Multiresistant Gram-negative bacteria: the role of high-risk clones in the dissemination of antibiotic resistance

Faecal carriage of Pseudomonas aeruginosa in healthy humans: antimicrobial susceptibility and global genetic lineages

The aim of this study was to analyse the Pseudomonas aeruginosa faecal carriage rate in 98 healthy humans and to perform the phenotypic and genotypic characterization of recovered isolates. The genetic relatedness among the isolates was analysed by pulsed-field gel electrophoresis and multilocus sequence typing that was compared with worldwide epidemic clones. Pseudomonas aeruginosa was isolated from eight healthy individuals (8.2%), and two of them remained colonized after 5 months (in one case by the same clone). All 10 isolates (one/sample) were susceptible to 14 tested antipseudomonal agents and lacked integron structures. Six pulsed-field gel electrophoresis patterns and six sequence types (ST245, ST253, ST254, ST274, ST663 and the new one, ST1059) were identified among them. Four groups of OprD alterations were detected based on mutations and deletions related to PAO1 reference strain in our carbapenem-susceptible strains. This is the first study focused on P. aeruginosa from faecal samples of healthy humans that provides additional insights into the antimicrobial resistance and genetic diversity of P. aeruginosa. Although the isolates were antimicrobial susceptible, most of the sequence types detected were genetically related to Spanish epidemic clones or globally spread sequence types, such as ST274 and ST253.

The resistome of Pseudomonas aeruginosa in relationship to phenotypic susceptibility

Many clinical isolates of Pseudomonas aeruginosa cause infections that are difficult to eradicate due to their resistance to a wide variety of antibiotics. Key genetic determinants of resistance were identified through genome sequences of 390 clinical isolates of P. aeruginosa, obtained from diverse geographic locations collected between 2003 and 2012 and were related to microbiological susceptibility data for meropenem, levofloxacin, and amikacin. β-Lactamases and integron cassette arrangements were enriched in the established multidrug-resistant lineages of sequence types ST111 (predominantly O12) and ST235 (O11). This study demonstrates the utility of next-generation sequencing (NGS) in defining relevant resistance elements and highlights the diversity of resistance determinants within P. aeruginosa. This information is valuable in furthering the design of diagnostics and therapeutics for the treatment of P. aeruginosa infections.

Emergence of blaKPC carbapenemase genes in Australia

blaKPC genes encoding resistance to carbapenems are increasingly widely reported and are now endemic in parts of several countries, but only one Klebsiella pneumoniae isolate carrying blaKPC-2 had previously been reported in Australia, in 2010. Here we characterised this isolate, six additional K. pneumoniae and one Escherichia coli carrying blaKPC and another K. pneumoniae lacking blaKPC, all isolated in Australia in 2012. Seven K. pneumoniae belonged to clonal complex (CC) 292, associated with blaKPC in several countries. Five with blaKPC-2 plus the isolate lacking a blaKPC gene were sequence type 258 (ST258) and the seventh was the closely related ST512 with blaKPC-3. The eighth K. pneumoniae isolate, novel ST1048, and the E. coli (ST131) also carried blaKPC-2. blaKPC genes were associated with the most common Tn4401a variant, which gives the highest levels of expression, in all isolates. The ST258 isolates appeared to share a similar set of plasmids, with IncFIIK, IncX3 and ColE-type plasmids identified in most isolates. All K. pneumoniae isolates had a characteristic insertion in the ompK35 gene resulting in a frameshift and early termination, but only the ST512 isolate had a GlyAsp insertion in loop 3 of OmpK36 that may contribute to increased resistance. The clinical epidemiology of blaKPC emergence in Australia thus appears to reflect the global dominance of K. pneumoniae CC292 (and perhaps E. coli ST131). Some, but not all, patients carrying these isolates had previously been hospitalised outside Australia, suggesting multiple discrete importation events of closely related strains, as well as undetected nosocomial spread.

Draft Genome Sequence of Colistin-Only-Susceptible Pseudomonas aeruginosa Strain ST235, a Hypervirulent High-Risk Clone in Spain

We report the genome of colistin-only-susceptible Pseudomonas aeruginosa strain ST235 (PA_ST235). This isolate was obtained in the setting of an outbreak in a tertiary hospital in Spain. This clone was apparently associated with a significantly higher mortality rate. The ST235 clone also appears to be associated with greater virulence.

Rapid identification of major Escherichia coli sequence types causing urinary tract and bloodstream infections

Escherichia coli sequence types (STs) 69, 73, 95, and 131 are collectively responsible for a large proportion of E. coli urinary tract and bloodstream infections, and they differ markedly in their antibiotic susceptibilities. Here, we describe a novel PCR method to rapidly detect and distinguish these lineages. Three hundred eighteen published E. coli genomes were compared in order to identify signature sequences unique to each of the four major STs. The specificities of these sequences were assessed in silico by seeking them in an additional 98 genomes. A PCR assay was designed to amplify size-distinguishable fragments unique to the four lineages and was validated using 515 E. coli isolates of known STs. Genome comparisons identified 22 regions ranging in size from 335 bp to 26.5 kb that are unique to one or more of the four predominant E. coli STs, with two to 10 specific regions per ST. These regions predominantly harbor genes encoding hypothetical proteins and are within or adjacent to prophage sequences. Most (13/22) were highly conserved (>96.5% identity) in the genomes of their respective ST. The new assay correctly identified all 142 representatives of the four major STs in the validation set (n = 515), with only two ST12 isolates misidentified as ST95. Compared with MLST, the assay has 100% sensitivity and 99.5% specificity. The rapid identification of major extraintestinal E. coli STs will benefit future epidemiological studies and could be developed to tailor antibiotic therapy to the different susceptibilities of these dominant lineages.

Concurrent interspecies and clonal dissemination of OXA-48 carbapenemase

Several isolates of four different carbapenemase-producing Enterobacteriaceae species were recovered from a patient hospitalized for 4 months in a teaching hospital in Madrid. These species comprised seven Klebsiella pneumoniae belonging to ST15, four Escherichia coli belonging to ST2531, two Serratia marcescens and one Citrobacter freundii. This patient was the index case of a small outbreak of four patients infected and/or colonized by carbapenemase-producing K. pneumoniae. Molecular results identified the bla(OXA-48) gene in all Enterobacteriaceae isolates from the index case and in all isolates from the other three patients, suggesting intra- and interpatient dissemination. Our results highlight the great ability of OXA-48 carbapenemase to spread among different enterobacterial species by both clonal and nonclonal dissemination.

Identification of VIM-2-producing Pseudomonas aeruginosa from Tanzania is associated with sequence types 244 and 640 and the location of blaVIM-2 in a TniC integron

Epidemiological data on carbapenemase-producing Gram-negative bacteria on the African continent are limited. Here, we report the identification of VIM-2-producing Pseudomonas aeruginosa isolates in Tanzania. Eight out of 90 clinical isolates of P. aeruginosa from a tertiary care hospital in Dar es Salaam were shown to harbor bla(VIM-2). The bla(VIM-2)-positive isolates belonged to two different sequence types (ST), ST244 and ST640, with bla(VIM-2) located in an unusual integron structure lacking the 3' conserved region of qacΔE1-sul1.

Mode of delivery and other risk factors for Escherichia coli infections in very low birth weight infants

Background

Infections in newborns remain one of the most significant problems in modern medicine. Escherichia coli is an important cause of neonatal bloodstream and respiratory tract infections and is associated with high mortality. The aim of our study was to investigate the epidemiology of E. coli infection in Polish neonatal intensive care units (NICUs) and resistance to antibiotics, with particular reference to the safety of very low birth weight infants.

Methods

Continuous prospective infection surveillance was conducted in 2009–2012 in five NICUs, including 1,768 newborns whose birth weight was <1.5 kg. Escherichia coli isolates from different diagnostic specimens including blood, tracheal/bronchial secretions and others were collected. All isolates were tested using disk diffusion antimicrobial susceptibility methods. Pulsed-field gel electrophoresis was used to determine the possible horizontal transfer of E. coli among patients.

