ISEcp1-mediated transposition of qnrB-like gene in Escherichia coli

High Prevalence of Plasmid-Mediated Quinolone Resistance among ESBL/AmpC-Producing Enterobacterales from Free-Living Birds in Poland

In this study, we investigated the occurrence of plasmid-mediated quinolone resistance (PMQR) in extended-spectrum β-lactamase- (ESBL) and/or AmpC-type β-lactamase-producing Enterobacterales isolates from free-living birds in Poland. The prevalence of the qnrB19 gene was 63%, and the distribution of isolates in terms of bacterial species was as follows: 67% (22/33) corresponded to Escherichia coli, 83% (5/6) to Rahnella aquatilis, 44% (4/9) to Enterobacter cloacae and 33% (1/3) to Klebsiella pneumoniae. The qnrB19 gene was also found in a single isolate of Citrobacter freundii. The molecular characteristics of qnrB19-positive isolates pointed to extended-spectrum beta lactamase CTX-M as the most prevalent one (89%) followed by TEM (47%), AmpC (37%) and SHV (16%). This study demonstrates the widespread occurrence of PMQR-positive and ESBL/AmpC-producing Enterobacterales isolates in fecal samples from wild birds. In this work, plasmid pAM1 isolated from Escherichia coli strain SN25556 was completely sequenced. This plasmid is 3191 nucleotides long and carries the qnrB19 gene, which mediates decreased susceptibility to quinolones. It shares extensive homology with other previously described small qnrB19-harboring plasmids. The nucleotide sequence of pAM1 showed a variable region flanked by an oriT locus and a Xer recombination site. The presence of a putative recombination site was detected, suggesting that interplasmid recombination events might have played a role in the development of pAM1. Our results highlight the broad geographical spread of ColE-type Qnr resistance plasmids in clinical and environmental isolates of Enterobacterales. As expected from the results of phenotypic susceptibility testing, no resistance genes other than qnrB19 were identified.

Global Distribution and Diversity of Prevalent Sewage Water Plasmidomes

Sewage water from around the world contains an abundance of short plasmids, several of which harbor antimicrobial resistance genes (ARGs). The global dynamics of plasmid-derived antimicrobial resistance and functions are only starting to be unveiled. Here, we utilized a previously created data set of 159,332 assumed small plasmids from 24 different global sewage samples. The detailed phylogeny, as well as the interplay between their protein domains, ARGs, and predicted bacterial host genera, were investigated to understand sewage plasmidome dynamics globally. A total of 58,429 circular elements carried genes encoding plasmid-related features, and MASH distance analyses showed a high degree of diversity. A single (yet diverse) cluster of 520 predicted Acinetobacter plasmids was predominant among the European sewage water. Our results suggested a prevalence of plasmid-backbone gene combinations over others. This could be related to selected bacterial genera that act as bacterial hosts. These combinations also mirrored the geographical locations of the sewage samples. Our functional domain network analysis identified three groups of plasmids. However, these backbone domains were not exclusive to any given group, and Acinetobacter was the dominant host genus among the theta-replicating plasmids, which contained a reservoir of the macrolide resistance gene pair msr(E) and mph(E). Macrolide resistance genes were the most common in the sewage plasmidomes and were found in the largest number of unique plasmids. While msr(E) and mph(E) were limited to Acinetobacter, erm(B) was disseminated among a range of Firmicutes plasmids, including Staphylococcus and Streptococcus, highlighting a potential reservoir of antibiotic resistance for these pathogens from around the globe. IMPORTANCE Antimicrobial resistance is a global threat to human health, as it inhibits our ability to treat infectious diseases. This study utilizes sewage water plasmidomes to identify plasmid-derived features and highlights antimicrobial resistance genes, particularly macrolide resistance genes, as abundant in sewage water plasmidomes in Firmicutes and Acinetobacter hosts. The emergence of macrolide resistance in these bacteria suggests that macrolide selective pressure exists in sewage water and that the resident bacteria can readily acquire macrolide resistance via small plasmids.

Epidemiologic and molecular characterization of β-lactamase-producing multidrug-resistant uropathogenic Escherichia coli isolated from asymptomatic hospitalized patients

Uropathogenic Escherichia coli (UPECs) are the predominant cause of asymptomatic bacteriuria (ABU) and symptomatic UTI. In this study, multidrug-resistant (MDR) ABU-UPECs from hospitalized patients of Kolkata, India, were characterized with respect to their ESBL phenotype, acquisition of β-lactamase genes, mobile genetic elements (MGEs), phylotype property, ERIC-PCR profile, sequence types (STs), clonal complexes (CCs) and evolutionary and quantitative relationships and compared to the symptomatic ones to understand their epidemiology and evolutionary origin. Statistically significant incidence of ESBL producers, β-lactamase genes, MGEs and novel phylotype property (NPP) among ABU-UPECs similar to the symptomatic ones indicated the probable incidence of chromosomal plasticity on resistance gene acquisition through MGEs due to indiscriminate drug usage. ERIC-PCR typing and MLST analysis showed clonal heterogeneity and predominance of ST940 (CC448) among asymptomatic isolates akin to symptomatic ones along with the evidence of zoonotic transmissions. Minimum spanning tree analysis showed a close association between ABU-UPEC with known and unidentified STs having NPPs with isolates that belonged to phylogroups clade I, D, and B2. This is the first study that reported the occurrence of MGEs and NPPs among ABU-UPECs with the predominance of ESBL production which displayed the deleterious effect of MDR among this pathogen demanding alternative therapeutic interventions. Moreover, this study for the first time attempted to introduce a new approach to ascertain the phylotype property of unassigned UPECs. Withal, increased recognition, proper understanding and characterization of ABU-UPECs with the implementation of appropriate therapeutic measures against them when necessary are the need of the era which otherwise might lead to serious complications in the vulnerable population.

