The enzymatic β-lactams resistance
Resistance to β-lactams has spread worldwide. The low toxicity of these molecules and the broad spectrum of action of some of them make β-lactams the most prescribed antibiotic drug class and propagation of resistance constitutes therefore a major clinical concern. Studies have highlighted that the rise of the bacterial resistance against β-lactams is related to the usage of the drug in clinics, both because of selection of resistant bacteria and by promoting the mobilization of the genes responsible for such resistances (Bush and Fisher, 2011). Similarly, the presence of antibiotics in water environments could promote the selection of antibiotic resistant strains. Detecting and measuring the concentration of antibiotics or intermediary products from their metabolization and degradation in water medium is difficult, mainly because of the lack of standardized methods (Pérez-Parada et al., 2011). However, different studies described analytical methods to investigate pollution of freshwater by antibiotic compounds (Bailon-Perez et al., 2009; Ibanez et al., 2009) and antibiotics, including β-lactams, have been found to contaminate significantly several rivers (Pei et al., 2006; Jiang et al., 2011; Yang et al., 2011). A recent report from Pérez-Parada et al. (2011) has demonstrated the presence of compounds derived from amoxicillin in river effluent water. Although a selection due to these compounds has not been demonstrated, a corresponding risk cannot be excluded.
The most prevalent mechanism of β-lactams resistance in Gram-negative bacteria has been, for a long time, the enzymatic inactivation mediated by penicillinases such as TEM, SHV, and the extended spectrum β-lactamases (ESBLs) derived from these families (Coque et al., 2008). In the last decade, blaTEM and blaSHV, genes have become less frequently detected in clinics and have been replaced by the more recently described blaCTX-M (Bonnet, 2004). CTX-M enzymes represent a special concern in clinics due to the extended spectrum of action and to its global, successful spread that has occurred in bacteria responsible for nosocomial and community acquired infections (Pitout et al., 2005). In 1963, blaTEM has been reported for the first time, located on a plasmid. All the currently known blaTEM genes have been documented to derive from the first characterized allele (Barlow and Hall, 2002). However, the origin of this mechanism has not been elucidated until now. The K. pneumoniae chromosome is thought to be the origin of blaSHV, even if the physiological role of this mechanism remains unknown (Haeggman et al., 2004). CTX-M enzymes have been extensively investigated in clinics and more recently reported from environmental samples. Presence of blaCTX-M in bacteria from freshwater (Dhanji et al., 2011; Lupo et al., submitted), water sediment (Lu et al., 2010), or water-associated birds (Randall et al., 2011) constitutes further reservoirs and shuttles for these resistance determinants (Table 1). Based on aminoacidic homology, the blaCTX-M genes are sorted in four groups: blaCTX-M-1, blaCTX-M-2, blaCTX-M-8, blaCTX-M-9 (Pitout et al., 2005). The progenitor of each gene group has been found located on the chromosome of Kluyvera spp., of the Enterobacteriaceae family. Mobilization events from the ancestor genes have given rise to the clinically relevant mechanisms. In detail, blaCTX-M-1 and blaCTX-M-2 derived from Kluyvera ascorbata (Humeniuk et al., 2002; Rodriguez et al., 2004), blaCTX-M-8 and blaCTX-M-9 from Kluyvera georgiana (Poirel et al., 2002; Canton and Coque, 2006). The Kluyvera genus seems to be a sink of blaCTX-M. Indeed, Kluyvera cryocrescens harbors a chromosomal β-lactamase, KLUC-1, which shares ca. 85% identity with CTX-M-1 (Bonnet, 2004). To the best of our knowledge, KLUC-1 has not been encountered in clinical isolates, but this species represents a reservoir of a new potential clinical ESBL. Although Kluyvera spp. are considered environmental bacteria and have been found also in water, elucidating the natural habitat of this species may help to evaluate the risk of the propagation of their β-lactamases. The CTX-M enzymes have been extensively investigated because of the clinical consequences that their spread has caused. However, many class A β-lactamases are chromosomally located in several members of Enterobacteriaceae and could constitute, if integrated on mobile elements, future mechanisms emerging in clinics. Bellais et al. (2001) discovered a chromosomal β-lactamase in Rahnella aquatilis (RAHN-1), which had similarities to blaCTX-M-1 and blaCTX-M-2; Arakawa et al. (1989) characterized KOXY from Klebsiella oxytoca; Perilli et al. (1991) MAL-1 in Citrobacter diversus; Peduzzi et al. (1994) CUM-A in P. vulgaris; Liassine et al. (2002) HUG-A from Proteus penneri; Peduzzi et al. (1997) SFO-1 from Serratia fonticola; Seoane and Garcia Lobo (1991) YENT from Yersinia enterocolitica; Vimont et al. (2002) ERP-1 from Erwinia persicina; Walckenaer et al. (2004) PLA-1 and ORN-1A from Raoultella planticola and Raoultella ornithinolytica, respectively. The above mentioned list provides only some examples: Bush and Fisher (2011) have reviewed that almost 600 class A β-lactamases naturally occur and have been reported in 2011. Worryingly, mechanisms exhibiting a spectrum of activity extended to carbapenems are