Results

The incidence of E. coli infections was 5.4% and 2.0/1,000 patient-days. The occurrence of E. coli infections depended significantly on the NICU and varied between 3.9% and 17.9%. Multivariate analysis that took into account the combined effect of demographic data (gender, gestational age and birth weight) and place of birth showed that only the place of hospitalisation had a significant effect on the E. coli infection risk. The highest levels of resistance among all E. coli isolates were observed against ampicillin (88.8%) and amoxicillin/clavulanic acid (62.2%). Among E. coli isolates, 17.7% were classified as multidrug resistant. Escherichia coli isolates showed different pulsotypes and dominant epidemic clones were not detected.

Conclusions

Our data indicate that antibiotic prophylaxis in the presence of symptoms such as chorioamnionitis and premature rupture of membranes did not help reduce the risk of E. coli infection. Multivariate analysis demonstrated only one significant risk factor for E. coli infection among infants with a birth weight <1.5 kg, that is, the impact of the NICU, it means that both neonatal care and care during pregnancy and labour were found to be significant.

High prevalence of carbapenem resistance among plasmid-mediated AmpC β-lactamase-producing Klebsiella pneumoniae during outbreaks in liver transplantation units

During a prospective surveillance using PCR for the detection of plasmid-mediated AmpC β-lactamase (pAmpC)-producing Enterobacteriaceae, outbreaks due to pAmpC-producing Klebsiella pneumoniae (pAmpC-Kp) occurred in an adult liver transplantation unit (aLTU) and a paediatric liver transplantation unit (pLTU), with carbapenem-resistant (CR) variants. Between April 2010 and March 2012, a total of 32 patients infected with pAmpC-Kp were found by prospective surveillance using PCR detection at a Japanese university hospital. Multilocus sequence typing, analysis of outer membrane proteins, and detection of carbapenemases were performed. Clinical courses of patients with bloodstream infection (BSI) were reviewed. Of 32 pAmpC-Kp isolates from each patient, 20 (18 from aLTU patients) were DHA-1-producing sequence type 11 (DHA-1-ST11), 9 were CMY-2-ST45/778 (all from pLTU patients) and the other 3 isolates had different sequence types. CR variants were isolated from 8 aLTU patients with DHA-1-ST11 and from 1 pLTU patient with CMY-2-ST45. All of the pAmpC-Kp isolates, including CR variants, were negative for carbapenemases. All of the DHA-1-ST11 and CMY-2-ST45 isolates lacked OmpK35, and seven CR variants also lacked OmpK36. BSIs due to DHA-1-ST11 isolates, including CR variants, occurred in six aLTU patients, four of whom died. The outbreaks were controlled after application of intensified infection control measures. During pAmpC-Kp outbreaks involving 27 liver transplants, CR variants with porin loss developed in nine patients, and DHA-1-ST11 K. pneumoniae caused BSIs with high mortality.

Activity of ceftaroline-avibactam tested against contemporary Enterobacteriaceae isolates carrying β-lactamases prevalent in the United States

Contemporary (2012) β-lactamase-producing isolates (n=493) from U.S. hospitals were tested against ceftaroline-avibactam. Klebsiella spp., Escherichia coli and Proteus mirabilis isolates displaying the Clinical and Laboratory Standards Institute (CLSI) screening criteria for extended spectrum β-lactamase (ESBL) production were evaluated. Isolates carried genes encoding CTX-M (n=316, CTX-M-14-like and -15-like), KPC (n=45), CMY-2-like (n=54), or SHV enzyme with ESBL activity (n=78). Ceftaroline-avibactam inhibited 98.2% of the isolates at ≤0.5 μg/mL, and all strains were inhibited by ≤2 μg/mL of this novel β-lactamase-inhibitor combination. These results confirm that ceftaroline-avibactam could be a useful therapeutic option for Enterobacteriaceae isolates producing β-lactamases that are prevalent in the United States.

Emerging rapid resistance testing methods for clinical microbiology laboratories and their potential impact on patient management

Atypical and multidrug resistance, especially ESBL and carbapenemase expressing Enterobacteriaceae, is globally spreading. Therefore, it becomes increasingly difficult to achieve therapeutic success by calculated antibiotic therapy. Consequently, rapid antibiotic resistance testing is essential. Various molecular and mass spectrometry-based approaches have been introduced in diagnostic microbiology to speed up the providing of reliable resistance data. PCR- and sequencing-based approaches are the most expensive but the most frequently applied modes of testing, suitable for the detection of resistance genes even from primary material. Next generation sequencing, based either on assessment of allelic single nucleotide polymorphisms or on the detection of nonubiquitous resistance mechanisms might allow for sequence-based bacterial resistance testing comparable to viral resistance testing on the long term. Fluorescence in situ hybridization (FISH), based on specific binding of fluorescence-labeled oligonucleotide probes, provides a less expensive molecular bridging technique. It is particularly useful for detection of resistance mechanisms based on mutations in ribosomal RNA. Approaches based on MALDI-TOF-MS, alone or in combination with molecular techniques, like PCR/electrospray ionization MS or minisequencing provide the fastest resistance results from pure colonies or even primary samples with a growing number of protocols. This review details the various approaches of rapid resistance testing, their pros and cons, and their potential use for the diagnostic laboratory.

MLST reveals potentially high-risk international clones of Enterobacter cloacae

OBJECTIVES

To perform the first multinational Enterobacter cloacae clonality study, using the MLST scheme newly developed in Japan.

METHODS

The analysis included 195 rectal carriage E. cloacae isolates resistant to expanded-spectrum cephalosporins (ESCs), collected from patients in 12 hospital units across Europe and Israel. All of the isolates were typed by PFGE and 173 isolates were subjected to MLST. ESC resistance was analysed phenotypically; genes encoding ESBLs and carbapenemases were identified by PCR and sequencing.

RESULTS

MLST distinguished 88 STs, which correlated with the PFGE data. PFGE was more discriminatory, producing 129 pulsotypes (169 patterns). Numerous STs were observed in several countries each. The most widespread were ST66, ST78, ST108 and ST114, each having at least 10 isolates from three to five countries, diversified into multiple pulsotypes, with clusters of related isolates in one or more centres. Analysis of the STs against the MLST database revealed several epidemic clonal complexes, such as those with central genotypes ST74 (including ST78) or ST114 (including ST66). ESC resistance was equally related to overexpression of the AmpC cephalosporinase and to ESBL production. Among ESBL producers some spreading subclones were identified, including specific ST66, ST78 and ST114 pulsotypes, associated with CTX-M-15 production. Several isolates produced carbapenemase VIM-1 or KPC-2.

CONCLUSIONS

Together with the information available in the MLST database, our results suggest that, like Escherichia coli and Klebsiella pneumoniae, E. cloacae harbours clonal lineages of increased epidemic potential that may be associated with resistance spread.

Similar frequencies of Pseudomonas aeruginosa isolates producing KPC and VIM carbapenemases in diverse genetic clones at tertiary-care hospitals in Medellín, Colombia

Carbapenem-resistant Pseudomonas aeruginosa has become a serious health threat worldwide due to the limited options available for its treatment. Understanding its epidemiology contributes to the control of antibiotic resistance. The aim of this study was to describe the clinical and molecular characteristics of infections caused by carbapenem-resistant P. aeruginosa isolates in five tertiary-care hospitals in Medellín, Colombia. A cross-sectional study was conducted in five tertiary-care hospitals from June 2012 to March 2014. All hospitalized patients infected by carbapenem-resistant P. aeruginosa were included. Clinical information was obtained from medical records. Molecular analyses included PCR for detection of bla(VIM), bla(IMP), bla(NDM), bla(OXA-48), and bla(KPC) genes plus pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) for molecular typing. A total of 235 patients were enrolled: 91.1% of them were adults (n = 214), 88.1% (n = 207) had prior antibiotic use, and 14.9% (n = 35) had urinary tract infections. The bla(VIM-2) and bla(KPC-2) genes were detected in 13.6% (n = 32) and 11.5% (n = 27), respectively, of all isolates. Two isolates harbored both genes simultaneously. For KPC-producing isolates, PFGE revealed closely related strains within each hospital, and sequence types (STs) ST362 and ST235 and two new STs were found by MLST. With PFGE, VIM-producing isolates appeared highly diverse, and MLST revealed ST111 in four hospitals and five new STs. These results show that KPC-producing P. aeruginosa is currently disseminating rapidly and occurring at a frequency similar to that of VIM-producing P. aeruginosa isolates (approximately 1:1 ratio) in Medellín, Colombia. Diverse genetic backgrounds among resistant strains suggest an excessive antibiotic pressure resulting in the selection of resistant strains.

