Commensal Fitness Advantage May Contribute to the Global Dissemination of Multidrug-Resistant Lineages of Bacteria-The Case of Uropathogenic E. coli.

It is widely accepted that favorable fitness in commensal colonization is one of the prime facilitators of clonal dissemination in bacteria. The question arises as to what kind of fitness advantage may be wielded by uropathogenic strains of the two predominant fluoroquinolone- and multidrug-resistant clonal groups of E. coli-ST131-H30 and ST1193, which has permitted their unprecedented pandemic-like global expansion in the last few decades. The colonization-associated genes' content, carriage of low-cost plasmids, and integrons with weak promoters could certainly contribute to the fitness of the pandemic groups, although those genetic factors are common among other clonal groups as well. Also, ST131-H30 and ST1193 strains harbor fluoroquinolone-resistance conferring mutations targeting serine residues in DNA gyrase (GyrA-S83) and topoisomerase IV (ParC-S80) that, in those clonal backgrounds, might result in a commensal fitness benefit, i.e., beyond the antibiotic resistance per se. This fitness gain might have contributed not only to the widespread dissemination of these major clones in the healthcare setting but also to their long-term colonization of healthy individuals and, thus, circulation in the community, even in a low or no fluoroquinolone use environment. This evolutionary shift affecting commensal E. coli, initiated by mutations co-favorable in both antibiotics-treated patients and healthy individuals warrants more in-depth studies to monitor further changes in the epidemiological situation and develop effective measures to reduce the antibiotic resistance spread.

Global Evolution of Pathogenic Bacteria With Extensive Use of Fluoroquinolone Agents.

It is well-established that the spread of many multidrug-resistant (MDR) bacteria is predominantly clonal. Interestingly the international clones/sequence types (STs) of most pathogens emerged and disseminated during the last three decades. Strong experimental evidence from multiple laboratories indicate that diverse fitness cost associated with high-level resistance to fluoroquinolones contributed to the selection and promotion of the international clones/STs of hospital-associated methicillin-resistant Staphylococcus aureus (HA-MRSA), extended-spectrum ß-lactamase-(ESBL)-producing Klebsiella pneumoniae, ESBL-producing Escherichia coli and Clostridioides difficile. The overwhelming part of the literature investigating the epidemiology of the pathogens as a function of fluoroquinolone use remain in concordence with these findings. Moreover, recent in vitro data clearly show the potential of fluoroquinolone exposure to shape the clonal evolution of Salmonella Enteritidis. The success of the international clones/STs in all these species was linked to the strains' unique ability to evolve multiple energetically beneficial gyrase and topoisomerase IV mutations conferring high-level resistance to fluorquinolones and concomittantly permitting the acquisition of an extra resistance gene load without evoking appreciable fitness cost. Furthermore, by analyzing the clonality of multiple species, the review highlights, that in environments under high antibiotic exposure virulence factors play only a subsidiary role in the clonal dynamics of bacteria relative to multidrug-resistance coupled with favorable fitness (greater speed of replication). Though other groups of antibiotics should also be involved in selecting clones of bacterial pathogens the role of fluoroquinolones due to their peculiar fitness effect remains unique. It is suggested that probably no bacteria remain immune to the influence of fluoroquinolones in shaping their evolutionary dynamics. Consequently a more judicious use of fluoroquinolones, attuned to the proportion of international clone/ST isolates among local pathogens, would not only decrease resistance rates against this group of antibiotics but should also ameliorate the overall antibiotic resistance landscape.

Transmissible silver resistance readily evolves in high-risk clone isolates of Klebsiella pneumoniae.

Silver is used extensively in both hospitals and outpatient clinics as a disinfectant coating agent on various devices. Resistance to silver was recently reported as an emerging problem in Enterobacteriaceae. Multidrug-resistant high-risk clones of Klebsiella pneumoniae are common causes of serious healthcare-associated infections worldwide posing a serious threat to patients. In this study, we investigated the capacity of both high-risk (CG14/15 and CG258) and minor clone strains of K. pneumoniae to develop resistance to silver. Resistance was induced in vitro in silver-susceptible but otherwise multidrug-resistant clinical isolates. Genetic alterations in the silver-resistant derivative strains with regard to the silver-susceptible isolates were investigated by whole-genome sequencing. The transferability of high-level resistance to silver was also tested. We demonstrated that the high-level resistance to silver can quickly evolve as a consequence of a single-point mutation either in the cusS gene of the chromosomally encoded CusCFBARS efflux system and/or in the silS gene of the plasmid-encoded Copper Homeostasis and Silver Resistance Island (CHASRI) coding also for a metallic efflux. The minimal inhibitory concentrations (MICs) of the strains increased from 4 mg/L (23.5 µM) AgNO3 to >8,500 mg/L (>50,000 µM) AgNO3 during induction. Harboring the CHASRI proved an important selective asset for K. pneumoniae when exposed to silver. Successful conjugation experiments using Escherichia coli K12 J5-3Rif as recipient showed that high-level silver resistance can transmit between strains of high-risk clones of K. pneumoniae (ST15 and ST11) and isolates from additional species of Enterobacteriaceae. The lack of fitness cost associated with the carriage of the CHASRI in a silver-free environment and the presence of the RelEB toxin-antitoxin system on the conjugative plasmids could advance the dissemination of silver resistance. Our results show that multidrug-resistant high-risk clones of K. pneumoniae are capable of evolving and transmitting high-level resistance to silver. This observation should warrant a more judicious use of silver coated-devices to prevent the extensive dissemination of silver resistance.