Molecular mechanisms associated with quinolone resistance in Enterobacteriaceae: review and update

BACKGROUND

Quinolones are broad-spectrum antibiotics, which are used for the treatment of different infectious diseases associated with Enterobacteriaceae. During recent decades, the wide use as well as overuse of quinolones against diverse infections has led to the emergence of quinolone-resistant bacterial strains. Herein, we present the development of quinolone antibiotics, their function and also the different quinolone resistance mechanisms in Enterobacteriaceae by reviewing recent literature.

METHODS

All data were extracted from Google Scholar search engine and PubMed site, using keywords; quinolone resistance, Enterobacteriaceae, plasmid-mediated quinolone resistance, etc.

RESULTS AND CONCLUSION

The acquisition of resistance to quinolones is a complex and multifactorial process. The main resistance mechanisms consist of one or a combination of target-site gene mutations altering the drug-binding affinity of target enzymes. Other mechanisms of quinolone resistance are overexpression of AcrAB-tolC multidrug-resistant efflux pumps and downexpression of porins as well as plasmid-encoded resistance proteins including Qnr protection proteins, aminoglycoside acetyltransferase (AAC(6')-Ib-cr) and plasmid-encoded active efflux pumps such as OqxAB and QepA. The elucidation of resistance mechanisms will help researchers to explore new drugs against the resistant strains.

A framework for identifying the recent origins of mobile antibiotic resistance genes

Since the introduction of antibiotics as therapeutic agents, many bacterial pathogens have developed resistance to antibiotics. Mobile resistance genes, acquired through horizontal gene transfer, play an important role in this process. Understanding from which bacterial taxa these genes were mobilized, and whether their origin taxa share common traits, is critical for predicting which environments and conditions contribute to the emergence of novel resistance genes. This knowledge may prove valuable for limiting or delaying future transfer of novel resistance genes into pathogens. The literature on the origins of mobile resistance genes is scattered and based on evidence of variable quality. Here, we summarize, amend and scrutinize the evidence for 37 proposed origins of mobile resistance genes. Using state-of-the-art genomic analyses, we supplement and evaluate the evidence based on well-defined criteria. Nineteen percent of reported origins did not fulfill the criteria to confidently assign the respective origin. Of the curated origin taxa, >90% have been associated with infection in humans or domestic animals, some taxa being the origin of several different resistance genes. The clinical emergence of these resistance genes appears to be a consequence of antibiotic selection pressure on taxa that are permanently or transiently associated with the human/domestic animal microbiome.

Ebmeyer and colleagues developed a genomic framework for identification and scrutiny of the origins of antibiotic resistance genes. Using data scoured from the literature and publicly available genomes, their results indicate that only 81% of previously reported origins are valid, and that the majority of resistance genes of which the origin is known to date emerged in taxa that have been associated with infection in humans and domesticated animals.

Transferable Mechanisms of Quinolone Resistance from 1998 Onward

While the description of resistance to quinolones is almost as old as these antimicrobial agents themselves, transferable mechanisms of quinolone resistance (TMQR) remained absent from the scenario for more than 36 years, appearing first as sporadic events and afterward as epidemics. In 1998, the first TMQR was soundly described, that is, QnrA. The presence of QnrA was almost anecdotal for years, but in the middle of the first decade of the 21st century, there was an explosion of TMQR descriptions, which definitively changed the epidemiology of quinolone resistance. Currently, 3 different clinically relevant mechanisms of quinolone resistance are encoded within mobile elements: (i) target protection, which is mediated by 7 different families of Qnr (QnrA, QnrB, QnrC, QnrD, QnrE, QnrS, and QnrVC), which overall account for more than 100 recognized alleles; (ii) antibiotic efflux, which is mediated by 2 main transferable efflux pumps (QepA and OqxAB), which together account for more than 30 alleles, and a series of other efflux pumps (e.g., QacBIII), which at present have been sporadically described; and (iii) antibiotic modification, which is mediated by the enzymes AAC(6')Ib-cr, from which different alleles have been claimed, as well as CrpP, a newly described phosphorylase.

Subtyping of plasmid-mediated quinolone resistance among Salmonella serotypes by whole genome sequencing

Most known plasmids are identified by conferring virulence or antimicrobial resistance phenotypes and such characteristics aid in the success of the dispersion of different plasmid types between bacteria from different sources. This study aimed to perform the subtyping of the plasmid-mediated quinolone resistance, detected in Salmonella spp. A total of 34 Salmonella strains non-susceptible to ciprofloxacin were evaluated. Strains were selected based on the presence of PMQR determined by Polymerase Chain Reaction and further submitted to Next Generation Sequencing. Most of the strains presented the qnrB19 in small ColE-like plasmids and qnrB2 gene associated with IncN/ST5 plasmids also detected. Our results indicated the co-occurrence of PMQR and ESBLs in plasmids that are a lineage of epidemic plasmids circulating in Salmonella in which additional resistances were detected, highlighting the potential threat of resistance Salmonella to public health, particularly in infections in which antimicrobial therapy is needed.

ISEcp1-mediated transposition of chromosome-borne blaCMY-2 into an endogenous ColE1-like plasmid in Escherichia coli

Background

CMY-2 is the most prevalent pAmpC β-lactamase, but the chromosomal bla_CMY-2 gene transfer via horizontal transmission has been seldom reported. This study aimed to describe an ISEcp1-mediated transposition of a chromosomal bla_CMY-2 gene from Escherichia coli into a small endogenous ColE1-like plasmid, resulting in elevated resistance to extended-spectrum cephalosporins.

Methods

Three ESCs-resistant ST641 E. coli strains EC6413, EC4103 and EC5106 harbored the bla_CMY-2 gene. S1-PFGE, I-ceu I-PFGE, Southern blotting and electroporation experiments were performed to investigate the location and transferability of bla_CMY-2. The genetic context and gene expression of bla_CMY-2 in the original isolates and the corresponding electroporants were explored by PCR mapping, primer walking strategy and RT-qPCR.