High prevalence of ST131 among CTX-M-producing Escherichia coli from community-acquired infections, in the Czech Republic

A total of 2,683 nonrepetitive Escherichia coli isolates were collected from microbiological laboratories covering all regions of the Czech Republic, during April 2011. Antimicrobial susceptibility patterns of E. coli were assessed. All 38 cefotaxime-resistant (CTX-R) isolates were found to be extended-spectrum β-lactamase (ESBL)-positive by the double-disc synergy test. Thirty-two of those isolates produced enzymes of CTX-M-1 family, five of CTX-M-9 family, and one isolate both CTX-M types. Genotyping by multilocus sequence typing classified all ESBL-producing isolates into 13 sequence types (STs). ST131 was the most prevalent and was exclusively correlated with E. coli belonging to the more-virulent phylogroup B2. blaCTX-M-15 and blaCTX-M-9-like genes were mainly carried by plasmids belonging to the IncF group, while replicon I1 was predominant among CTX-M-1-encoding plasmids. Additionally, 63% of the ESBL-producing isolates were also resistant to ciprofloxacin. Sequence analysis of quinolone resistance-determining regions of gyrA and parC revealed the presence of amino acid substitutions in 22 out of 23 ciprofloxacin-resistant isolates. The acc(6')-Ib-cr and qnrB1 plasmid-mediated quinolone resistance genes were also detected in some of the isolates. This is the first report on the emergence and spread of CTX-M-producing E. coli in the community of the Czech Republic, indicating the high prevalence of ST131 clone among CTX-M producers.

Inappropriate use of antibiotics in hospitals: the complex relationship between antibiotic use and antimicrobial resistance

Hospitals are considered an excellent compartment for the selection of resistant and multi-drug resistant (MDR) bacteria. The overuse and misuse of antimicrobial agents are considered key points fuelling this situation. Antimicrobial stewardship programs have been designed for better use of these compounds to prevent the emergence of resistant microorganisms and to diminish the upward trend in resistance. Nevertheless, the relationship between antibiotic use and antimicrobial resistance is complex, and the desired objectives are difficult to reach. Various factors affecting this relationship have been advocated including, among others, antibiotic exposure and mutant selection windows, antimicrobial pharmacodynamics, the nature of the resistance (natural or acquired, including mutational and that associated with horizontal gene transfer) and the definition of resistance. Moreover, antimicrobial policies to promote better use of these drugs should be implemented not only in the hospital setting coupled with infection control programs, but also in the community, which should also include animal and environmental compartments. Within hospitals, the restriction of antimicrobials, cycling and mixing strategies and the use of combination therapies have been used to avoid resistance. Nevertheless, the results have not always been favorable and resistant bacteria have persisted despite the theoretical benefits of these strategies. Mathematical models as well as microbiological knowledge can explain this failure, which is mainly related to the current scenario involving MDR bacteria and overcoming the fitness associated with resistance. New antimicrobials, rapid diagnostic and antimicrobial susceptibility testing and biomarkers will be useful for future antimicrobial stewardship interventions.

Population structure of clinical Pseudomonas aeruginosa from West and Central African countries

BACKGROUND

Pseudomonas aeruginosa (PA) has a non-clonal, epidemic population with a few widely distributed and frequently encountered sequence types (STs) called 'high-risk clusters'. Clinical P. aeruginosa (clinPA) has been studied in all inhabited continents excepted in Africa, where a very few isolates have been analyzed. Here, we characterized a collection of clinPA isolates from four countries of West and Central Africa.

METHODOLOGY

184 non-redundant isolates of clinPA from hospitals of Senegal, Ivory Coast, Nigeria, and Central African Republic were genotyped by MLST. We assessed their resistance level to antibiotics by agar diffusion and identified the extended-spectrum β-lactamases (ESBLs) and metallo-β-lactamases (MBLs) by sequencing. The population structure of the species was determined by a nucleotide-based analysis of the entire PA MLST database and further localized on the phylogenetic tree (i) the sequence types (STs) of the present collection, (ii) the STs by continents, (iii) ESBL- and MBL-producing STs from the MLST database.

PRINCIPAL FINDINGS

We found 80 distinct STs, of which 24 had no relationship with any known STs. 'High-risk' international clonal complexes (CC155, CC244, CC235) were frequently found in West and Central Africa. The five VIM-2-producing isolates belonged to CC233 and CC244. GES-1 and GES-9 enzymes were produced by one CC235 and one ST1469 isolate, respectively. We showed the spread of 'high-risk' international clonal complexes, often described as multidrug-resistant on other continents, with a fully susceptible phenotype. The MBL- and ESBL-producing STs were scattered throughout the phylogenetic tree and our data suggest a poor association between a continent and a specific phylogroup.

CONCLUSIONS

ESBL- and MBL-encoding genes are borne by both successful international clonal complexes and distinct local STs in clinPA of West and Central Africa. Furthermore, our data suggest that the spread of a ST could be either due to its antibiotic resistance or to features independent from the resistance to antibiotics.

Prevalence and characteristics of lactose non-fermenting Escherichia coli in urinary isolates

Recently, serotype O75 was found to be prominent among the non-ST131 ciprofloxacin-resistant Escherichia coli, and they were all lactose non-fermenters. In this study, we investigated the prevalence and characteristics of lactose non-fermenters in urinary isolates of E. coli. A total of 167 E. coli isolates was collected. Antimicrobial susceptibility tests were determined by VITEK 2 (bioMerieux, France). The lactose non-fermenters underwent PCR-based O typing, multilocus sequence typing (MLST) analysis, phylogenetic grouping. For ciprofloxacin-resistant isolates, the resistance mechanisms were investigated. Thirty-three (19.7%) isolates were lactose non-fermenters and the ciprofloxacin resistance rate was significantly higher than in lactose fermenters (66.7% vs. 31.6%, P = 0.0002). According to the serotype, O75 was the most common (42.4%, 14/33) and was followed by O16 (5/33), O2 (4/33), O25b (3/33), O15 (1/33), O6 (1/33), O1 (1/33). All the O75 isolates were ciprofloxacin-resistant and belonged to ST1193. By MLST, they were resolved into 11 STs. ST1193 was the most common (14/33) and was followed by ST131 (8/33). Interestingly, 8 isolates of ST131 were divided into three O types [O16 (4 isolates), O25b (3), and non-typeable (1)]. The ciprofloxacin resistance rate was high in isolates of O75-ST1193 and O25b-ST131 but low in O16-ST131 and O2-ST95. All the ciprofloxacin-resistant isolates showed identical triple mutations in gyrA and parC but the serotype O25b isolates had an additional mutation in parC (E84V). Only one isolate harbored aac(6')-Ib-cr variant and no qnr gene was detected. Continuous monitoring of the prevalence and clonal composition of the lactose non-fermenters is needed.

Dominance of international 'high-risk clones' among metallo-β-lactamase-producing Pseudomonas aeruginosa in the UK

OBJECTIVES

Carbapenem-resistant isolates of Pseudomonas aeruginosa producing metallo-β-lactamases (MBLs) are increasingly reported worldwide and often belong to particular 'high-risk clones'. This study aimed to characterize a comprehensive collection of MBL-producing P. aeruginosa isolates referred to the UK national reference laboratory from multiple UK laboratories over a 10 year period.

METHODS

Isolates were referred to the UK national reference laboratory between 2003 and 2012 for investigation of resistance mechanisms and/or outbreaks. MBL genes were detected by PCR. Typing was carried out by nine-locus variable-number tandem repeat (VNTR) analysis and MLST.