Double-Serine Fluoroquinolone Resistance Mutations Advance Major International Clones and Lineages of Various Multi-Drug Resistant Bacteria.

The major international sequence types/lineages of methicillin-resistant Staphylococcus aureus (MRSA), extended-spectrum ß-lactamase (ESBL)-producing Klebsiella pneumoniae and ESBL-producing E. coli were demonstrated to have been advanced by favorable fitness balance associated with high-level resistance to fluoroquinolones. The paper shows that favorable fitness in the major STs/lineages of these pathogens was principally attained by the capacity of evolving mutations in the fluoroquinolone-binding serine residues of both the DNA gyrase and topoisomerase IV enzymes. The available information on fitness balance incurred by individual and various combinations of mutations in the enzymes is reviewed in multiple species. Moreover, strong circumstantial evidence is presented that major STs/lineages of other multi-drug resistant bacteria, primarily vancomycin-resistant Enterococcus faecium (VRE), emerged by a similar mechanism. The reason(s) why the major ST/lineage strains of various pathogens proved more adept at evolving favorable mutations than most isolates of the same species remains to be elucidated.

Dissimilar Fitness Associated with Resistance to Fluoroquinolones Influences Clonal Dynamics of Various Multiresistant Bacteria.

Fitness cost associated with resistance to fluoroquinolones was recently shown to vary across clones of methicillin-resistant Staphylococcus aureus and extended-spectrum ß-lactamase-producing Klebsiella pneumoniae. The resulting dissimilar fitness should have influenced the clonal dynamics and thereby the rates of resistance for these pathogens. Moreover, a similar mechanism was recently proposed for the emergence of the H30 and H30R lineages of ESBL-producing E. coli and the major international clone (ribotype 027) of Clostridium difficile. Furthermore, several additional international clones of various multiresistant bacteria are suspect to have been selected by an analogous process. An ability to develop favorable mutations in the gyrase and topoisomerase IV genes seems to be a prerequisite for pathogens to retain fitness while showing high-level resistance to fluoroquinolones. Since, the consumption of other "non-fluoroquinolone" groups of antibiotics have also contributed to the rise in resistance rates a more judicious use of antibiotics in general and of fluoroquinolones in particular could ameliorate the international resistance situation.

Has the use of fluoroquinolones facilitated the widespread dissemination of methicillin-resistant Staphylococcus aureus and extended-spectrum ß-lactamase-producing Klebsiella pneumoniae in the healthcare setting?

Our group recently demonstrated that diverse fitness cost associated with resistance to fluoroquinolones allowed the extensive dissemination of the major international clones of both methicillin-resistant Staphylococcus aureus (MRSA) and multiresistant Klebsiella pneumoniae in the healthcare setting. The mechanism described by us was subsequently confirmed by British authors investigating the dynamics of MRSA clones in England. Our results imply that the use of fluoroquinolones should impact the incidence for both MRSA and multiresistant K. pneumoniae. A review of the related clinical studies mostly support this notion and shows that changes in the consumption of fluoroquinolone type antibiotics and the rates for both MRSA and multiresistant ESBL-producing K. pneumoniae remain usually in accordance. Though the association seems strong and the mechanism behind it unequivocal the use of fluoroquinolones should not be abandoned; a more judicious application can be recommended.

Serogrouping and pulsed-field gel electrophoresis analysis of Listeria monocytogenes isolates from cases of human infection in Hungary 2004­2012 molecular typing of Listeria monocytogenes in Hungary.

