Genetic and Biochemical Characterization of an Acquired Subgroup B3 Metallo-β-Lactamase Gene,
            <i>bla</i>
            <sub>AIM-1</sub>
            , and Its Unique Genetic Context in Pseudomonas aeruginosa from Australia

fThe origin of carbapenem-hydrolyzing metallo-␤-lactamases (MBLs) acquired by clinical bacteria is largely unknown. We investigated the frequency, host range, diversity, and functionality of MBLs in the soil microbiota. Twenty-five soil samples of different types and geographical origins were analyzed by antimicrobial selective culture, followed by phenotypic testing and expression of MBL-encoding genes in Escherichia coli, and whole-genome sequencing of MBL-producing strains was performed. Carbapenemase activity was detected in 29 bacterial isolates from 13 soil samples, leading to identification of seven new MBLs in presumptive Pedobacter roseus (PEDO-1), Pedobacter borealis (PEDO-2), Pedobacter kyungheensis (PEDO-3), Chryseobacterium piscium (CPS-1), Epilithonimonas tenax (ESP-1), Massilia oculi (MSI-1), and Sphingomonas sp. (SPG-1). Carbapenemase production was likely an intrinsic feature in Chryseobacterium and Epilithonimonas, as it occurred in reference strains of different species within these genera. The amino acid identity to MBLs described in clinical bacteria ranged between 40 and 69%. Remarkable features of the new MBLs included prophage integration of the encoding gene (PEDO-1), an unusual amino acid residue at a key position for MBL structure and catalysis (CPS-1), and overlap with a putative OXA ␤-lactamase (MSI-1). Heterologous expression of PEDO-1, CPS-1, and ESP-1in E. coli significantly increased the MICs of ampicillin, ceftazidime, cefpodoxime, cefoxitin, and meropenem. Our study shows that MBL producers are widespread in soil and include four genera that were previously not known to produce MBLs. The MBLs produced by these bacteria are distantly related to MBLs identified in clinical samples but constitute resistance determinants of clinical relevance if acquired by pathogenic bacteria.

Section: Resultsmentioning

confidence: 99%

The Soil Microbiota Harbors a Diversity of Carbapenem-Hydrolyzing β-Lactamases of Potential Clinical Relevance

Gudeta

Bortolaia

Amos

et al. 2016

“…Altogether, these findings suggested that, similar to other ␤-lactamases, including some acquired MBLs, namely, bla SPM-1 and bla AIM-1 (32,33), an ISCR element was involved in the capture and mobilization of bla FIM-1 and underscored the potential role of (27)(28)(29) or deduced using the SignalP software. The sequence sources were as follows: FIM-1 (the present study), NDM-1 (GenBank/EMBL accession no.…”

Section: Resultsmentioning

confidence: 89%

FIM-1, a New Acquired Metallo-β-Lactamase from a Pseudomonas aeruginosa Clinical Isolate from Italy