emerging in clinics (Rossolini, 2005; Queenan and Bush, 2007). VIM, IMP, KPC, some OXA, and the newly described NDM-1 represent examples of these enzymes. The emergence of KPC (K. pneumoniae carbapenemase) was described in 2001 (Yigit et al., 2001) and this enzyme has been found to spread worldwide and among several bacterial species such as Enterobacteriaceae, P. aeruginosa, and A. baumannii (Bush and Fisher, 2011). The crucial molecular vector of its spread has been recognized by Naas et al. (2008), who characterized the location of blaKPC gene on a Tn-3-like transposon, the Tn4401, probably responsible for the original mobilization of this gene. The transposon contains several sequences encoding transposases or insertion sequences derived from environmental bacterial species, but the ancestral host of this enzyme has not been identified, so far. Recently Chagas et al. (2011) have detected K. pneumoniae producing KPC in an effluent receiving hospital waste water, highlighting an environmental vector for the dissemination of these enzymes (Table 1). VIM enzymes have been rarely reported from environmental isolates. Scotta et al. (2011) isolated Brevundimonas diminuta, Rhizobium radiobacter, Pseudomonas monteilii, P. aeruginosa, O. anthropi, and Enterobacter ludwigii strains producing VIM enzymes, again from an effluent receiving the waste water of a hospital. Previously, Quinteira et al. (2005) isolated a strain of Pseudomonas pseudoalcaligenes harboring blaVIM from a hospital wastewater effluent (Table 1). Probably, the presence of VIM producer species in the environment is due to nosocomial selective conditions and contamination by wastewater from hospitals. However, the detection of blaVIM in different environmental species from freshwater highlights the potential of water as a reservoir for these genes and as a vector facilitating their spread. Concerning IMP enzymes, so far, a unique report has been provided by Pellegrini et al. (2009), in a strain of P. fluorescens recovered from waste water (Table 1). A carbapenemase activity is also exhibited by several class D β-lactamases, among which the families of OXA-23, OXA-40, OXA-58, and OXA-51 are associated to A. baumannii (Poirel et al., 2010). This opportunistic pathogen, provided with an intrinsic but silent blaOXA51-like gene, is widely distributed in nature. The origin of blaOXA-40 and blaOXA-58-like genes remains unknown but Poirel et al. (2008) have characterized a blaOXA-23-like chromosomally located in Acinetobacter radioresistens, suggesting that this species is the progenitor for OXA-23. Moreover, A. baumannii isolates carrying blaOXA-23 have been detected in river (Girlich et al., 2010) and wastewater from hospitals (Ferreira et al., 2011, Table 1). OXA-48 represents another class D carbapenemase that dramatically spreads among Enterobacteriaceae. This latter enzyme is supposed to originate from the chromosome of the water borne species S. oneidensis (Poirel et al., 2004). Recently, S. marcescens strains harboring blaOXA-48 have been isolated from a river in Morocco (Potron et al., 2011), demonstrating the risks for their dissemination in water habitats (Table 1). The recent emergence and dramatic spread of NDM-1 enzyme in clinical isolates of A. baumannii and Enterobacteriaceae, has focused major attentions. Usually, strains harboring this broad spectrum carbapenemase gene demonstrate a multi-drug resistant phenotype and a wide set of virulence genes (Walsh et al., 2011). The carriage of bacteria harboring blaNDM-1 by healthy individuals has lead researchers to investigate the source of this gene. Walsh et al. (2011) recently demonstrated the presence of different bacterial species (P. aeruginosa, Achromobacter spp., and Kingella denitrificans) harboring blaNDM-1 in tap water used as drinking water in India (Table 1). This finding is closing the transmission circle and explains the fast and successful dissemination of this gene. Several genes encoding carbapenemase enzymes have been found chromosomally located in bacterial species of environmental origin and water related, for instance the sme gene on the chromosome of S. marcescens, and the sfc gene on the S. fonticola chromosome (Naas and Nordmann, 1994; Henriques et al., 2004). The water borne S. maltophilia also harbors a gene coding for the L1 carbapenemase. Avison et al. (2001) have elucidated that this gene is located on a plasmid-like element considered intrinsic to S. maltophilia.
Class C β-lactamases located on plasmids (CMY, MIR, DHA, and ACT) have been found worldwide from several sources (Jacoby, 2009). Water borne bacteria, such as A. hydrophila, M. morganii, H. alvei, and shuttle species between water and gut such as Citrobacter freundii, Enterobacter asburiae, have been proposed to be the progenitors of the most commonly encountered plasmidic ampC genes detected in clinical isolates. These genes have been reported from Canadian and Korean water bodies (Kim et al., 2008; Mataseje et al., 2009). Schwartz et al. (2003) detected ampC in waste, surface, and drinking water biofilms (Table 1). The presence of antibiotic resistance genes in biofilm matrices, especially in those located in drinking water supplies is of particular concern. Indeed, such biofilm matrices can be a long lasting source of antibiotic resistance genes that can directly spread via the food chain.