Eighty isolates of Listeria monocytogenes cultured from human infections in Hungary between 2004 and 2012 were serotyped by the PCR technique of Doumithet al. [9] and characterised by pulsed-field gel electrophoresis (PFGE). Most of the isolates belonged to two serogroups: 53 isolates (66.3%) to serovar group 4b,4d,4e and 21isolates (25.8%) to serogroup 1/2a,3a. Although many pulsotypes were identified a particular pulsotype proved highly excelling comprising of 31 isolates after digestion by both ApaI and AscI restriction enzymes. All strains from this pulsotype belonged toserovar group 4b,4d,4e. Interestingly 24% of isolates from invasive samples(cerebrospinal fluid, blood) belonged to two distinct pulsotypes in the less common serovar group 1/2a,3a. Several small clusters of cases caused by isolates with identical pulsotypes were identified.

Identification of two multidrug-resistant Pseudomonas aeruginosa clonal lineages with a countrywide distribution in Hungary.

The aim of this study was to identify class 1 integrons from extended-spectrum and metallo-beta-lactamase-negative, multidrug-resistant Pseudomonas aeruginosa clinical isolates from Hungary and to characterize the isolates by phenotypic and molecular methods. Fourteen selected P. aeruginosa isolates resistant to ceftazidime, gentamicin, and ciprofloxacin were subjected to serotyping, random amplification of polymorphic DNA (RAPD), integron content analysis, and a phenotypic test to detect high-level production of AmpC. Four representative isolates were further analyzed by multilocus sequence typing. Two P. aeruginosa multidrug-resistant clonal lineages were identified with a countrywide distribution. The first lineage is characterized by serotype O4, RAPD genotype A, sequence type ST175, and the presence of a class 1 integron harbouring aadB and aadA13 gene cassettes in its variable region. The second lineage is characterized by serotype O6, RAPD genotype B, sequence type ST395, and a class 1 integron carrying a single aadB cassette. The corresponding isolates were recovered from altogether 11 towns in Hungary. ST175 and ST395 are the presently calculated founders of two distinct P. aeruginosa clonal complexes that appear to have a wide geographical distribution also outside Hungary. The multidrug-resistant phenotype associated with these two clonal lineages might have contributed to an increase in their frequency and to their subsequent diversification. Both P. aeruginosa lineages displayed > or =8-fold synergy with boronic acid/ceftazidime combinations, suggesting an AmpC-mediated resistance to ceftazidime. Our observations underscore the role of class 1 integrons in the spread of aminoglycoside resistance by clonal dissemination among P. aeruginosa clinical isolates in Hungary.

Identification of PER-1 extended-spectrum beta-lactamase producing Pseudomonas aeruginosa clinical isolates of the international clonal complex CC11 from Hungary and Serbia.

PER-1 extended-spectrum beta-lactamase-producing Pseudomonas aeruginosa clinical isolates from Budapest, Hungary, and Belgrade, Serbia, were characterized by molecular methods. Two PER-1-positive isolates were recovered from sporadic cases in Budapest and a small cluster of PER-1-positive infections involving four patients were identified at a Belgrade hospital. A class 1 integron harbouring a bla(OXA-2)beta-lactamase gene and four other gene cassettes was detected in both the Budapest and the Belgrade isolates. The two P. aeruginosa isolates from Budapest also carried another class 1 integron containing bla(OXA-74), aac(6')-Ib-cr and cmlA7 genes in its variable region. The aac(6')-Ib-cr fluoroquinolone-acetylating aminoglycoside acetyltransferase gene is described here for the first time in P. aeruginosa. Multilocus sequence typing (MLST) revealed that the PER-1 positive P. aeruginosa isolates identified in this study display ST235, a sequence type that belongs to clonal complex CC11. Two bla(PER-1)-positive P. aeruginosa reference isolates from France and Belgium could also be assigned to complex CC11 by MLST. Our results underscore the role of complex CC11 in the dissemination of bla(PER-1) among P. aeruginosa clinical isolates.

Expansion and countrywide dissemination of ST11, ST15 and ST147 ciprofloxacin-resistant CTX-M-15-type beta-lactamase-producing Klebsiella pneumoniae epidemic clones in Hungary in 2005--the new 'MRSAs'?