RESULTS

MBL-producing P. aeruginosa isolates were referred from 267 source patients and 89 UK laboratories. The most common isolation sites were urine (24%), respiratory (18%), wounds (17%) and blood (13%). VIM-type MBLs predominated (91% of all MBLs found), but a few IMP- and NDM-type enzymes were also identified. Diverse VNTR types were seen, but 86% of isolates belonged to six major complexes. MLST of representative isolates from each complex showed that they corresponded to STs 111, 233, 235, 357, 654 and 773, respectively. Isolates belonging to these complexes were received from between 9 and 25 UK referring laboratories each.

CONCLUSIONS

The incidence of MBL-producing P. aeruginosa is increasing in the UK. The majority of these isolates belong to several 'high-risk clones', which have been previously reported internationally as host clones of MBLs.

The characterization and antibiotic resistance profiles of clinical Escherichia coli O25b-B2-ST131 isolates in Kuwait

Background

Escherichia coli O25b-B2-ST131 are considered virulent extra-intestinal pathogens causing serious clinical complications such as urinary tract infection and bacteraemia. Our main objectives in this study were to characterise the multi-drug resistant (MDR) isolates of this lineage in Kuwait, and to demonstrate whether reduced susceptibility is spread clonally.

Results

A subset of 83 (10%) non-duplicate and non-selective E. coli O25b-B2-ST131 out of 832 MDR E. coli was identified and collected. Minimum inhibitory concentrations of the isolates were determined and pulsed-field gel electrophoresis was used for typing.

The majority (95.2%) of the 83 E. coli O25b-B2-ST131 harboured at least one bla gene with bla_CTX-M-15 being the most prevalent. bla_CTX-M-2 was present in one isolate. Also one isolate harboured bla_CTX-M-56, qnrB1 and bla_CMY-2 genes and carried IncF1 plasmids of about 97 kb and160 kb. qnrB and qnrS were found in 8 other bla_CTX-M-15 containing isolates. The bla_NDM, bla_IMP, bla_VIM and qnrA were not detected, however, the bla_OXA-48 was present in two (2.4%).

Conclusions

The majority of isolates harbouring qnr genes demonstrated relatedness (≥85%) by PFGE. However, the diversity in PFGE profiles for the other MDR isolates reflected the changes in population genetics of E. coli O25b-B2-ST131. We identified for the first time the appearance of bla_CTX-M-2 in the Middle East and bla_CTX-M-56 outside the Latin American countries. The isolate harbouring bla_CTX-M-56 also contained qnrB1 and bla_CMY-2 genes and carried IncF1 plasmids. The appearance of a highly virulent E. coli O25b-ST131 that is resistant to penicillins, most cephalosproins, β-lactamase inhibitors as well as fluoroquinolones is a cause for concern.

Electronic supplementary material

The online version of this article (doi:10.1186/s12866-014-0214-6) contains supplementary material, which is available to authorized users.

Antibiotic resistance and extended spectrum beta-lactamases: Types, epidemiology and treatment

Antibiotic resistance is a problem of deep scientific concern both in hospital and community settings. Rapid detection in clinical laboratories is essential for the judicious recognition of antimicrobial resistant organisms. Production of extended-spectrum β-lactamases (ESBLs) is a significant resistance-mechanism that impedes the antimicrobial treatment of infections caused by Enterobacteriaceae and is a serious threat to the currently available antibiotic armory. ESBLs are classified into several groups according to their amino acid sequence homology. Proper infection control practices and barriers are essential to prevent spread and outbreaks of ESBL producing bacteria. As bacteria have developed different strategies to counter the effects of antibiotics, the identification of the resistance mechanism may help in the discovery and design of new antimicrobial agents. The carbapenems are widely regarded as the drugs of choice for the treatment of severe infections caused by ESBL-producing Enterobacteriaceae, although comparative clinical trials are scarce. Hence, more expeditious diagnostic testing of ESBL-producing bacteria and the feasible modification of guidelines for community-onset bacteremia associated with different infections are prescribed.

Extensively drug-resistant pseudomonas aeruginosa isolates containing blaVIM-2 and elements of Salmonella genomic island 2: a new genetic resistance determinant in Northeast Ohio

Carbapenems are a mainstay of treatment for infections caused by Pseudomonas aeruginosa. Carbapenem resistance mediated by metallo-β-lactamases (MBLs) remains uncommon in the United States, despite the worldwide emergence of this group of enzymes. Between March 2012 and May 2013, we detected MBL-producing P. aeruginosa in a university-affiliated health care system in northeast Ohio. We examined the clinical characteristics and outcomes of patients, defined the resistance determinants and structure of the genetic element harboring the blaMBL gene through genome sequencing, and typed MBL-producing P. aeruginosa isolates using pulsed-field gel electrophoresis (PFGE), repetitive sequence-based PCR (rep-PCR), and multilocus sequence typing (MLST). Seven patients were affected that were hospitalized at three community hospitals, a long-term-care facility, and a tertiary care center; one of the patients died as a result of infection. Isolates belonged to sequence type 233 (ST233) and were extensively drug resistant (XDR), including resistance to all fluoroquinolones, aminoglycosides, and β-lactams; two isolates were nonsusceptible to colistin. The blaMBL gene was identified as blaVIM-2 contained within a class 1 integron (In559), similar to the cassette array previously detected in isolates from Norway, Russia, Taiwan, and Chicago, IL. Genomic sequencing and assembly revealed that In559 was part of a novel 35-kb region that also included a Tn501-like transposon and Salmonella genomic island 2 (SGI2)-homologous sequences. This analysis of XDR strains producing VIM-2 from northeast Ohio revealed a novel recombination event between Salmonella and P. aeruginosa, heralding a new antibiotic resistance threat in this region's health care system.

Polyclonal spread and outbreaks with ESBL positive gentamicin resistant Klebsiella spp. in the region Kennemerland, The Netherlands

Objective

The objective of this study was to analyze the transmission dynamics of ESBL positive Klebsiella spp. with an additional resistance towards gentamicin (ESBL-G) in a Dutch region of 650,000 inhabitants in 2012.

Methods

All patient related ESBL-G isolates isolated in 2012 were genotyped using both Amplification Fragment Length Polymorphism (AFLP) and High-throughput MultiLocus Sequence Typing (HiMLST). HiMLST was used to analyze the presence of (unidentified) clusters of ESBL-G positive patients. Furthermore, all consecutive ESBL-G isolates within patients were studied in order to evaluate the intra-patient variation of antibiotic phenotypes.

Results

There were 38 ESBL-G isolates, which were classified into 18 different sequence types (STs) and into 21 different AFLP types. Within the STs, four clusters were detected from which two were unknown resulting in a transmission index of 0.27. An analysis of consecutive ESBL-G isolates (with similar STs) within patients showed that for 68.8% of the patients at least one isolate had a different consecutive antibiotic phenotype.

Conclusion

The transmission of ESBL-G in the region Kennemerland in 2012 was polyclonal with several outbreaks (with a high level of epidemiological linkage). Furthermore, clustering by antibiotic phenotype characterization seems to be an inadequate approach in this setting. The routine practice of molecular typing of collected ESBL-G isolates may help to detect transmission in an early stage, which opens the possibility of a rapid response.

Experimental protection of diabetic mice against Lethal P. aeruginosa infection by bacteriophage

The emergence of antibiotic-resistant bacterial strains has become a global crisis and is vulnerable for the exploration of alternative antibacterial therapies. The present study emphasizes the use of bacteriophage for the treatment of multidrug resistant P. aeruginosa. P. aeruginosa was used to induce septicemia in streptozotocin (STZ) induced diabetic and nondiabetic mice by intraperitoneal (i.p.) injection of 3 × 10⁸ CFU, resulting in a fatal bacteremia within 48 hrs. A single i.p. injection of 3 × 10⁹ PFU phage GNCP showed efficient protection in both diabetic (90%) and nondiabetic (100%) bacteremic mice. It was further noted that the protection rate was reduced in diabetic mice when phage GNCP was administered after 4 h and 6 h of lethal bacterial challenge. In contrast, nondiabetic bacteremic mice were rescued even when treatment was delayed up to 20 h after lethal bacterial challenge. Evaluation of results confirmed that a single intraperitoneal injection of the phage dose (3 × 10⁹ PFU/mL) was more effective than the multiple doses of imipenem. These results uphold the efficacy of phage therapy against pernicious P. aeruginosa infections, especially in cases of immunocompromised host.