Results

The bla_CMY-2-containing region (ISEcp1-bla_CMY-2-∆blc-∆yggR-∆tnp1-orf7-orf8-orf9-∆tnp2-∆hsdR) was transposed into endogenous ColE1-like plasmid pSC137 in the process of electroporation at very low frequencies (10^-8-10^-9). The transpositions resulted in novel larger bla_CMY-2-harboring ColE1-like plasmids with size of 14,845 bp, enabling increase in MICs of 2 to 8-fold for cefotaxime, ceftiofur, and ceftazidime in recipient strains over their respective original counterparts. Transcriptional level analysis revealed that the increased bla_CMY-2 expression was correlated with elevated MIC values of cephalosporins. The bla_CMY-2 transposition unit was identical to that in a clinical isolate E. coli TN44889 from France isolated in 2004.

Conclusions

Our results firstly demonstrated that ISEcp1 mediated a transposition of chromosome-borne bla_CMY-2 into an endogenous ColE1-like plasmid by electroporation. Amplification of the bla_CMY-2 gene facilitates the strain adaptation to a changed environment with an elevated antibiotic pressure.

The impact of insertion sequences on bacterial genome plasticity and adaptability

Transposable elements (TE), small mobile genetic elements unable to exist independently of the host genome, were initially believed to be exclusively deleterious genomic parasites. However, it is now clear that they play an important role as bacterial mutagenic agents, enabling the host to adapt to new environmental challenges and to colonize new niches. This review focuses on the impact of insertion sequences (IS), arguably the smallest TE, on bacterial genome plasticity and concomitant adaptability of phenotypic traits, including resistance to antibacterial agents, virulence, pathogenicity and catabolism. The direct consequence of IS transposition is the insertion of one DNA sequence into another. This event can result in gene inactivation as well as in modulation of neighbouring gene expression. The latter is usually mediated by de-repression or by the introduction of a complete or partial promoter located within the element. Furthermore, transcription and transposition of IS are affected by host factors and in some cases by environmental signals offering the host an adaptive strategy and promoting genetic variability to withstand the environmental challenges.

Plasmid-mediated quinolone resistance in Enterobacteriaceae: a systematic review with a focus on Mediterranean countries

Quinolones are a family of synthetic broad-spectrum antimicrobial drugs. These molecules have been widely prescribed to treat various infectious diseases and have been classified into several generations based on their spectrum of activity. Quinolones inhibit bacterial DNA synthesis by interfering with the action of DNA gyrase and topoisomerase IV. Mutations in the genes encoding these targets are the most common mechanisms of high-level fluoroquinolone resistance. Moreover, three mechanisms for plasmid-mediated quinolone resistance (PMQR) have been discovered since 1998 and include Qnr proteins, the aminoglycoside acetyltransferase AAC(6')-Ib-cr, and plasmid-mediated efflux pumps QepA and OqxAB. Plasmids with these mechanisms often encode additional antimicrobial resistance (extended spectrum beta-lactamases [ESBLs] and plasmidic AmpC [pAmpC] ß-lactamases) and can transfer multidrug resistance. The PMQR determinants are disseminated in Mediterranean countries with prevalence relatively high depending on the sources and the regions, highlighting the necessity of long-term surveillance for the future monitoring of trends in the occurrence of PMQR genes.

Complex Class 1 Integron Carrying qnrB62 and blaVIM-2 in a Citrobacter freundii Clinical Isolate

The coexistence of qnrB62 and bla_VIM-2 was detected in a Citrobacter clinical isolate. The reduced fluoroquinolone susceptibility is attributable to qnrB62, mutations of quinolone-resistance-determining regions, and an efflux pump or pumps. The genetic context surrounding chromosomal qnrB62 was a novel complex class 1 integron (In1184::ISCR1::qnrB62) containing a unique gene array (bla_VIM-2-aacA4'-8-gucD). An 18-nucleotide deletion at the 3' end of the pspA gene [pspA(Δ18)], upstream of qnrB62, and an inverted repeat region (IRR2) were detected in In1184::ISCR1::qnrB62, indicating past transposition events.

Prevalence of Plasmid-Mediated Quinolone Resistance Genes in Clinical Enterobacteria from Argentina

This first nationwide study was conducted to analyze the prevalence of plasmid-mediated quinolone resistance (PMQR) genes in phenotypically unselected (consecutive) clinical enterobacteria. We studied 1,058 isolates that had been consecutively collected in 66 hospitals of the WHONET-Argentina Resistance Surveillance Network. Overall, 26% of isolates were nonsusceptible to at least one of the three quinolones tested (nalidixic acid, ciprofloxacin, and levofloxacin). The overall prevalence of PMQR genes was 8.1% (4.6% for aac(6')-Ib-cr; 3.9% for qnr genes; and 0.4% for oqxA and oqxB, which were not previously reported in enterobacteria other than Klebsiella spp. from Argentina). The PMQR prevalence was highly variable among the enterobacterial species or when the different genes were considered. The prevalent PMQR genes were located in class 1 integrons [qnrB2, qnrB10, and aac(6')-Ib-cr]; in the ColE1-type plasmid pPAB19-1 or Tn2012-like transposons (qnrB19); and in Tn6238 or bracketed by IS26 and bla_OXA-1 [aac(6')-Ib-cr]. The mutations associated with quinolone resistance that were located in the quinolone resistance-determining region (QRDR mutations) of gyrA, parC, and gyrB were also investigated. The occurrence of QRDR mutations was significantly associated with the presence of PMQR genes: At least one QRDR mutation was present in 82% of the PMQR-harboring isolates but in only 23% of those without PMQR genes (p < 0.0001, Fisher's Test). To the best of our knowledge, this is the first report on the prevalence of PMQR genes in consecutive clinical enterobacteria where all the genes currently known have been screened.

Acquisition of Broad-Spectrum Cephalosporin Resistance Leading to Colistin Resistance in Klebsiella pneumoniae

An extended-spectrum β-lactamase (ESBL)-producing and colistin-resistant Klebsiella pneumoniae clinical isolate was recovered from a patient who was treated with cefotaxime. This isolate harbored a blaCTX-M-15 ESBL gene that was associated with an ISEcp1 insertion sequence. Transposition of that tandem occurred within the chromosomal mgrB gene, leading to inactivation of the mgrB gene and consequently to acquired resistance to colistin. We showed here a coselection of colistin resistance as a result of a broad-spectrum cephalosporin selective pressure.

