Expanded-spectrum beta-lactamase PER-1 in an environmental Aeromonas media isolate from Switzerland

Genomic epidemiology and ceftazidime-avibactam high-level resistance mechanisms of Pseudomonas aeruginosa in China from 2010 to 2022

Ceftazidime-avibactam (CZA) resistance is a huge threat in the clinic; however, the underlying mechanism responsible for high-level CZA resistance in Pseudomonas aeruginosa (PA) isolates remains unknown. In this study, a total of 5,763 P. aeruginosa isolates were collected from 2010 to 2022 to investigate the ceftazidime-avibactam (CZA) high-level resistance mechanisms of Pseudomonas aeruginosa (PA) isolates in China. Fifty-six PER-producing isolates were identified, including 50 isolates carrying blaPER-1 in PA, and 6 isolates carrying blaPER-4. Of these, 82.1% (46/56) were classified as DTR-PA isolates, and 76.79% (43/56) were resistant to CZA. Importantly, blaPER-1 and blaPER-4 overexpression led to 16-fold and >1024-fold increases in the MICs of CZA, respectively. WGS revealed that the blaPER-1 gene was located in two different transferable IncP-2-type plasmids and chromosomes, whereas blaPER-4 was found only on chromosomes and was carried by a class 1 integron embedded in a Tn6485-like transposon. Overexpression of efflux pumps may be associated with high-level CZA resistance in blaPER-1-positive strains. Kinetic parameter analysis revealed that PER-4 exhibited a similar kcat/Km with ceftazidime and a high (∼3359-fold) IC50 value with avibactam compared to PER-1. Our study found that overexpression of PER-1 combined with enhanced efflux pump expression and the low affinity of PER-4 for avibactam contributes to high-level resistance to CZA. Additionally, the Tn6485-like transposon plays a significant role in disseminating blaPER. Urgent active surveillance is required to prevent the further spread of high-level CZA resistance in DTR-PA isolates.

Characterization of virulence and antimicrobial resistance genes of Aeromonas media strain SD/21-15 from marine sediments in comparison with other Aeromonas spp

Aeromonas media is a Gram-negative bacterium ubiquitously found in aquatic environments. It is a foodborne pathogen associated with diarrhea in humans and skin ulceration in fish. In this study, we used whole genome sequencing to profile all antimicrobial resistance (AMR) and virulence genes found in A. media strain SD/21-15 isolated from marine sediments in Denmark. To gain a better understanding of virulence and AMR genes found in several A. media strains, we included 24 whole genomes retrieved from the public databanks whose isolates originate from different host species and environmental samples from Asia, Europe, and North America. We also compared the virulence genes of strain SD/21-15 with A. hydrophila, A. veronii, and A. salmonicida reference strains. We detected Msh pili, tap IV pili, and lateral flagella genes responsible for expression of motility and adherence proteins in all isolates. We also found hylA, hylIII, and TSH hemolysin genes in all isolates responsible for virulence in all isolates while the aerA gene was not detected in all A. media isolates but was present in A. hydrophila, A. veronii, and A. salmonicida reference strains. In addition, we detected LuxS and mshA-Q responsible for quorum sensing and biofilm formation as well as the ferric uptake regulator (Fur), heme and siderophore genes responsible for iron acquisition in all A. media isolates. As for the secretory systems, we found all genes that form the T2SS in all isolates while only the vgrG1, vrgG3, hcp, and ats genes that form parts of the T6SS were detected in some isolates. Presence of bla MOX-9 and bla OXA-427 β-lactamases as well as crp and mcr genes in all isolates is suggestive that these genes were intrinsically encoded in the genomes of all A. media isolates. Finally, the presence of various transposases, integrases, recombinases, virulence, and AMR genes in the plasmids examined in this study is suggestive that A. media has the potential to transfer virulence and AMR genes to other bacteria. Overall, we anticipate these data will pave way for further studies on virulence mechanisms and the role of A. media in the spread of AMR genes.

