) and amikacin (≥32 μg ml(-1) ), were observed for 92, 77 and 73% of the strains tested respectively. This study may be used as a guideline for antimicrobial therapy against bite wound infections caused by Pasteurellaceae originating from the oral cavity of Tasmanian devils.

SIGNIFICANCE AND IMPACT OF THE STUDY

Tasmanian devils' aggressive behaviour makes bite wounds in fellow devils and human caretakers a common entity. Pasteurellaceae bacteria are common inhabitants of the oral microbiota of Tasmanian devils and a likely cause of bite wound infections. Here, for the first time, we report antimicrobial sensitivity profiles from a broad collection of Pasteurellaceae isolates obtained from the oral cavity of Tasmanian devils. Low MIC values were observed for the majority of the 22 antimicrobial agents included, yet nearly all strains were tolerant to clindamycin and the aminoglycosides. The work can serve as a guide for clinicians involved in treatment of bite wounds inflicted by devils in animals and humans.

Novel blaROB-1-bearing plasmid conferring resistance to β-lactams in Haemophilus parasuis isolates from healthy weaning pigs

Haemophilus parasuis, the causative agent of Glässer's disease, is one of the early colonizers of the nasal mucosa of piglets. It is prevalent in swine herds, and lesions associated with disease are fibrinous polyserositis and bronchopneumonia. Antibiotics are commonly used in disease control, and resistance to several antibiotics has been described in H. parasuis. Prediction of H. parasuis virulence is currently limited by our scarce understanding of its pathogenicity. Some genes have been associated with H. parasuis virulence, such as lsgB and group 1 vtaA, while biofilm growth has been associated with nonvirulent strains. In this study, 86 H. parasuis nasal isolates from farms that had not had a case of disease for more than 10 years were obtained by sampling piglets at weaning. Isolates were studied by enterobacterial repetitive intergenic consensus PCR and determination of the presence of lsgB and group 1 vtaA, biofilm formation, inflammatory cell response, and resistance to antibiotics. As part of the diversity encountered, a novel 2,661-bp plasmid, named pJMA-1, bearing the blaROB-1 β-lactamase was detected in eight colonizing strains. pJMA-1 was shown to share a backbone with other small plasmids described in the Pasteurellaceae, to be 100% stable, and to have a lower biological cost than the previously described plasmid pB1000. pJMA-1 was also found in nine H. parasuis nasal strains from a separate collection, but it was not detected in isolates from the lesions of animals with Glässer's disease or in nontypeable Haemophilus influenzae isolates. Altogether, we show that commensal H. parasuis isolates represent a reservoir of β-lactam resistance genes which can be transferred to pathogens or other bacteria.

Molecular organization of small plasmids bearing blaTEM-1 and conferring resistance to β-lactams in Haemophilus influenzae

TEM-1 is the dominant β-lactamase of Haemophilus influenzae and can be located on small plasmids. Three distinct plasmids with sizes from 4,304 to 5,646 nucleotides (nt) were characterized: pA1606, pA1209, and pPN223. In addition to TEM-1 and a replication enzyme of the Rep 3 superfamily, pA1606 carries a Tn3 resolvase gene and pA1606 and pA1209 carry an open reading frame (ORF) similar to a plasmid recombination enzyme gene described in Gram-positive bacteria. The plasmids transformed strain Rd to the ampicillin-resistant phenotype.

Antimicrobial susceptibilities and resistance genes of Canadian isolates of Actinobacillus pleuropneumoniae

Actinobacillus pleuropneumoniae is the causative agent of porcine pleuropneumonia, a severe and highly contagious respiratory disease responsible for economic losses in the swine industry worldwide. Although antimicrobial resistance in A. pleuropneumoniae has been recently reported in different countries, the current situation in Canada is unknown. The aim of the current study was to determine the antimicrobial susceptibilities of 43 strains of A. pleuropneumoniae isolated in Canada. In addition, antimicrobial resistance genes were detected with an oligonucleotide microarray. The impact of biofilm formation on susceptibility to antimicrobials was also evaluated. All isolates were susceptible to ceftiofur, florfenicol, enrofloxacin, erythromycin, clindamycin, trimethoprim/sulfamethoxazole, and tilmicosin. A low level of resistance was observed toward tiamulin, penicillin, and ampicillin as well as danofloxacin. We observed a high level of resistance to chlortetracycline (88.4%) and oxytetracycline (90.7%). The strains showing resistance to tetracycline antimicrobials contained at least one of the following tet genes: tetB, tetO, tetH, or tetC. Five isolates showed multiresistance to penicillins (bla(ROB-1)), streptomycin [aph3'' (strA)], sulfonamides (sulII), and tetracyclines (tetO) antimicrobials whereas three others showed multiresistance to streptomycin [aph3'' (strA)], sulfonamides (sulII), and tetracyclines (tetB, tetO, or tetB/tetH) antimicrobials. To the best of our knowledge, this is the first description of tetC gene in Pasteurellaceae. Finally, cells of A. pleuropneumoniae in a biofilm were 100 to 30,000 times more resistant to antimicrobials than their planktonic counterparts.

Beta-lactam resistance in Haemophilus parasuis Is mediated by plasmid pB1000 bearing blaROB-1

beta-Lactam resistance in Haemophilus parasuis is an emerging phenomenon that has not yet been characterized from a molecular perspective. Clinical high-level beta-lactam-resistant isolates from Spain bore a novel plasmid, pB1000, expressing a functionally active ROB-1 beta-lactamase. Pulsed-field gel electrophoresis was applied for the first time to H. parasuis and showed that beta-lactam resistance is due to clonal spread of a resistant strain, BB1018, bearing pB1000.