Plasmid-mediated quinolone resistance

Three mechanisms for plasmid-mediated quinolone resistance (PMQR) have been discovered since 1998. Plasmid genes qnrA, qnrB, qnrC, qnrD, qnrS, and qnrVC code for proteins of the pentapeptide repeat family that protects DNA gyrase and topoisomerase IV from quinolone inhibition. The qnr genes appear to have been acquired from chromosomal genes in aquatic bacteria, are usually associated with mobilizing or transposable elements on plasmids, and are often incorporated into sul1-type integrons. The second plasmid-mediated mechanism involves acetylation of quinolones with an appropriate amino nitrogen target by a variant of the common aminoglycoside acetyltransferase AAC(6')-Ib. The third mechanism is enhanced efflux produced by plasmid genes for pumps QepAB and OqxAB. PMQR has been found in clinical and environmental isolates around the world and appears to be spreading. The plasmid-mediated mechanisms provide only low-level resistance that by itself does not exceed the clinical breakpoint for susceptibility but nonetheless facilitates selection of higher-level resistance and makes infection by pathogens containing PMQR harder to treat.

Escherichia coli of sequence type 3835 carrying bla NDM-1, bla CTX-M-15, bla CMY-42 and bla SHV-12

New Delhi metallo-β-lactamase (NDM) represents a serious challenge for treatment and public health. A carbapenem-resistant Escherichia coli clinical strain WCHEC13-8 was subjected to antimicrobial susceptibility tests, whole genome sequencing and conjugation experiments. It was resistant to imipenem (MIC, >256 μg/ml) and meropenem (MIC, 128 μg/ml) and belonged to ST3835. bla NDM-1 was the only carbapenemase gene detected. Strain WCHEC13-8 also had a plasmid-borne AmpC gene (bla CMY-42) and two extended-spectrum β-lactamase genes (bla CTX-M-15 and bla SHV-12). bla NDM-1 and bla SHV-12 were carried by a 54-kb IncX3 self-transmissible plasmid, which is identical to plasmid pNDM-HF727 from Enterobacter cloacae. bla CMY-42 was carried by a 64-kb IncI1 plasmid and bla CTX-M-15 was located on a 141-kb plasmid with multiple F replicons (replicon type: F36:A4:B1). bla CMY-42 was in a complicated context and the mobilisation of bla CMY-42 was due to the transposition of ISEcp1 by misidentifying its right-end boundary. Genetic context of bla NDM-1 in strain WCHEC13-8 was closely related to those on IncX3 plasmids in various Enterobacteriaceae species in China. In conclusion, a multidrug-resistant ST3835 E. coli clinical strain carrying bla NDM-1, bla CTX-M-15, bla CMY-42 and bla SHV-12 was identified. IncX3 plasmids may be making a significant contribution to the dissemination of bla NDM among Enterobacteriaceae in China.

Mechanisms of drug resistance: quinolone resistance

Quinolone antimicrobials are synthetic and widely used in clinical medicine. Resistance emerged with clinical use and became common in some bacterial pathogens. Mechanisms of resistance include two categories of mutation and acquisition of resistance-conferring genes. Resistance mutations in one or both of the two drug target enzymes, DNA gyrase and DNA topoisomerase IV, are commonly in a localized domain of the GyrA and ParE subunits of the respective enzymes and reduce drug binding to the enzyme-DNA complex. Other resistance mutations occur in regulatory genes that control the expression of native efflux pumps localized in the bacterial membrane(s). These pumps have broad substrate profiles that include quinolones as well as other antimicrobials, disinfectants, and dyes. Mutations of both types can accumulate with selection pressure and produce highly resistant strains. Resistance genes acquired on plasmids can confer low-level resistance that promotes the selection of mutational high-level resistance. Plasmid-encoded resistance is due to Qnr proteins that protect the target enzymes from quinolone action, one mutant aminoglycoside-modifying enzyme that also modifies certain quinolones, and mobile efflux pumps. Plasmids with these mechanisms often encode additional antimicrobial resistances and can transfer multidrug resistance that includes quinolones. Thus, the bacterial quinolone resistance armamentarium is large.

Phylogeny and Comparative Genomics Unveil Independent Diversification Trajectories of qnrB and Genetic Platforms within Particular Citrobacter Species

To gain insights into the diversification trajectories of qnrB genes, a phylogenetic and comparative genomics analysis of these genes and their surrounding genetic sequences was performed. For this purpose, Citrobacter sp. isolates (n = 21) and genome or plasmid sequences (n = 56) available in public databases harboring complete or truncated qnrB genes were analyzed. Citrobacter species identification was performed by phylogenetic analysis of different genotypic markers. The clonal relatedness among isolates, the location of qnrB genes, and the genetic surroundings of qnrB genes were investigated by pulsed-field gel electrophoresis (PFGE), S1-/I-CeuI-PFGE and hybridization, and PCR mapping and sequencing, respectively. Identification of Citrobacter isolates was achieved using leuS and recN gene sequences, and isolates characterized in this study were diverse and harbored chromosomal qnrB genes. Phylogenetic analysis of all known qnrB genes revealed seven main clusters and two branches, with most of them included in two clusters. Specific platforms (comprising pspF and sapA and varying in synteny and/or identity of other genes and intergenic regions) were associated with each one of these qnrB clusters, and the reliable identification of all Citrobacter isolates revealed that each platform evolved in different recognizable (Citrobacter freundii, C. braakii, C. werkmanii, and C. pasteurii) and putatively new species. A high identity was observed between some of the platforms identified in the chromosome of Citrobacter spp. and in different plasmids of Enterobacteriaceae. Our data corroborate Citrobacter as the origin of qnrB and further suggest divergent evolution of closely related qnrB genes/platforms in particular Citrobacter spp., which were delineated using particular genotypic markers.