Pollini

Maradei

Pecile³

et al. 2013

Acquired metallo-␤-lactamases (MBLs) are resistance determinants of increasing clinical importance in Gram-negative bacterial pathogens, which confer a broad-spectrum ␤-lactam resistance, including carbapenems. Several such enzymes have been described since the 1990s. In the present study, a novel acquired MBL, named FIM-1, was identified and characterized. The bla FIM-1 gene was cloned from a multidrug-resistant Pseudomonas aeruginosa clinical isolate (FI-14/157) cultured from a patient with a vascular graft infection in Florence, Italy. The isolate belonged in the sequence type 235 epidemic clonal lineage. The FIM-1 enzyme is a member of subclass B1 and, among acquired MBLs, exhibited the highest similarity (ca. 40% amino acid identity) with NDM-type enzymes. In P. aeruginosa FI-14/157, the bla FIM-1 gene was apparently inserted into the chromosome and associated with ISCR19-like elements that were likely involved in the capture and mobilization of this MBL gene. Transfer experiments of the bla FIM-1 gene to an Escherichia coli strain or another P. aeruginosa strain by conjugation or electrotransformation were not successful. The FIM-1 protein was produced in E. coli and purified by two chromatography steps. Analysis of the kinetic parameters, carried out with the purified enzyme, revealed that FIM-1 has a broad substrate specificity, with a preference for penicillins (except the 6␣-methoxy derivative temocillin) and carbapenems. Aztreonam was not hydrolyzed. Detection of this novel type of acquired MBL in a P. aeruginosa clinical isolate underscores the increasing diversity of such enzymes that can be encountered in the clinical setting.A cquired metallo-␤-lactamases (MBLs) are resistance determinants of increasing clinical importance in Gram-negative bacterial pathogens, including Pseudomonas aeruginosa, Enterobacteriaceae, and other Gram-negative nonfermenters. These enzymes can degrade most ␤-lactams, including carbapenems, and escape inhibition by the conventional ␤-lactamase inhibitors or avibactam. Thus, they are able to confer an extended ␤-lactam resistance profile to the bacterial host that is not reversible by ␤-lactamase inhibitors (1).Acquired MBLs were detected since the early 1990s, the first representatives being IMP-and VIM-type enzymes (2-4). Thereafter, a number of additional lineages of acquired MBLs have been described, including the SPM-, GIM-, SIM-, KHM-, NDM-, AIM-, DIM-, SMB-, and TMB-type enzymes (5, 6; see also reference 1 and references therein). By convention, different MBL types diverge from each other at by least 30% at the amino acid sequence level (7). Enzymes of different types may differ in functional properties, and the corresponding genes may be associated with different types of mobile genetic elements responsible for their dissemination, such as mobile gene cassettes inserted into integrons, ISCR elements, or composite transposons (8, 9).We report here on the identification and characterization of a new type of acquired MBL, named FIM-1, in a multidrug-resistant clinical ...

“…For example, Klebsiella pneumoniae carbapenemase (KPC) is the carbapenemase found most frequently in Enterobacteriaceae in the United States (1), while NDM is frequently found in the Indian subcontinent (2) and SPM is found in Brazil (3). Despite the fact that there have been reports of KPC (4), NDM (5,6), OXA-48 (7) and even a unique carbapenemase, AIM-1 (8), in Australia, none have become dominant there. In Australia, IMP-producing Enterobacteriaceae, particularly Enterobacter cloacae, have been reported to be the predominant form of CPE (9)(10)(11).…”

mentioning

confidence: 99%

Dominance of IMP-4-Producing Enterobacter cloacae among Carbapenemase-Producing Enterobacteriaceae in Australia

Sidjabat

Townell

Nimmo

et al. 2015

eThe prevalence of carbapenemase-producing Enterobacteriaceae (CPE) has been increasing worldwide. bla IMP has been reported to be the predominant carbapenemase-encoding gene within Enterobacteriaceae in Australia. However, there are limited data currently available on CPE from Queensland, Australia. A total of 58 CPE isolates were isolated between July 2009 and March 2014 from Queensland hospitals. The clonality of isolates was determined by Diversilab repetitive sequence-based PCR. The isolates were investigated for the resistance mechanisms carbapenemase, extended-spectrum ␤-lactamase, and AmpC ␤-lactamase and for aminoglycoside resistance and plasmid-mediated quinolone resistance genes by PCR. The plasmid types associated with carbapenemase-encoding genes were characterized. The majority of the CPE were Enterobacter cloacae (n ‫؍‬ 29). The majority of Queensland CPE isolates were IMP producers and comprised 11 species (n ‫؍‬ 48). Nine NDM-producing Enterobacteriaceae were identified. One NDM-producing Klebsiella pneumoniae isolate coproduced OXA-48. One K. pneumoniae isolate was an OXA-181 producer. The incidence of IMP producers increased significantly in 2013. bla IMP-4 was found in all IMP-producing isolates. bla TEM , qnrB, and aacA4 were common among IMP-4 producers. The HI2 (67%) and L/M (21%) replicons were associated with bla IMP-4 . All HI2 plasmids were of sequence type 1 (ST1). All but one of the NDM producers possessed bla CTX-M-15 . The 16S rRNA methylase genes found among NDM producers were armA, rmtB, rmtC, and rmtF. The substantial increase in the prevalence of CPE in Queensland has been associated mainly with the emergence E. cloacae strains possessing HI2 plasmids carrying bla IMP-4 over the past 2 years. The importation of NDM producers and/or OXA-48-like producers in patients also contributed to the increased emergence of CPE.