PER extended-spectrum β-lactamases originate from Pararheinheimera spp

To investigate the origin of PER extended-spectrum β-lactamases, publicly available sequence databases were searched for bla_PER-like genes. Three genomes from Pararheinheimera, a genus associated with water and soil environments, were found to carry bla_PER-like genes but lacked the ISCR1/ISPa12/ISPa13 insertion sequences commonly associated with bla_PER in clinical isolates. Sequence analysis revealed 78-96% nucleotide identity and conserved synteny between the clinical mobile genetic elements (MGEs) encoding bla_PER-1 and the bla_PER locus in the Pararheinheimera genomes. Notably, bla_PER genes were only identified in 3 of 21 Pararheinheimera and Rheinheimera genomes, whereas the genetic environment of bla_PER genes as found in clinical MGEs was conserved in all Pararheinheimera and Rheinheimera genomes. These findings indicate that bla_PER genes were likely acquired by a branch of the Pararheinheimera genus long before the antibiotic era. Later, bla_PER genes were mobilised, likely through the involvement of insertion sequences, from one or several Pararheinheimera species, allowing their dissemination into human pathogens.

Transposition of Tn1213 Encoding the PER-1 Extended-Spectrum β-Lactamase

PER-1 is an extended-spectrum β-lactamase that is encoded by a gene located in composite transposon Tn1213 made by two distinct insertion sequences, namely, ISPa12 and ISPa13. In vitro mobilization performed in Escherichia coli shows that Tn1213 is functional and is able to mobilize the blaPER-1 gene, although at a very low frequency (ca. 1 × 10-9).

Delineation of Taxonomic Species within Complex of Species: Aeromonas media and Related Species as a Test Case

Aeromonas media is an opportunistic pathogen for human and animals mainly found in aquatic habitats and which has been noted for significant genomic and phenotypic heterogeneities. We aimed to better understand the population structure and diversity of strains currently affiliated to A. media and the related species A. rivipollensis. Forty-one strains were included in a population study integrating, multilocus genetics, phylogenetics, comparative genomics, as well as phenotypics, lifestyle, and evolutionary features. Sixteen gene-based multilocus phylogeny delineated three clades. Clades corresponded to different genomic groups or genomospecies defined by phylogenomic metrics ANI (average nucleotide identity) and isDDH (in silico DNA-DNA hybridization) on 14 whole genome sequences. DL-lactate utilization, cefoxitin susceptibility, nucleotide signatures, ribosomal multi-operon diversity, and differences in relative effect of recombination and mutation (i.e., in evolution mode) distinguished the two species Aeromonas media and Aeromonas rivipollensis. The description of these two species was emended accordingly. The genome metrics and comparative genomics suggested that a third clade is a distinct genomospecies. Beside the species delineation, genetic and genomic data analysis provided a more comprehensive knowledge of the cladogenesis determinants at the root and inside A. media species complex among aeromonads. Particular lifestyles and phenotypes as well as major differences in evolution modes may represent putative factors associated with lineage emergence and speciation within the A. media complex. Finally, the integrative and populational approach presented in this study is considered broadly in order to conciliate the delineation of taxonomic species and the population structure in bacterial genera organized in species complexes.

PER-8, a Novel Extended-Spectrum β-Lactamase PER Variant, from an Acinetobacter baumannii Clinical Isolate in Nepal

A novel PER-type extended-spectrum β-lactamase, PER-8, was identified in an Acinetobacter baumannii clinical isolate obtained in Nepal. The amino acid sequence of PER-8 has a substitution at position 39 (Gly to Glu) compared with that of PER-7. The k_cat/K_m ratio of PER-8 for aztreonam was lower than that of PER-7, while the k_cat/K_m ratio of PER-8 for imipenem was higher than that of PER-7. The genomic environment surrounding bla_PER-8 was intI1 bla_PSE-1qacEDI sulI ISCR1-bla_PER-8gts sulI orfX on a 100-kb plasmid.

Multidrug-resistant (MDR) Aeromonas recovered from the metropolitan area of Valencia (Spain): diseases spectrum and prevalence in the environment

Aeromonas infections are rare in Europe and often related to traveller's diarrhoea. A total of 185 Aeromonas isolates from river water, fish and clinical sources, recovered during a 1-year period, were used to investigate the disease spectrum and impact of multidrug-resistant (MDR) strains. They were all identified by biochemical tests and 25% of them were also identified by sequencing of the 16S rRNA gene. The minimum inhibitory concentrations (MICs) of 21 antimicrobials were determined for all isolates by broth microdilution/E-strips methods, and susceptibility was assessed according to the Clinical and Laboratory Standards Institute (CLSI). Strains pathogenicity was determined by using Swiss Webster mice as the animal model. Aeromonas diseases had an incidence of around 20 cases/million inhabitants in the metropolitan area of Valencia (Spain). Acute gastroenteritis in children with no history of travel abroad was the main pathology. These cases were related to A. caviae, A. veronii biovar sobria, A. hydrophila and A. dhakensis. A significant incidence of A. caviae in humans was found, while the other species were equally present in clinical and environmental origins. A. jandaei, A. bestiarum and A. media had mainly an environmental distribution. The prevalence of MDR Aeromonas was maximal in clinical samples, and resistance phenotypes were significantly related to this source. 7.2% of environmental Aeromonas was resistant to at least five drugs; most of them were moderately virulent for mice and, in addition, belonged to clinically significant species. The present study demonstrates a diseases spectrum similar to that reported in tropical countries, and also that pathogenic and heavily MDR Aeromonas are present in environmental reservoirs. MDR Aeromonas from any source analysed were susceptible to aztreonam, netilmicin, cefotaxime, ceftazidime, cefepime and fluoroquinolones.