Prevalence and characterization of hybrid blaCTX-M among Escherichia coli isolates from livestock and other animals

This study investigated 248 extended-spectrum β-lactamase-producing Escherichia coli isolates from 2012 to 2013 for hybrid blaCTX-M genes. blaCTX-M genes were detected in 228 isolates of which 14 isolates were hybrid blaCTX-M positive (6 blaCTX-M-123, 6 blaCTX-M-64, and 2 blaCTX-M-132). The 14 hybrid blaCTX-M-carrying isolates (8 from chickens, 2 each from pigs and cattle, 1 each from dog and rodent) were genetically diverse. All but 2 hybrid blaCTX-M were carried on IncI1 (5 blaCTX-M-123) and IncI2 (6 blaCTX-M-64 and one blaCTX-M-132) plasmids. Our IncI1 and IncI2 plasmids had pHNAH4-1-like and pHN1122-1-like restriction fragment length polymorphism patterns, respectively. Genetic relatedness of the plasmids to pHNAH4-1 and pHN1122-1 were confirmed by complete sequencing of 3 plasmids, pCTXM123_C0996, pCTXM64_C0967, and pCTXM132_P0421. Plasmids closely related to pHNAH4-1 and pHN1122-1 and carrying different blaCTX-M alleles have been reported from multiple geographic areas in China previously. The findings highlighted the wide dissemination of hybrid blaCTX-M variants in different parts of China.

Mobile insertion cassette elements found in small non-transmissible plasmids in Proteeae may explain qnrD mobilization

qnrD is a plasmid mediated quinolone resistance gene from unknown origin, recently described in Enterobacteriaceae. It encodes a pentapeptide repeat protein 36-60% different from the other Qnr (A, B, C, S and VC). Since most qnrD-positive strains were described as strains belonging to Proteus or Providencia genera, we hypothesized that qnrD originated in Proteeae before disseminating to other enterobacterial species. We screened 317 strains of Proteeae for qnrD and its genetic support by PCR. For all the seven qnrD-positive strains (4 Proteus mirabilis, 1 Proteus vulgaris and 2 Providencia rettgeri) the gene was carried onto a small non-transmissible plasmid, contrarily to other qnr genes that are usually carried onto large multi-resistant plasmids. Nucleotide sequences of the qnrD-bearing plasmids were 96% identical. Plasmids contained 3 ORFs apart from qnrD and belonged to an undescribed incompatibility group. Only one plasmid, in P. vulgaris, was slightly different with a 1,568-bp insertion between qnrD and its promoter, leading to absence of quinolone resistance. We sought for similar plasmids in 15 reference strains of Proteeae, but which were tested negative for qnrD, and found a 48% identical plasmid (pVERM) in Providencia vermicola. In order to explain how qnrD could have been inserted into such native plasmid, we sought for gene mobilization structures. qnrD was found to be located within a mobile insertion cassette (mic) element which sequences are similar to one mic also found in pVERM. Our conclusions are that (i) the small non-transmissible qnrD-plasmids described here may result from the recombination between an as-yet-unknown progenitor of qnrD and pVERM, (ii) these plasmids are maintained in Proteeae being a qnrD reservoir (iii) the mic element may explain qnrD mobilization from non-transmissible plasmids to mobilizable or conjugative plasmids from other Enterobacteriaceae, (iv) they can recombined with larger multiresistant plasmids conjugated in Proteeae.

Incidence, clinical presentation, and antimicrobial resistance trends in Salmonella and Shigella infections from children in Yucatan, Mexico

BACKGROUND

Salmonella and Shigella cause significant morbidity and mortality among children worldwide. Increased antimicrobial resistance results in greater burden of disease.

MATERIALS AND METHODS

From 2005 to 2011, Salmonella and Shigella isolates collected from ill children at a major hospital in Yucatan, Mexico, were subjected to serotyping and antimicrobial susceptibility testing by disk diffusion and agar dilution. The identification of bla CTX, bla CMY, bla SHV, bla TEM, and bla OXA and qnr resistance genes was conducted by PCR and sequencing.

RESULTS

Among 2344 children with acute gastroenteritis, salmonellosis decreased from 17.7% in 2005 to 11.2% in 2011 (p < 0.001). In contrast, shigellosis increased from 8.3% in 2010 to 12.1% in 2011. Compared to children with Salmonella, those with Shigella had significantly more bloody stools (59 vs 36%, p < 0.001), dehydration (27 vs 15%, p = 0.031), and seizures (11 vs 3%, p = 0.03). In Salmonella (n = 365), there was a significant decrease in resistance to ampicillin (43 to 16%, p < 0.001), trimethoprim-sulfamethoxazole (44 to 26%, p = 0.014), and extended-spectrum cephalosporins (27 to 10%, p = 0.009). Reduced susceptibility to ciprofloxacin in Salmonella rose from 30 to 41% (p < 0.001). All ceftriaxone-resistant isolates harbored the bla CMY-2 gene. qnr genes were found in 42 (36%) of the 117 Salmonella isolates with a ciprofloxacin MIC ≥ 0.125 μg/ml. Four were qnrA1 and 38 were qnrB19. Resistance to ampicillin (40%) and trimethoprim-sulfamethoxazole (58%) was common in Shigella (n = 218), but isolates remained fully susceptible to ceftriaxone and ciprofloxacin.

CONCLUSION

Illness from Salmonella has decreased while severe Shigella infections have increased among children with gastroenteritis in the Yucatan Peninsula. While Shigella resistance to clinically important antibiotics remained unchanged, resistance to most of these, except ciprofloxacin, declined in Salmonella. bla CMY-2 and qnr genes are common in Salmonella isolates.