High dissemination of extended-spectrum β-lactamase-producing Enterobacteriaceae in effluents from wastewater treatment plants

Water environments play an important role in the dissemination of antibiotic-resistant bacteria among humans, animals and agricultural sources. In order to assess the spread of extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae, we analyzed 279 effluent samples from 21 wastewater treatment plants in Navarra (northern Spain). A total of 185 cefpodoxime-resistant bacteria were isolated on ChromID ESBL agar plates, with high predominance of Escherichia coli among isolated species (73%). ESBL production was determined by different methods, concluding its presence in 86.5% of the isolates by the combination disk test, 75.7% by double-disk synergy test and 73.5% by MicroScan(®) NM37 automated system. PCR and sequencing analysis showed that the predominant β-lactamases (bla) genes were blaCTx-M (67.4%) followed by blaTEM (47%), blaSHV (17.4%) and blaOxA (8.3%); furthermore, two or more β-lactamases genes were found in 34.9% of the isolates. The results demonstrate the high prevalence of ESBL-producing Enterobacteriaceae in effluent water from wastewater treatment plants and confirm the need to optimize current disinfection procedures and to improve management of wastewater in an effort to minimize reservoirs of resistant bacteria. Further studies are needed for examining the presence of these bacteria in other environments and for determining the potential dissemination routes of these resistances as well as their impact on human health.

Bacterial infections in cirrhosis: a position statement based on the EASL Special Conference 2013

Bacterial infections are very common and represent one of the most important reasons of progression of liver failure, development of liver-related complications, and mortality in patients with cirrhosis. In fact, bacterial infections may be a triggering factor for the occurrence of gastrointestinal bleeding, hypervolemic hyponatremia, hepatic encephalopathy, kidney failure, and development of acute-on-chronic liver failure. Moreover, infections are a very common cause of repeated hospitalizations, impaired health-related quality of life, and increased healthcare costs in cirrhosis. Bacterial infections develop as a consequence of immune dysfunction that occurs progressively during the course of cirrhosis. In a significant proportion of patients, infections are caused by gram-negative bacteria from intestinal origin, yet gram-positive bacteria are a frequent cause of infection, particularly in hospitalized patients. In recent years, infections caused by multidrug-resistant bacteria are becoming an important clinical problem in many countries. The reduction of the negative clinical impact of infections in patients with cirrhosis may be achieved by a combination of prophylactic measures, such as administration of antibiotics, to reduce the occurrence of infections in high-risk groups together with early identification and management of infection once it has developed. Investigation on the mechanisms of altered gut microflora, translocation of bacteria, and immune dysfunction may help develop more effective and safe methods of prevention compared to those that are currently available. Moreover, research on biomarkers of early infection may be useful in early diagnosis and treatment of infections. The current manuscript reports an in-depth review and a position statement on bacterial infections in cirrhosis.

Clonal dissemination of extensively drug-resistant Acinetobacter baumannii producing an OXA-23 β-lactamase at a teaching hospital in Shanghai, China

BACKGROUND/PURPOSE

Extensively drug-resistant (XDR) Acinetobacter baumannii presents a serious therapeutic and infection control challenge. This study aimed to explore the causes for the rapid increase of XDR A. baumannii at a teaching hospital in Shanghai.

METHODS

All consecutive clinical isolates of XDR A. baumannii were collected from January to December 2010 at Huashan Hospital in Shanghai. The prevalence of carbapenemase genes was investigated by polymerase chain reaction (PCR) amplification. Genetic relatedness of the isolates was determined by enterobacterial repetitive intergenic consensus-PCR and multilocus sequence typing. A retrospective case-control study was performed for the identification of risk factors of XDR A. baumannii infections.

RESULTS

All 106 XDR A. baumannii isolates carried the blaOxA-23 gene and were resistant to all antimicrobial agents tested, except colistin, tigecycline and cefoperazone-sulbactam. One hundred and five of the strains belonged to clonal complex 92 by multilocus sequence typing, and 78 were classified as clone A1 by enterobacterial repetitive intergenic consensus-PCR. Intensive care unit residency at the time of isolation, recent general anesthesia, the number of previous antibiotic classes administered and previous hospitalization were identified as risk factors by case-control study. Efficacy rates were 62.5% (5/8), 47.4% (9/19), and 42.9% (3/7) when the XDR patients were treated with cefoperazone-sulbactam, carbapenems, or both cefoperazone-sulbactam and carbapenem, alone or in combination with other agents, respectively.

CONCLUSION

XDR A. baumannii producing OXA-23 β-lactamase was clonally disseminated at a university hospital in Shanghai. Cefoperazone-sulbactam and carbapenems alone or combined with other antibiotics may benefit XDR A. baumannii infections in the absence of other effective antibiotics.

High prevalence of cross-resistance to aminoglycosides in fluoroquinolone-resistant Escherichia coli clinical isolates

BACKGROUND

Multidrug-resistant Escherichia coli, especially a lineage of O25b:H4-ST131, has increased and spread worldwide. The surveillance of cross-resistance of E. coli is necessary.

METHODS

Cross-resistance to fluoroquinolones (FQs) and aminoglycosides (AGs) was examined in E. coli isolated in Hokkaido Prefecture, Japan, between 2008 and 2009.

RESULTS

Gentamicin (GEN) resistance was more common in FQ-resistant isolates (30/112 strains; 26.8%) than in FQ-susceptible isolates (2/100 strains; 2%). The frequency of GEN resistance was similar in two groups of FQ-resistant strains, O25b:H4-ST131 genotype (22/87 strains; 25.3%) and a group of other FQ-resistant genotypes (8/25 strains; 32.0%). The main AG resistance gene was aac(3)-II (87.5% of GEN-resistant strains). The only amikacin-resistant strain which was FQ resistant carried the aac(6')-Ib-cr gene. CTX-M type extended-spectrum β-lactamase (ESBL) genes were also found in FQ-resistant strains at a high frequency. However, the number of strains with both ESBL and AG-modifying enzyme genes was relatively low (8 strains).

CONCLUSION

All FQ-resistant strains, not only O25b:H4-ST131, appeared to preferentially acquire ESBL genes and/or genes encoding AG-modifying enzymes; however, the acquisitions of these genes seemed to occur independently.

Expansion and evolution of a virulent, extensively drug-resistant (polymyxin B-resistant), QnrS1-, CTX-M-2-, and KPC-2-producing Klebsiella pneumoniae ST11 international high-risk clone

In this study, we report the early expansion, evolution, and characterization of a multiresistant Klebsiella pneumoniae clone that was isolated with increasing frequency from inpatients in a tertiary-care university hospital in Brazil. Seven carbapenem- and quinolone-resistant and polymyxin B-susceptible or -resistant K. pneumoniae isolates isolated between December 2012 and February 2013 were investigated. Beta-lactamase- and plasmid-mediated quinolone resistance (PMQR)-encoding genes and the genetic environment were investigated using PCR, sequencing, and restriction fragment length polymorphism (RFLP). Clonal relatedness was established using XbaI-pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST), and phylogenetic group characterization. Plasmid analyses included PCR-based replicon typing (PBRT) and hybridization of the S1-PFGE product, plasmid MLST, and conjugation experiments. Virulence potential was assessed by PCR by searching for 10 virulence factor-encoding genes (ureA, fimH, kfuBC, uge, wabG, magA, mrkD, allS, rmpA, and cf29a) and by phenotypic tests to analyze the hypermucoviscous phenotype. The genetic context of a multidrug-resistant and extensively drug-resistant K. pneumoniae ST11-KpI clone harboring IncFIIk-Tn4401a-blaKPC-2, qnrS1, and blaCTX-M-2 was found. Moreover, three isolates displayed high resistance to polymyxin B (MICs = 32, 32, and 128 mg/liter) as well as mucous and hypermucoviscous phenotypes. These bacteria also harbored ureA, fimH, uge, wabG, and mrkD, which code for virulence factors associated with binding, biofilm formation, and the ability to colonize and escape from phagocytosis. Our study describes the association of important coresistance and virulence factors in the K. pneumoniae ST11 international high-risk clone, which makes this pathogen successful at infections and points to the quick expansion and evolution of this multiresistant and virulent clone, leading to a pandrug-resistant phenotype and persistent bacteria in a Brazilian hospital.