Studies on the mechanisms of β-lactam resistance in Bordetella bronchiseptica

OBJECTIVES

Little is currently known about beta-lactam resistance in Bordetella bronchiseptica. So far, only a single beta-lactamase gene, bla(BOR-1), has been identified. In a previous study, high MICs of ampicillin, cefalotin and ceftiofur were determined among 349 porcine B. bronchiseptica isolates. The aim of this study was to identify genes associated with elevated MICs of beta-lactams and their transferability.

METHODS

Selected isolates were investigated by PCR for commonly found bla genes and class 1 integrons; selected amplicons were sequenced. Plasmid location of resistance genes was confirmed by conjugation. Beta-lactamases were characterized by SDS-PAGE and isoelectric focusing. The genomic relatedness of the isolates was investigated by XbaI macrorestriction analysis. Inhibition studies with efflux pump inhibitors were conducted. The permeability of cephalosporins into intact cells was measured exemplarily for one isolate.

RESULTS

Of the 349 B. bronchiseptica isolates, eight isolates carried a class 1 integron with a bla(OXA-2) cassette on a conjugative plasmid of ca. 50 kb. In addition, one plasmid-free isolate also carried this class 1 integron. Besides bla(BOR-1), no other beta-lactamase gene was detected in the remaining isolates with high MICs of ampicillin of >or= 32 mg/L. Inhibition experiments suggested that efflux does not play a role in beta-lactam resistance. Instead, membrane permeability for cephalosporins was reduced as shown for B. bronchiseptica isolate B543.

CONCLUSIONS

This is to the best of our knowledge the first report of a mobile bla gene in B. bronchiseptica. Reduced membrane permeability of B. bronchiseptica seems to decrease susceptibility against cephalosporins.

Antimicrobial susceptibility and plasmid analysis of Actinobacillus pleuropneumoniae isolated in Taiwan

Sixty Actinobacillus pleuropneumoniae (App) strains from pigs in Taiwan were examined. Serotyping revealed that these belonged to serovars 1 (n=53), 2 (n=3), and 5 (n=4). Agar disk diffusion susceptibility testing of the isolates showed 55 (92%) were resistant to three or more antimicrobial agents. Six resistance patterns were observed. Ampicillin-chloramphenicol-flumequine-nalidixic acid-streptomycin-sulfonamide/trimethoprim-tetracycline was the most common multi-resistance pattern. Minimal inhibitory concentration of 14 antimicrobial agents was determined. The isolates were highly susceptible to ceftiofur and trimethoprim in vitro. Isolates were resistant to streptomycin, ampicillin, and nalidixic acid. All isolates were examined for the presence of plasmids using the alkaline lysis method. Forty three (72%) isolates had four plasmid bands with an approximate sizes of 3.5, 4.3, 5.8 and 6.0 kb; 12 (20%) had three bands at 3.5, 4.3 and 5.2 kb, and 5 (8%) had no plasmid bands. Antimicrobial resistance plasmids were detected in resistant strains of App. Three antimicrobial resistance plasmids were transformed into E. coli DH5 alpha. pTMY1 (4.3 kb) encoded a streptomycin kinase and a dihydropteroate synthase; pTMY2 (6.0 kb) encoded ROB-1 beta-lactamase and aminoglycoside 3'-phosphotransferase; pTMY3 (5.2 kb) encoded only ROB-1 beta-lactamase. The 4.3 kb plasmid was sequenced and consisted of 4242 bp with 42.9% GC content. The 4.3 kb plasmid DNA sequence was 98% homologous to a plasmid previously isolated from Pasteurella haemolytica.

Morphological changes and lysis induced by beta-lactams associated with the characteristic profiles of affinities of penicillin-binding proteins in actinobacillus pleuropneumoniae

Actinobacillus pleuropneumoniae, which was formerly classified in the genus Haemophilus, is a pathogen causing swine pleuropneumonia. We found that aspoxicillin showed strong activity and that meropenem had better lytic activity against this pathogen. In the present study, we for the first time identified penicillin-binding proteins (PBPs) of A. pleuropneumoniae in order to elucidate the relationship between the antibacterial and lytic activities of beta-lactam antibiotics and affinities of the PBPs. The competitive assay using (3)H-labeled benzylpenicillin revealed seven PBPs in A. pleuropneumoniae; they were determined to be PBPs 1a, 1b, 2, 3, 4, 5, and 6, and the molecular masses of these PBPs were estimated to be 92, 80, 76, 72, 50, 44, and 30 kDa, respectively, by comparison with those of Haemophilus influenzae. Our detailed analysis of the affinities of the PBPs of A. pleuropneumoniae and of the bacterial lysis kinetics for several beta-lactam antibiotics revealed that the strong antibacterial activity of aspoxicillin against this strain could be related to the higher affinity of PBP 3 and that preferential inactivation of PBP 1b could cause rapid lysis.

Antimicrobial susceptibility of equine isolates of Actinobacillus spp. and identification of beta-lactamases in some strains

A total number of 149 Actinobacillus strains isolated from clinical samples (73 strains) and from the oral cavity of healthy horses (76 strains) were tested for their susceptibility to 17 antimicrobial substances. The antibiograms were generally very similar between the various strains and no differences could be clearly correlated to either phenotype or source of isolates. However, when tested against penicillin, ampicillin, trimethoprim-sulfa, and streptomycin, small groups of strains with what appeared to be acquired resistance could be identified. Eight of the penicillin-resistant strains were found to produce beta-lactamase. The beta-lactamases appeared to be bound tightly to the cell wall, thereby frustrating further characterization by isoelectric focusing. Plasmids of approximately 3 kb were found in four out of seven beta-lactamase-producing strains submitted to plasmid analysis.