OBJECTIVES: To investigate the molecular epidemiology of ciprofloxacin-resistant CTX-M-15-producing Klebsiella pneumoniae epidemic clones (ECs) isolated from six nosocomial outbreaks and sporadic cases during 2005 in Hungary. METHODS: Two hundred and eighty-one extended-spectrum beta-lactamase (ESBL)-producing K. pneumoniae clinical isolates collected from 41 centres were submitted to the National ESBL Reference Laboratory for further investigations. Of the 281 strains, 75 isolates proved to be SHV producers, whereas 6 isolates were ciprofloxacin-susceptible CTX-M-type ESBL producers. One hundred and ninety-six ciprofloxacin-resistant CTX-M-type beta-lactamase-producing isolates collected from 35 centres were subjected to macrorestriction profile analysis. Furthermore, molecular typing was performed by PCR and sequencing of several antibiotic resistance genes, plasmid profile analysis, transfer of resistance determinants and multilocus sequence typing (MLST). RESULTS: PFGE revealed the existence of three genetic clusters defined as ECs, where 129 isolates belonged to the previously described Hungarian EC (HEC), 46 isolates to epidemic clone II (EC II) and 21 isolates to epidemic clone III (EC III), respectively. All isolates harboured plasmids ranging from 2.0 to 230 kb. PstI digestion of plasmid DNA from transconjugants/transformants revealed diverse restriction patterns from distinct ECs. Sequence analysis of beta-lactamase genes from 19 selected isolates detected bla(CTX-M-15) and bla(OXA-1) in strains from all three ECs and bla(TEM-1) in EC III isolates located on large plasmids. ISEcpI associated with CTX-M-15 was detected only on a 50 kb non-conjugative plasmid from EC III. MLST identified three allelic profiles: ST 15 (HEC), ST 11 (EC III) and the novel ST 147 (EC II), which correspond to the PFGE clusters, respectively. CONCLUSIONS: In 2005, 97% of all CTX-M-producing K. pneumoniae isolates detected across Hungary were highly ciprofloxacin-resistant CTX-M-15 producers and represented just three stable genetic clones.

Molecular characterization of vancomycin-resistant Enterococcus spp. clinical isolates from Hungary and Serbia.

The objectives of this work were to collect and characterize vancomycin-resistant Enterococcus faecium (VREF) clinical isolates from Hungary and Serbia and to analyse their genetic relatedness. VREF isolates were initially typed by PFGE. A selection of VREF isolates representing all participating hospitals was further examined by multiple-locus variable-number tandem repeat analysis (MLVA) and multilocus sequence typing (MLST). VanB VREF isolates (n=18) recovered from blood, urine and faecal cultures at a Budapest hospital between August 2003 and December 2004 were molecularly characterized. Macrorestriction analysis of the isolates revealed their monoclonal relatedness. A cluster of infections caused by 2 distinct VanA VREF clones recovered from 6 departments was identified in a Belgrade hospital in Serbia. The vanA resistance determinant was transferable by in vitro conjugation experiments. We also identified 2 vanA-positive E. gallinarum blood culture isolates in this Belgrade hospital. Molecular typing of representative VREF isolates from Hungary and Serbia by MLVA and MLST revealed that all tested isolates belonged to MLST complex CC17 and the corresponding MLVA cluster 1. Our results extend the documented occurrence of CC17 to a new region in Europe.

Identification of the first VIM metallo-beta-lactamase-producing multiresistant Aeromonas hydrophila strain.

A VIM metallo-beta-lactamase-producing Aeromonas hydrophila strain carrying an integron-borne bla(VIM-4) gene was isolated from a cirrhotic patient's fecal sample in a Budapest hospital. The variable region of this integron is identical with that of a previously characterized integron from Pseudomonas aeruginosa clinical isolates in Pécs in southern Hungary.

Molecular typing indicates an important role for two international clonal complexes in dissemination of VIM-producing Pseudomonas aeruginosa clinical isolates in Hungary.

VIM metallo-beta-lactamase-producing serotype O11 or O12 Pseudomonas aeruginosa isolates infecting or colonising 19 patients from seven hospitals were reported in Hungary between 2003 and 2005. In this study we characterised VIM-producing Pseudomonas spp. clinical isolates from two novel locations in Hungary; we identified three new bla(VIM) carrying integron types and the presence of the bla(VIM-2) allele in Hungary. By applying various typing techniques, including multilocus sequence typing, we revealed an important role of two international clonal complexes, CC4 and CC11, in the dissemination of bla(VIM)-positive P. aeruginosa in hospitals in Hungary. Isolate P12-Q, a representative strain from France of the major European multiresistant P12 clone, displayed ST111 which, according to eBURST analysis, is the presently calculated founder sequence type of CC4. This is in accordance with the wide geographic distribution of the P12 clone. Our data indicate that, although the CC4 clonal complex includes serotype O1 and O6 isolates as well, it also contains the P12 clone. We characterised a P. aeruginosa nosocomial clone with a singleton sequence type (ST313), that may have acquired bla(VIM-2) and bla(VIM-4) gene cassettes from a yet unidentified local gene pool in Hungary.