Molecular characterization of clinical multidrug-resistant Klebsiella pneumoniae isolates

Background

Klebsiella pneumoniae is a frequent nosocomial pathogen, with the multidrug-resistant (MDR) K. pneumoniae being a major public health concern, frequently causing difficult-to-treat infections worldwide. The aim of this study was to investigate the molecular characterization of clinical MDR Klebsiella pneumoniae isolates.

Methods

A total of 27 non-duplicate MDR K. pneumoniae isolates with a CTX-CIP-AK resistance pattern were investigated for the prevalence of antimicrobial resistance genes including extended spectrum β-lactamase genes (ESBLs), plasmid-mediated quinolone resistance (PMQR) genes, 16S rRNA methylase (16S-RMTase) genes, and integrons by polymerase chain reaction (PCR) amplification and DNA sequencing. Plasmid replicons were typed by PCR-based replicon typing (PBRT). Multi-locus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE) were carried out to characterize the strain relatedness.

Results

All the isolates co-harbored 3 or more resistance determinants. OqxAB, CTX-M-type ESBLs and RmtB were the most frequent determinants, distributed among19 (70.4%),18 (66.7%) and 8 (29.6%) strains. Fourteen isolates harbored class 1 integrons, with orfD-aacA4 being the most frequent gene cassette array. Class 3 integrons were less frequently identified and contained the gene cassette array of bla_GES-1-bla_OXA-10-aac(6′)-Ib. IncFII replicon was most commonly found in this collection. One cluster was observed with ≥80% similarity among profiles obtained by PFGE, and one sequence type (ST) by MLST, namely ST11, was observed in the cluster.

Conclusion

K. pneumoniae carbapenemase (KPC)–producing ST11 was the main clone detected. Of particular concern was the high prevalence of multiple resistance determinants, classs I integrons and IncFII plasmid replicon among these MDR strains, which provide advantages for the rapid development of MDR strains.

Diagnostic potential of monoclonal antibodies specific to the unique O-antigen of multidrug-resistant epidemic Escherichia coli clone ST131-O25b:H4

The Escherichia coli lineage sequence type 131 (ST131)-O25b:H4 is a globally spread multidrug-resistant clone responsible for a great proportion of extraintestinal infections. Driven by the significant medical needs associated with this successful pathogenic lineage, we generated murine monoclonal antibodies (MAbs) against its lipopolysaccharide (LPS) O25b antigen in order to develop quick diagnostic tests. Murine monoclonal antibodies were generated by immunizing mice with whole killed nonencapsulated ST131-O25b E. coli cells and screening hybridoma supernatants for binding to purified LPS molecules obtained from an E. coli ST131-O25b clinical isolate. The MAbs selected for further study bound to the surface of live E. coli O25b strains irrespective of the capsular type expressed, while they did not bind to bacteria or purified LPS from other serotypes, including the related classical O25 antigen (O25a). Using these specific MAbs, we developed a latex bead-based agglutination assay that has greater specificity and is quicker and simpler than the currently available typing methods. The high specificities of these MAbs can be explained by the novel structure of the O25b repeating unit elucidated in this article. Based on comparative analysis by nuclear magnetic resonance (NMR) and mass spectrometry, the N-acetyl-fucose in the O25a O-antigen had been replaced by O-acetyl-rhamnose in the O25b repeating unit. The genetic determinants responsible for this structural variation were identified by aligning the corresponding genetic loci and were confirmed by trans-complementation of a rough mutant by the subserotype-specific fragments of the rfb operons.

Inhibitor-resistant TEM- and OXA-1-producing Escherichia coli isolates resistant to amoxicillin-clavulanate are more clonal and possess lower virulence gene content than susceptible clinical isolates

In a previous prospective multicenter study in Spain, we found that OXA-1 and inhibitor-resistant TEM (IRT) β-lactamases constitute the most common plasmid-borne mechanisms of genuine amoxicillin-clavulanate (AMC) resistance in Escherichia coli. In the present study, we investigated the population structure and virulence traits of clinical AMC-resistant E. coli strains expressing OXA-1 or IRT and compared these traits to those in a control group of clinical AMC-susceptible E. coli isolates. All OXA-1-producing (n = 67) and IRT-producing (n = 45) isolates were matched by geographical and temporal origin to the AMC-susceptible control set (n = 56). We performed multilocus sequence typing and phylogenetic group characterization for each isolate and then studied the isolates for the presence of 49 virulence factors (VFs) by PCR and sequencing. The most prevalent clone detected was distinct for each group: group C isolates of sequence type (ST) 88 (C/ST88) were the most common in OXA-1 producers, B2/ST131 isolates were the most common in IRT producers, and B2/ST73 isolates were the most common in AMC-susceptible isolates. The median numbers of isolates per ST were 3.72 in OXA-1 producers, 2.04 in IRT producers, and 1.69 in AMC-susceptible isolates; the proportions of STs represented by one unique isolate in each group were 19.4%, 31.1%, and 48.2%, respectively. The sum of all VFs detected, calculated as a virulence score, was significantly higher in AMC-susceptible isolates than OXA-1 and IRT producers (means, 12.5 versus 8.3 and 8.2, respectively). Our findings suggest that IRT- and OXA-1-producing E. coli isolates resistant to AMC have a different and less diverse population structure than AMC-susceptible clinical E. coli isolates. The AMC-susceptible population also contains more VFs than AMC-resistant isolates.

Extended-spectrum β-lactamase-producing Escherichia coli isolated from poultry: a review of current problems, illustrated with some laboratory findings

Extended-spectrum β-lactamase (ESBL)-producing Escherichia coli has been documented in humans as well as in food-producing birds, including chickens, and for unknown reasons the prevalence has increased significantly during the last decade. With E. coli as a major opportunistic pathogen in chickens and with a potential for zoonotic transfer to human beings, ESBL-producing E. coli represents a major risk both to poultry production and to human health. This review presents some of the current problems with ESBL-producing E. coli in relation to poultry production, with a focus on chickens. To illustrate issues in relation to screening and typing, two case studies are included where one collection of ESBL-producing E. coli isolates was obtained from asymptomatic carrier chickens while the other was obtained from lesions in chickens. Pulsed-field gel electrophoresis and multi-locus sequence typing revealed a highly heterogeneous population of ESBL-producing E. coli. All isolates harboured between one and three large plasmids (>100 kb). Among isolates associated with asymptomatic chickens, the ESBL types SHV and TEM dominated, while CTX-M-1 dominated in disease-associated isolates. The isolates from diseased birds were occasionally of sequence types often associated with human infections, such as ST131. With improved tools to trace and screen for ESBL-producing E. coli at farm level, strategies can be selected that aim to reduce or eliminate the presence of ESBL-producing E. coli in poultry and poultry products meant for human consumption.

Successful control of a neonatal outbreak caused mainly by ST20 multidrug-resistant SHV-5-producing Klebsiella pneumoniae, Greece

Background

Extended spectrum beta-lactamase-producing Klebsiella pneumoniae (ESBL-Kp) infection can cause significant morbidity and mortality in neonates. We investigated a nosocomial ESBL-Kp outbreak in a neonatal intensive care unit (NICU) of the University Hospital of Larissa (UHL), Central Greece.

Methods

A total of sixty-four ESBL-Kp were studied; twenty six isolates were recovered from the NICU and were compared with thirty-eight randomly selected isolates from different wards of the hospital during the period March- December 2012. All isolates were characterized by antimicrobial susceptibility testing, ESBL-production by double-disk synergy test, molecular typing using BOX-PCR, whereas selected isolates were further characterized by beta lactamase and virulence gene content, multilocus sequence typing and phylogenetic analysis. All neonates affected by ESBL-Kp were put under strict contact isolation, along with appropriate infection control measures.