The complex genetic context of blaPER-1 flanked by miniature inverted-repeat transposable elements in Acinetobacter johnsonii

On a large plasmid of Acinetobacter johnsonii strain XBB1 from hospital sewage, bla_PER-1 and ISCR1 were found in a complex Tn402-like integron carrying an arr3-aacA4 cassette array. The integron was truncated by the same 439-bp miniature inverted-repeat transposable element (MITE) at both ends. bla_PER-1 and its complex surroundings might have been mobilized by the MITEst into an orf of unknown function, evidenced by the presence of the characteristic 5-bp direct target repeats. The same 439-bp MITEs have also been found flanking class 1 integrons carrying metallo-β-lactamases genes bla_IMP-1, bla_IMP-5 and bla_VIM-2 before but without ISCR1. Although the cassette arrays are different, integrons have always been truncated by the 439-bp MITEs at the exact same locations. The results suggested that MITEs might be able to mobilize class 1 integrons via transposition or homologous recombination and therefore represent a possible common mechanism for mobilizing antimicrobial resistance determinants.

Occurrence and antibiotic susceptibility profiles of Burkholderia cepacia complex in coastal marine environment

During an environmental study of bacterial resistance to antibiotics in coastal waters of the Kaštela Bay, Adriatic Sea, Croatia, 47 Burkholderia cepacia complex (Bcc) isolates were recovered from seawater and mussel (Mytilus galloprovincialis) samples. All isolates showed multiple antibiotic resistance. Among the isolates, two Burkholderia cenocepacia isolates produced chromosomally encoded TEM-116 extended-spectrum β-lactamase (ESBL). Analysis of outer membrane proteins revealed that decreased expression of a 36-kDa protein could be associated with a high level of β-lactam resistance in both isolates. Phenotypic study of efflux system also indicated an over-expression of Resistance-Nodulation-Cell Division (RND) efflux-mediated mechanism in one of the isolates. This study demonstrated the presence of Bcc in seawater and M. galloprovincialis, which gives evidence that coastal marine environment, including mussels, could be considered as a reservoir for Bcc species. Detection of ESBL-encoding genes indicates the potential role of these bacteria in the maintenance and dispersion of antibiotic resistance genes.

Antibiotic susceptibility profiles and first report of TEM extended-spectrum β-lactamase in Pseudomonas fluorescens from coastal waters of the Kaštela Bay, Croatia

The aim of this study was to investigate the antibiotic susceptibility profiles and the presence of extended-spectrum-β-lactamases (ESBLs) in Pseudomonas fluorescens isolates from coastal waters of the Kaštela Bay, Croatia. Twenty-two water samples were collected during 2009. Isolates were tested for susceptibilities to 13 antibiotics by Etest. ESBL production was confirmed by double-disk synergy test carried out on Mueller-Hinton agar plates containing efflux pump inhibitor Phe-Arg-β-naphthylamide dihydrochloride. PCR and DNA sequencing analysis were used to identify ESBL-encoding genes. The transferability of cephalosporin resistance was tested by conjugation experiments. Genetic relatedness of ESBL-producing isolates was determined by random amplified polymorphic DNA (RAPD) analysis. Out of 185 P. fluorescens isolates recovered, 70 (37.8%) demonstrated multiresistance phenotype with highest rates of resistance to tetracycline (61.6%), aztreonam (31.9%), meropenem (17.3%), ceftazidime (15.1%) and cefotaxime (12.4%). Ten (5.4%) isolates were identified as ESBL producers. All isolates carried chromosomally located bla (TEM-116) gene. RAPD analysis identified four different genotypes. Here, we demonstrated a baseline profiles of antimicrobial resistance of P. fluorescens from coastal waters of the Kaštela Bay, Croatia. To our knowledge, this is the first report of the presence of TEM-type ESBL in P. fluorescens, indicating this bacterium as a reservoir of antibiotic resistance genes with clinical relevance.