Characterization of fluoroquinolone resistance and qnr diversity in Enterobacteriaceae from municipal biosolids

Municipal biosolids produced during activated sludge treatment applied in wastewater treatment plants, are significant reservoirs of antibiotic resistance, since they assemble both natural and fecal microbiota, as well as residual concentrations of antibiotic compounds. This raises major concerns regarding the environmental and epidemiological consequences of using them as fertilizers for crops. The second generation fluoroquinolone ciprofloxacin is probably the most abundant antibiotic compound detected in municipal biosolids due to its widespread use and sorption properties. Although fluoroquinolone resistance was originally thought to result from mutations in bacterial gyrase and topoisomerase IV genes, it is becoming apparent that it is also attributed to plasmid-associated resistance factors, which may propagate environmental antibiotic resistance. The objective of this study was to assess the impact of the activated sludge process on fluoroquinolone resistance. The scope of resistances and mobile genetic mechanisms associated with fluoroquinolone resistance were evaluated by screening large collections of ciprofloxacin-resistant Enterobacteriaceae strains from sludge (n = 112) and from raw sewage (n = 89). Plasmid-mediated quinolone resistance determinants (qnrA, B, and S) were readily detected in isolates from both environments, the most dominant being qnrS. Interestingly, all qnr variants were significantly more abundant in sludge isolates than in the isolates from raw sewage. Almost all ciprofloxacin-resistant isolates were resistant to multiple antibiotic compounds. The sludge isolates were on the whole resistant to a broader range of antibiotic compounds than the raw sewage isolates; however, this difference was not statistically significant. Collectively, this study indicates that the activated sludge harbors multi-resistant bacterial strains, and that mobile quinolone-resistance elements may have a selective advantage in the activated sludge.

Impact of low-level fluoroquinolone resistance genes qnrA1, qnrB19 and qnrS1 on ciprofloxacin treatment of isogenic Escherichia coli strains in a murine urinary tract infection model

OBJECTIVES

To study the impact of qnrA1, qnrB19 and qnrS1 on the ciprofloxacin treatment of urinary tract infection (UTI).

METHODS

From a wild-type (wt) Escherichia coli UTI isolate, three isogenic strains were constructed carrying low-level ciprofloxacin resistance genes qnrA1, qnrB19 or qnrS1 (ciprofloxacin MIC range: 0.19-0.38 mg/L). Time-kill studies were performed for all four isogenic strains at the following concentrations: 1×, 2×, 4×, 8× and 16× MIC. Ciprofloxacin serum and urine pharmacokinetics was determined to calculate a murine dose equivalent (AUC(24)) to the standard human dose of 500 mg twice daily, which corresponded to 0.2 mg/mouse four times daily. In the murine UTI model, mice infected with each of the isogenic qnr strains or the wt strain were treated with ciprofloxacin (0.2 mg/mouse) or saline (only the E. coli wt) subcutaneously four times daily for 3 days starting 24 h after bacterial inoculation.

RESULTS

In vitro, the strains responded to ciprofloxacin concentrations of 4-16× MIC by several log(10) reductions. In vivo, despite ciprofloxacin reaching urine concentrations far exceeding the MICs for the strains (500 mg/L), ciprofloxacin was significantly less efficient at reducing the urine and bladder bacterial counts of qnrA1-, qnrB19- and qnrS1-positive strains compared with the ciprofloxacin-treated wt strain (P < 0.05). None of the four strains infected the kidneys well, with median cfu counts of <1 log(10).

CONCLUSIONS

Although qnr genes only confer low levels of resistance to ciprofloxacin, a reduced bactericidal activity of ciprofloxacin was observed in both urine and bladder in the murine model of UTI.

Plasmid-Mediated Quinolone Resistance; Interactions between Human, Animal, and Environmental Ecologies

Resistance to quinolones and fluoroquinolones is being increasingly reported among human but also veterinary isolates during the last two to three decades, very likely as a consequence of the large clinical usage of those antibiotics. Even if the principle mechanisms of resistance to quinolones are chromosome-encoded, due to modifications of molecular targets (DNA gyrase and topoisomerase IV), decreased outer-membrane permeability (porin defect), and overexpression of naturally occurring efflux, the emergence of plasmid-mediated quinolone resistance (PMQR) has been reported since 1998. Although these PMQR determinants confer low-level resistance to quinolones and/or fluoroquinolones, they are a favorable background for selection of additional chromosome-encoded quinolone resistance mechanisms. Different transferable mechanisms have been identified, corresponding to the production of Qnr proteins, of the aminoglycoside acetyltransferase AAC(6′)-Ib-cr, or of the QepA-type or OqxAB-type efflux pumps. Qnr proteins protect target enzymes (DNA gyrase and type IV topoisomerase) from quinolone inhibition. The AAC(6′)-Ib-cr determinant acetylates several fluoroquinolones, such as norfloxacin and ciprofloxacin. Finally, the QepA and OqxAB efflux pumps extrude fluoroquinolones from the bacterial cell. A series of studies have identified the environment to be a reservoir of PMQR genes, with farm animals and aquatic habitats being significantly involved. In addition, the origin of the qnr genes has been identified, corresponding to the waterborne species Shewanella sp. Altogether, the recent observations suggest that the aquatic environment might constitute the original source of PMQR genes, that would secondly spread among animal or human isolates.

Small plasmids harboring qnrB19: a model for plasmid evolution mediated by site-specific recombination at oriT and Xer sites

Plasmids pPAB19-1, pPAB19-2, pPAB19-3, and pPAB19-4, isolated from Salmonella and Escherichia coli clinical strains from hospitals in Argentina, were completely sequenced. These plasmids include the qnrB19 gene and are 2,699, 3,082, 2,989, and 2,702 nucleotides long, respectively, and they share extensive homology among themselves and with other previously described small qnrB19-harboring plasmids. The genetic environment of qnrB19 in all four plasmids is identical to that in these other plasmids and in transposons such as Tn2012, Tn5387, and Tn5387-like. Nucleotide sequence comparisons among these and previously described plasmids showed a variable region characterized by being flanked by an oriT locus and a Xer recombination site. We propose that this arrangement could play a role in the evolution of plasmids and present a model for DNA swapping between plasmid molecules mediated by site-specific recombination events at oriT and a Xer target site.