Epidemiology of SHV-type beta-lactamase-producing Klebsiella spp. from outbreaks in five geographically distant Hungarian neonatal intensive care units: widespread dissemination of epidemic R-plasmids.

One hundred and twenty-six extended-spectrum beta-lactamase-producing clinical isolates of Klebsiella spp. were collected in 1998, 2002 and 2003 from seven outbreaks in neonatal intensive care units (NICUs) of five Hungarian county and teaching hospitals. The isolates were multidrug resistant but were susceptible to ciprofloxacin. Pulsed-field gel electrophoresis revealed the existence of 12 distinct genetic clones, 10 of which proved epidemic in the studied NICUs. All isolates harboured plasmids ranging from 2.3 kb to 228 kb, representing 12 diverse plasmid profiles. Sequence analysis of SHV-specific polymerase chain reaction products from 13 representative isolates detected the bla(SHV-2a) gene in three and the bla(SHV-5) gene in seven epidemic clones, respectively. In the majority of isolates the bla(SHV) genes were on transferable plasmids of 94kb. EcoRI and PstI digestion of plasmid DNA from transconjugants revealed identical or closely related restriction patterns in nine bla(SHV-5)-harbouring R-plasmids and in two bla(SHV-2a)-harbouring R-plasmids carried by strains obtained from geographically distant NICUs. Endemic clones in individual wards or epidemic clones affecting multiple healthcare facilities were not found. However, similarities observed in the size and restriction pattern of the plasmids hints at the multiple transfer of epidemic R-plasmids responsible for a sequence of outbreaks in Hungary.

Metallo-beta-lactamases as emerging resistance determinants in Gram-negative pathogens: open issues.

The rapid spread of acquired metallo-beta-lactamases (MBLs) among major Gram-negative pathogens is a matter of particular concern worldwide and primarily in Europe, one of first continents where the emergence of acquired MBLs has been reported and possibly the geographical area where the increasing diversity of these enzymes and the number of bacterial species affected are most impressive. This spread has not been paralleled by accuracy/standardisation of detection methods, completeness of epidemiological knowledge or a clear understanding of what MBL production entails in terms of clinical impact, hospital infection control and antimicrobial chemotherapy. A number of European experts in the field met to review the current knowledge on this phenomenon, to point out open issues and to reinforce and relate to one another the existing activities set forth by research institutes, scientific societies and European Union-driven networks.

Establishing clonal relationships between VIM-1-like metallo-beta-lactamase-producing Pseudomonas aeruginosa strains from four European countries by multilocus sequence typing.

Ten multidrug-resistant Pseudomonas aeruginosa strains producing VIM-1-like acquired metallo-beta-lactamases (MBLs), isolated from four European countries (Greece, Hungary, Italy, and Sweden), were analyzed for genetic relatedness by several methodologies, including fliC sequence analysis, macrorestriction profiling of genomic DNA by pulsed-field gel electrophoresis (PFGE), random amplification of polymorphic DNA (RAPD), and multilocus sequence typing (MLST). The four approaches yielded consistent results overall but showed different resolution powers in establishing relatedness between isolates (PFGE>RAPD>MLST>fliC typing) and could usefully complement each other to address issues in the molecular epidemiology of P. aeruginosa strains producing acquired MBLs. In particular, the recently developed MLST approach was useful in revealing clonal relatedness between isolates when this was not readily apparent using RAPD and PFGE, and it suggested a common ancestry for some of the VIM-1-like MBL-positive P. aeruginosa strains currently spreading in Europe. The MBL producers belonged in three clonal complexes/burst groups (BGs). Of these, one corresponded to the previously described BG4 and included serotype O12 strains from Hungary and Sweden, while the other two were novel and included serotype O11 or nonserotypable strains from Greece, Sweden, and/or Italy. Comparison of the integrons carrying blaVIM-1-like cassettes of various isolates revealed a remarkable structural heterogeneity, suggesting the possibility that multiple independent events of acquisition of different blaVIM-containing integrons had occurred in members of the same clonal lineage, although a contribution of integrase-mediated cassette shuffling or other recombination mechanisms during the evolution of similar strains could also have played a role in determining this variability.

Molecular epidemiology of VIM-4 metallo-beta-lactamase-producing Pseudomonas sp. isolates in Hungary.

VIM metallo-beta-lactamase-producing serotype O11 or O12 Pseudomonas aeruginosa isolates infecting or colonizing 19 patients from seven hospitals in Hungary were characterized between October 2003 and November 2005. Macrorestriction analysis revealed the involvement of hospitals from three different towns in northwest Hungary in an outbreak caused by VIM-4-producing P. aeruginosa.