Carbapenem-hydrolyzing GES-5-encoding gene on different plasmid types recovered from a bacterial community in a sewage treatment plant

Plasmids pRSB113 and pRSB115 were recovered from an activated sludge bacterial community of a municipal wastewater treatment plant in Germany. Both plasmids carry the same bla(GES-5) carbapenemase gene, located within two distinct class 1 integrons. These plasmids have different backbones, belong to different incompatibility groups, and could replicate in both Pseudomonas aeruginosa and Escherichia coli.

Bacteremia due to extended-spectrum-β-lactamase-producing Aeromonas spp. at a medical center in Southern Taiwan

Although extended-spectrum-β-lactamase (ESBL)-producing aeromonads have been increasingly reported in recent years, most of them were isolates from case reports or environmental isolates. To investigate the prevalence of ESBL producers among Aeromonas blood isolates and the genes encoding ESBLs, consecutive nonduplicate Aeromonas blood isolates collected at a medical center in southern Taiwan from March 2004 to December 2008 were studied. The ESBL phenotypes were examined by clavulanate combination disk test and the cefepime-clavulanate ESBL Etest. The presence of ESBL-encoding genes, including bla(TEM), bla(PER), bla(CTX-M), and bla(SHV) genes, was evaluated by PCR and sequence analysis. The results showed that 4 (2.6%) of 156 Aeromonas blood isolates, 1 Aeromonas hydrophila isolate and 3 Aeromonas caviae isolates, expressed an ESBL-producing phenotype. The ESBL gene in two A. caviae isolates was bla(PER-3), which was located in both chromosomes and plasmids, as demonstrated by Southern hybridization. Of four patients with ESBL-producing Aeromonas bacteremia, two presented with catheter-related phlebitis and the other two with primary bacteremia. Three patients had been treated with initial noncarbapenem β-lactams for 5 to 10 days, and all survived. In conclusion, ESBL producers exist among Aeromonas blood isolates, and clinical suspicion of ESBL production should be raised in treating infections due to cefotaxime-resistant Aeromonas isolates.

PER-7, an extended-spectrum beta-lactamase with increased activity toward broad-spectrum cephalosporins in Acinetobacter baumannii

Acinetobacter baumannii isolate AP2 was recovered from a bronchial lavage sample of a patient hospitalized in Paris, France. A. baumannii AP2 was resistant to all β-lactams, including carbapenems, and expressed the extended-spectrum β-lactamase (ESBL) PER-7, which differs from PER-1 by 4 amino acid substitutions. Compared to PER-1, PER-7 possessed higher-level hydrolytic activities against cephalosporins and aztreonam. The blaPER-7 gene was chromosomally located and associated with a mosaic class 1 integron structure. Additionally, isolate AP2 expressed the carbapenem-hydrolyzing oxacillinase OXA-23 and the 16S RNA methylase ArmA, conferring high-level resistance to aminoglycosides.

Diversity of clavulanic acid-inhibited extended-spectrum β-lactamases in Aeromonas spp. from the Seine River, Paris, France

Environmental Aeromonas sp. isolates resistant to ceftazidime were recovered during an environmental survey performed with water samples from the Seine River, in Paris, France, in November 2009. Selected isolates were identified by sequencing of the 16S rRNA and rpoB genes. PCR and cloning experiments were used to identify broad-spectrum-β-lactamase-encoding genes and their genetic context. Clavulanic acid-inhibited extended-spectrum-β-lactamase (ESBL) genes were identified in 71% of the Aeromonas sp. isolates. A variety of ESBL genes were detected, including bla(VEB-1a), bla(SHV-12), bla(PER-1), bla(PER-6), bla(TLA-2), and bla(GES-7), suggesting an aquatic reservoir of those ESBL genes. Moreover, the repeated elements and different insertion sequences were identified in association with the bla(PER-6) and the bla(VEB-1a) genes, respectively, indicating a wide diversity of mobilization events, making Aeromonas spp. a vehicle for ESBL dissemination.

PER-6, an extended-spectrum beta-lactamase from Aeromonas allosaccharophila

An Aeromonas allosaccharophila environmental isolate recovered from the Seine River (Paris, France) produced a novel extended-spectrum beta-lactamase, PER-6, that shared 92% amino acid identity with the closest ss-lactamase, PER-2. The kinetic properties of PER-6 showed a slightly increased affinity for carbapenems. The bla(PER-6) gene was chromosomally located and bracketed by non-transposon-related structures.