Description of a 2,683-base-pair plasmid containing qnrD in two Providencia rettgeri isolates

qnr genes are plasmid-mediated quinolone resistance genes mainly harbored on large conjugative multiresistant plasmids. The qnrD gene was recently observed in Salmonella enterica on a small nonconjugative plasmid (p2007057). We describe two strains of Providencia rettgeri harboring qnrD on nonconjugative plasmids. The plasmids were 99% identical, with 2,683 bp and four open reading frames, including qnrD, but exhibited only 53% identity with the plasmid found in S. enterica.

Novel variants of the qnrB gene, qnrB31 and qnrB32, in Klebsiella pneumoniae

Quinolone resistance in the family Enterobacteriaceae is mostly attributed to the accumulation of mutations in the bacterial enzymes targeted by fluoroquinolones: DNA gyrase and DNA topoisomerase IV. Here we isolated the Klebsiella pneumoniae strains KP3606 and KP4707 from different specimens from 2008 to 2010 in Taizhou Municipal Hospital of China, and discovered a new subtype qnrB31, for which the GenBank accession number is HQ418999, and another new subtype qnrB32, for which the GenBank accession number is HQ704413. Susceptibility testing showed that KP3606 had a reduced susceptibility (MIC ≥0.5 µg ml(-1)) to quinolones, while KP4707 was resistant to quinolones. Of all qnrB alleles, the novel variants the qnrB32 gene and qnrB31 gene have the highest amino acid identity. The results suggested that of all the various genes involved in resistance to quinolones, the qnrB gene is the most likely to be mutated, and plasmids might play a role in the dissemination and evolution of qnrB genes.

Effect of spacer sequences between bla(CTX-M) and ISEcp1 on bla(CTX-M) expression

Spacer sequences of 42 and 127 bp, respectively, between the ISEcp1 insertion sequence and bla(CTX-M) have been observed in Klebsiella pneumoniae. However, it is not known whether different spacers upstream of bla(CTX-M) and a promoter within the 127 bp spacer influence cephalosporin resistance. Three recombinant plasmids with different spacers and with or without ISEcp1 were constructed to compare bla(CTX-M-3) expression and susceptibility to cephalosporins. Our experiment revealed enhanced bla(CTX-M-3) expression and a relatively high level resistance to cefotaxime and cefepime in recombinant plasmid IS42CTX-M-3, which contained ISEcp1 and the 42 bp spacer. A minor difference in bla(CTX-M-3) expression was observed in recombinants IS127CTX-M-3 and 127CTX-M-3, which contained a 127 bp spacer with or without ISEcp1, respectively. In conclusion, the promoter within ISEcp1 and a shorter spacer (42 bp but not 127 bp) between ISEcp1 and bla(CTX-M) are necessary for high-level bla(CTX-M-3) expression.

Gene flow, mobile genetic elements and the recruitment of antibiotic resistance genes into Gram-negative pathogens

Antibiotics were one of the great discoveries of the 20th century. However, resistance appeared even in the earliest years of the antibiotic era. Antibiotic resistance continues to become worse, despite the ever-increasing resources devoted to combat the problem. One of the most important factors in the development of resistance to antibiotics is the remarkable ability of bacteria to share genetic resources via Lateral Gene Transfer (LGT). LGT occurs on a global scale, such that in theory, any gene in any organism anywhere in the microbial biosphere might be mobilized and spread. With sufficiently strong selection, any gene may spread to a point where it establishes a global presence. From an antibiotic resistance perspective, this means that a resistance phenotype can appear in a diverse range of infections around the globe nearly simultaneously. We discuss the forces and agents that make this LGT possible and argue that the problem of resistance can ultimately only be managed by understanding the problem from a broad ecological and evolutionary perspective. We also argue that human activities are exacerbating the problem by increasing the tempo of LGT and bacterial evolution for many traits that are important to humans.

Characterisation of qnr plasmid-mediated quinolone resistance in Enterobacteriaceae from Italy: association of the qnrB19 allele with the integron element ISCR1 in Escherichia coli

The spread of plasmid-mediated quinolone resistance determinants (qnr-like determinants) was evaluated in a collection of 232 ciprofloxacin-resistant or extended-spectrum beta-lactamase (ESBL)-producing enterobacterial isolates recovered between November 2007 and May 2008 at Padua University Hospital, Italy. qnr genes were mainly found in Klebsiella pneumoniae (68%) and to a lesser extent in Escherichia coli (5.1%). Among the qnrA1, qnrS1 and qnrB19 alleles found, the latter was by far the most frequent. Genetic environment analysis revealed that one qnrB19 gene in E. coli was embedded in an ISCR1 complex class 1 integron. All other qnrB19 genes were flanked by an ISEcp1C region as part of the Tn2012 transposon. qnrA1- and qnrS1-containing strains were not clonally related. Both topoisomerase II mutations and ESBL (mainly SHV-12, TEM-1 and TEM-150 types) were present in most of the qnr-positive strains. qnrB19 is extremely frequent in K. pneumoniae isolates from Italy. In addition, association of qnrB19 with the ISCR1 mobile element in E. coli suggests a broad distribution of this resistance gene in the near future.

Plasmid-mediated quinolone resistance: a multifaceted threat

Although plasmid-mediated quinolone resistance (PMQR) was thought not to exist before its discovery in 1998, the past decade has seen an explosion of research characterizing this phenomenon. The best-described form of PMQR is determined by the qnr group of genes. These genes, likely originating in aquatic organisms, code for pentapeptide repeat proteins. These proteins reduce susceptibility to quinolones by protecting the complex of DNA and DNA gyrase or topoisomerase IV enzymes from the inhibitory effect of quinolones. Two additional PMQR mechanisms were recently described. aac(6')-Ib-cr encodes a variant aminoglycoside acetyltransferase with two amino acid alterations allowing it to inactivate ciprofloxacin through the acetylation of its piperazinyl substituent. oqxAB and qepA encode efflux pumps that extrude quinolones. All of these genes determine relatively small increases in the MICs of quinolones, but these changes are sufficient to facilitate the selection of mutants with higher levels of resistance. The contribution of these genes to the emergence of quinolone resistance is being actively investigated. Several factors suggest their importance in this process, including their increasing ubiquity, their association with other resistance elements, and their emergence simultaneous with the expansion of clinical quinolone resistance. Of concern, these genes are not yet being taken into account in resistance screening by clinical microbiology laboratories.