Results

The outbreak strain of ST20 multidrug-resistant SHV-5-producing K. pneumoniae was identified in all infected (n = 13) and three colonized neonates. A novel ST (ST1114) was also identified among SHV-5 producers (n = 10) recovered from nine colonized infants, but it was not related with ST20. Both STs were identified only in the NICU and not in other wards of the hospital. No ESBL-Kp were isolated from the hands of the nursing staff and the environment. Although we were not able to identify the source of the outbreak, no ESBL-Kp were isolated in the NICU after this period and we assumed that the outbreak was successfully controlled. All neonates received parenteral nutrition and most of them were delivered by caesarean section and showed low gestational age (<32 weeks) and low birth weights (<1500 g).

Conclusion

According to our knowledge, this is the first description of an outbreak of multidrug-resistant SHV-5 producing K. pneumoniae assigned to ST20.

Changing options for prevention and treatment of infections in cirrhosis

OPINION STATEMENT

Bacterial infections are more frequent and severe in cirrhosis. Most prevalent infections are spontaneous bacterial peritonitis (SBP) and urinary infections followed by pneumonia, cellulitis and bacteremia. Cirrhosis increases the risk of sepsis, severe sepsis and death. Early diagnosis and adequate treatment of infections is essential in the management of cirrhotic patients. Recent data show that currently recommended empirical antibiotic therapy, mainly based on the use of β-lactams, is effective in community-acquired infections, but frequently fails in nosocomial and healthcare-associated infections. A marked increase in the prevalence of multidrug resistant (MDR) bacteria in the healthcare environment explains this finding. Patients developing nosocomial infections or with extended lengths of hospitalization are at higher risk for second infections that are associated with poor prognosis. Antibiotic strategies should therefore be selected according to the type, severity and site of acquisition of infection, and be adapted to the local epidemiological pattern of antibiotic resistance. Treatment of MDR bacteria requires the use of broader spectrum antibiotics (carbapenems) or those active against specific resistant bacteria (glycopeptides, linezolid, daptomycin, amikacin, colistin). Restriction of antibiotic prophylaxis to the high-risk populations, prevention of antibiotic overuse, and early de-escalation policies are also mandatory to prevent the spread of MDR bacteria in cirrhosis.

Genotypic characteristics of multidrug-resistant Escherichia coli isolates associated with urinary tract infections

Escherichia coli is an important pathogen involved in community-acquired urinary tract infections (CA-UTIs). In this study, we analyzed the prevalence of frequently occurring genes and the distribution of integrons in 51 multidrug-resistant (MDR) E. coli isolates associated with CA-UTIs. The clonality of these strains was investigated by phylogrouping, multi-locus sequence typing, and pulsed-field gel electrophoresis (PFGE). All these strains were found to produce two or more resistance determinants, ceftazidime-hydrolyzing CTX-M-type extended-spectrum β-lactamases (ESBLs) and plasmid-mediated quinolone resistance determinants were the most prevalent (92.2% and 51.0%, respectively). A sulfhydryl variable-61-producing E. coli strain was identified for the first time in China. The prevalence of class 1 integrons was 54.9%, class 2 integrons were detected in three isolates but no isolate contained a class 3 integron. Phylogenetic group D was the dominant, observed in 70.6% of the isolates. PFGE analysis revealed a high level of diversity. Twenty-four distinctive sequence types (STs) including four major STs (ST648, ST224, ST38, and ST405) were identified. To our knowledge, this is the first report on the characterization of MDR E. coli isolates associated with CA-UTIs in China; our results suggest that an MDR D-ST648 clone producing CTX-M-ESBLs has emerged as a major clone in the community setting.

Carbapenem-resistant Klebsiella pneumoniae exhibit variability in capsular polysaccharide and capsule associated virulence traits

BACKGROUND

Novel therapies are urgently needed to treat carbapenem-resistant Klebsiella pneumoniae (CR-Kp)-mediated infection, which constitute a major health threat in the United States. In order to assess if it is feasible to develop anticapsular antibodies as a potential novel therapy, it is crucial to first systematically characterize capsular polysaccharide (CPS) and virulence traits in these strains.

METHODS

Forty CR-Kp were genotyped by pulsed field gel electrophoresis, multilocus sequence typing (MLST), and molecular capsule typing (C-patterns and wzi sequencing). Their biofilm formation, serum resistance, macrophage-mediated killing, and virulence in Galleria mellonella were compared. MAb (1C9) was generated by co-immunization with 2 CPSs, and cross-reactivity was investigated.

RESULTS

MLST assigned 80% of CR-Kp isolates to the ST258-clone. Molecular capsule typing identified new C-patterns, including C200/wzi-154, which was widely represented and associated with blaKPC-3-bearing strains. Heterogeneity was detected in biofilm formation and macrophage-mediated killing. Differences in serum resistance correlated with virulence in G. mellonella. ST258 strains carrying blaKPC-3 were less virulent than those with blaKPC-2. MAb 1C9 cross-reacted with 58% of CR-Kp CPSs.

CONCLUSIONS

CR-Kp ST258 strains exhibit variability of virulence-associated traits. Differences were associated with the type of KPC gene and CPS. Identification of cross-reacting anti-CPS mAbs encourages their development as adjunctive therapy.

MALDI-TOF mass spectrometry as a tool for the discrimination of high-risk Escherichia coli clones from phylogenetic groups B2 (ST131) and D (ST69, ST405, ST393)

Reliable, quick and low-cost methods are needed for the early detection of multidrug-resistant and highly virulent high-risk B2 and D Escherichia coli clones or clonal complexes (HiRCC). Matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS) seems to have a good discriminatory potential at different subspecies levels, but it was never evaluated for the discrimination of E. coli clones. We assessed the potential of MALDI-TOF MS coupled to multivariate data analysis to discriminate representative E. coli B2 and D HiRCC. Seventy-three E. coli isolates from B2 (including ST131 and B2 non-ST131 clones) and D (ST69, ST393, ST405) with variable pulsed-field gel electrophoresis (PFGE) patterns, origins and dates (1980-2010) were tested. MS spectra were acquired from independent extracts obtained from different plate cultures in two different Microflex LT MALDI-TOF devices (Bruker) after a standard extraction procedure. MALDI-TOF MS fingerprinting analysis revealed a good discriminatory ability between the four HiRCC analysed (ST131, ST69, ST405, ST393) and between B2 ST131 and other B2 non-ST131 isolates. Clusters defined by MALDI-TOF MS were consistent with the clonal complexes assigned by multilocus sequence typing (MLST), although differences were detected regarding the composition of clusters obtained by the comparison of PFGE profiles. We demonstrate, for the first time, that characteristic mass fingerprints of different E. coli HiRCC are sufficiently discriminatory and robust to enable their differentiation by MALDI-TOF MS, which might represent a promising tool for the optimisation of infection control, individual patient management and large-scale epidemiological studies of public health relevance. The good correlation between phenotypic and genotypic features further corroborates phylogenetic relationships delineated by MLST.

Travel-related carbapenemase-producing Gram-negative bacteria in Alberta, Canada: the first 3 years

We describe here the characteristics of Alberta, Canada, patients with infections or colonizations with carbapenemase-producing Gram-negative bacteria during 2010 to 2013 that were linked to recent travel outside Canada. Antimicrobial susceptibility was determined by broth microdilution, and isolates were characterized using PCR, sequencing, and multilocus sequencing typing. A broth mating study was used to assess the transferability of resistance plasmids, which were subsequently characterized. All the patients (n=12) included in our study had contact with a health care system while abroad. Most of the patients presented with urinary tract infections (UTIs) and were admitted to hospitals within weeks after their return to Alberta. Secondary spread occurred in 1 case, resulting in the death of another patient. The carbapenemase-producing bacteria (n=17) consisted of Escherichia coli (sequence type 101 [ST101], ST365, ST405, and ST410) with NDM-1, Klebsiella pneumoniae (ST15, ST16, ST147, ST258, ST340, ST512, and ST972) with NDM-1, OXA-181, KPC-2, and KPC-3, Acinetobacter baumannii with OXA-23, Providencia rettgeri with NDM-1, Enterobacter cloacae with KPC-2, and Citrobacter freundii with NDM-1. The blaNDM-1 gene was associated with various narrow- (i.e., IncF) and broad- (i.e., IncA/C and IncL/M) host-range plasmids with different addiction factors. Our results show that NDM-producing K. pneumoniae, belonging to a variety of sequence types with different plasmid scaffolds, are regularly imported from India into Alberta. Clinical microbiology laboratories should remain vigilant in detecting bacteria with carbapenemases.