Characterization of small ColE-like plasmids mediating widespread dissemination of the qnrB19 gene in commensal enterobacteria

In this work, we have characterized two small ColE-like plasmids (pECY6-7, 2.7 kb in size, and pECC14-9, of 3.0 kb), encoding the QnrB19 quinolone resistance determinant, that were carried by several clonally unrelated quinolone-resistant commensal Escherichia coli strains isolated from healthy children living in different urban areas of Peru and Bolivia. The two plasmids are closely related to each other and carry the qnrB19 gene as the sole resistance determinant, located in a conserved genetic context between the plasmid RNAII sequence (which controls plasmid replication) and the plasmid Xer site (involved in plasmid dimer resolution). ISEcp1-like or other putative insertion sequences are not present in the qnrB19-flanking regions or elsewhere on the plasmids. Since we previously observed a high prevalence (54%) of qnrB genes in the metagenomes of commensal enterobacteria from the same population of healthy children, the presence of pECY6-7- and pECC14-9-like plasmids in those qnrB-positive metagenomes was investigated by PCR mapping. Both plasmids were found to be highly prevalent (67% and 16%, respectively) in the qnrB-positive metagenomes, suggesting that dissemination of these small plasmids played a major role in the widespread dissemination of qnrB genes observed in commensal enterobacteria from healthy children living in those areas.

The SOS response promotes qnrB quinolone-resistance determinant expression

The qnr genes are plasmid-borne fluoroquinolone-resistance determinants widespread in Enterobacteriaceae. Three families of qnr determinants (qnrA, B and S) have been described, but little is known about their expression and regulation. Two new determinants, qnrC and qnrD, have been found recently. Here, we describe the characterization of the qnrB2 promoter and the identification of a LexA-binding site in the promoter region of all qnrB alleles. LexA is the central regulator of the SOS response to DNA damage. We show that qnrB2 expression is regulated through the SOS response in a LexA/RecA-dependent manner, and that it can be induced by the quinolone ciprofloxacin, a known inducer of the SOS system. This is the first description of direct SOS-dependent regulation of an antibiotic-resistance mechanism in response to the antibiotic itself.

Characterization of the plasmid-borne quinolone resistance gene qnrB19 in Salmonella enterica serovar Typhimurium

A qnrB19 gene variant, carried by an IncL/M-like plasmid, was detected in a multidrug Salmonella enterica serovar Typhimurium human strain with reduced susceptibility to ciprofloxacin. The genetic environment around the gene was fully sequenced (20 kb). A large gene cluster, containing the aph, qnrB19, and blaSHV-12-like resistance genes, is inserted inside a Tn3 transposon.

Genetic and biochemical characterization of the first extended-spectrum CARB-type beta-lactamase, RTG-4, from Acinetobacter baumannii

Acinetobacter baumannii isolate KAR was uncommonly more resistant to cefepime and cefpirome than to ceftazidime and cefotaxime. Cloning and expression of the beta-lactamase gene content of this isolate into Escherichia coli TOP10 identified ss-lactamase RTG-4 (or CARB-10), which corresponds to the first reported extended-spectrum CARB-type enzyme. RTG-4 is a plasmid-encoded Ambler class A beta-lactamase whose sequence differs by 4 amino acid substitutions from the narrow-spectrum beta-lactamase RTG-3. RTG-4 hydrolyzes cefepime and cefpirome and weakly hydrolyzes ceftazidime due to the single Ser-to-Thr substitution at Ambler position 69. RTG-4 is less susceptible to inhibition by tazobactam and sulbactam than RTG-3. Expression of beta-lactamase RTG-4 in a wild-type A. baumannii reference strain showed that it conferred resistance to cefepime and cefpirome. The genetic environment of the bla(RTG-4) gene was made of a peculiar transposon located on a ca. 50-kb plasmid. ISAba9, located upstream of bla(RTG-4), may be responsible for its acquisition by recognizing a secondary right inverted repeat sequence, thus acting by a one-ended transposition process.

New plasmid-mediated quinolone resistance gene, qnrC, found in a clinical isolate of Proteus mirabilis

Since the discovery of qnrA in 1998, two additional qnr genes, qnrB and qnrS, have been described. These three plasmid-mediated genes contribute to quinolone resistance in gram-negative pathogens worldwide. A clinical strain of Proteus mirabilis was isolated from an outpatient with a urinary tract infection and was susceptible to most antimicrobials but resistant to ampicillin, sulfamethoxazole, and trimethoprim. Plasmid pHS10, harbored by this strain, was transferred to azide-resistant Escherichia coli J53 by conjugation. A transconjugant with pHS10 had low-level quinolone resistance but was negative by PCR for the known qnr genes, aac(6')-Ib-cr and qepA. The ciprofloxacin MIC for the clinical strain and a J53/pHS10 transconjugant was 0.25 microg/ml, representing an increase of 32-fold relative to that for the recipient, J53. The plasmid was digested with HindIII, and a 4.4-kb DNA fragment containing the new gene was cloned into pUC18 and transformed into E. coli TOP10. Sequencing showed that the responsible 666-bp gene, designated qnrC, encoded a 221-amino-acid protein, QnrC, which shared 64%, 42%, 59%, and 43% amino acid identity with QnrA1, QnrB1, QnrS1, and QnrD, respectively. Upstream of qnrC there existed a new IS3 family insertion sequence, ISPmi1, which encoded a frameshifted transposase. qnrC could not be detected by PCR, however, in 2,020 strains of Enterobacteriaceae. A new quinolone resistance gene, qnrC, was thus characterized from plasmid pHS10 carried by a clinical isolate of P. mirabilis.