NBTI 5463 is a novel bacterial type II topoisomerase inhibitor with activity against gram-negative bacteria and in vivo efficacy

The need for new antibiotics that address serious Gram-negative infections is well recognized. Our efforts with a series of novel bacterial type II topoisomerase inhibitors (NBTIs) led to the discovery of NBTI 5463, an agent with improved activity over other NBTIs against Gram-negative bacteria, in particular against Pseudomonas aeruginosa (F. Reck, D. E. Ehmann, T. J. Dougherty, J. V. Newman, S. Hopkins, G. Stone, N. Agrawal, P. Ciaccio, J. McNulty, H. Barthlow, J. O'Donnell, K. Goteti, J. Breen, J. Comita-Prevoir, M. Cornebise, M. Cronin, C. J. Eyermann, B. Geng, G. R. Carr, L. Pandarinathan, X. Tang, A. Cottone, L. Zhao, N. Bezdenejnih-Snyder, submitted for publication). In the present work, NBTI 5463 demonstrated promising activity against a broad range of Gram-negative pathogens. In contrast to fluoroquinolones, the compound did not form a double-strand DNA cleavable complex with Escherichia coli DNA gyrase and DNA, but it was a potent inhibitor of both DNA gyrase and E. coli topoisomerase IV catalytic activities. In studies with P. aeruginosa, NBTI 5463 was bactericidal. Resistant mutants arose at a low rate, and the mutations were found exclusively in the nfxB gene, a regulator of the MexCD-OprJ efflux system. Levofloxacin-selected resistance mutations in GyrA did not result in decreased susceptibility to NBTI 5463. Animal infection studies demonstrated that NBTI 5463 was efficacious in mouse models of lung, thigh, and ascending urinary tract infections.

Acinetobacter phage genome is similar to Sphinx 2.36, the circular DNA copurified with TSE infected particles

While analyzing plasmids of Acinetobacter sp. DS002 we have detected a circular DNA molecule pTS236, which upon further investigation is identified as the genome of a phage. The phage genome has shown sequence similarity to the recently discovered Sphinx 2.36 DNA sequence co-purified with the Transmissible Spongiform Encephalopathy (TSE) particles isolated from infected brain samples collected from diverse geographical regions. As in Sphinx 2.36, the phage genome also codes for three proteins. One of them codes for RepA and is shown to be involved in replication of pTS236 through rolling circle (RC) mode. The other two translationally coupled ORFs, orf106 and orf96, code for coat proteins of the phage. Although an orf96 homologue was not previously reported in Sphinx 2.36, a closer examination of DNA sequence of Sphinx 2.36 revealed its presence downstream of orf106 homologue. TEM images and infection assays revealed existence of phage AbDs1 in Acinetobacter sp. DS002.

Characterization of third-generation cephalosporin-resistant Escherichia coli from bloodstream infections in Denmark

The aim of the study was to investigate the molecular epidemiology of 87 third-generation cephalosporin-resistant Escherichia coli (3GC-R Ec) from bloodstream infections in Denmark from 2009. Sixty-eight of the 87 isolates were extended-spectrum beta-lactamase (ESBL) producers, whereas 17 isolates featured AmpC mutations only (without a coexpressed ESBL enzyme) and 2 isolates were producing CMY-22. The majority (82%) of the ESBL-producing isolates in our study were CTX-M-15 producers and primarily belonged to phylogroup B2 (54.4%) or D (23.5%). Further, one of the two CMY-22-producing isolates belonged to B2, whereas only few of the other AmpCs isolates belonged to B2 and D. Pulsed-field gel electrophoresis revealed that both clonal and nonclonal spread of 3GC-R Ec occurred. ST131 was detected in 50% of ESBL-producing isolates. The remaining ESBL-producing isolates belonged to 17 other sequence types (STs), including several other internationally spreading STs (e.g., ST10, ST69, and ST405). The majority (93%) of the ESBL-producing isolates and one of the CMY-22-producing isolates were multiresistant. In conclusion, 3GC-R in bacteriaemic E. coli in Denmark was mostly due to ESBL production, overexpression of AmpC, and to a lesser extent to plasmid-mediated AmpC. The worldwide disseminated CTX-M-15-ST131 was strongly represented in this collection of Danish, bacteriaemic E. coli isolates.

Comparative study of genotype and virulence in CTX-M-producing and non-extended-spectrum-β-lactamase-producing Klebsiella pneumoniae isolates

Molecular and virulence characteristics of CTX-M-producing and non-extended-spectrum-β-lactamase (non-ESBL)-producing Klebsiella pneumoniae isolates were compared. Lack of shared characteristics between the two groups suggested that most CTX-M-producing K. pneumoniae isolates in South Korea did not occur by transfer of blaCTX-M into susceptible strains. Conjugation assays confirmed that the plasmid with the blaCTX-M-15 gene confers virulence as well as antimicrobial resistance, suggesting that a CTX-M-15-producing clone such as ST11 may have a selective advantage even without antibiotic pressure.

Carbapenem-resistant Pseudomonas aeruginosa strains from a Spanish hospital: characterization of metallo-beta-lactamases, porin OprD and integrons

Molecular typing and mechanisms of carbapenem resistance such as alterations in porin OprD and presence of metallo-beta-lactamases (MBLs), as well as integrons have been studied in a collection of carbapenem-resistant Pseudomonas aeruginosa (CRPA) isolates from a Spanish hospital. One hundred and twenty-three CRPA isolates were recovered from different samples of 80 patients. Clonal relationship among CRPA was analyzed by SpeI-PFGE. Susceptibility testing to 11 antibiotics and MBL phenotype was determined by microdilution, IP/IPI E-test and double disc method. The oprD gene was studied by PCR and sequencing, and mutations were determined comparing with P. aeruginosa PAO1 sequence. Characterization of MBLs, and class 1 and 2 integrons were studied by PCR and sequencing. SDS-PAGE analysis of outer membrane proteins of selected strains was performed. Seventy-four-per-cent of patients with CRPA were hospitalised in the ICU setting and 50% had long hospitalization stays. Sixty-four different PFGE patterns were detected, and 87 CRPA strains were further analyzed. MBL phenotype was detected in 43 of 87 strains (49.4%), which contained blaVIM-2 gene inside class 1 integrons. VIM-2-producing strains belonged to lineages ST175, ST235, and ST973. A great diversity of nucleotide insertions, deletions, and mutations in oprD gene, and the presence of a new insertion sequence (ISPa45) truncating oprD were identified among CRPA strains. Class 1 integrons were detected in 75% of CRPA strains, blaVIM-2 and the new arrangement aac(3)-Ia+ISPa34+aadA1 (named as In661) being the most frequent gene-cassette arrays detected. Other gene cassettes detected in integrons were: aadB, aadA6, aadA7, aac(6')-Ib', and blaOXA-46.

Comparison of local features from two Spanish hospitals reveals common and specific traits at multiple levels of the molecular epidemiology of metallo-β-lactamase-producing Pseudomonas spp

Twenty-seven well-characterized metallo-β-lactamase (MBL)-producing Pseudomonas strains from two distantly located hospitals were analyzed. The results revealed specific features defining the multilevel epidemiology of strains from each hospital in terms of species, clonality, predominance of high-risk clones, composition/diversity of integrons, and linkages of Tn402-related structures. Therefore, despite the global trends driving the epidemiology of MBL-producing Pseudomonas spp., the presence of local features has to be considered in order to understand this threat and implement proper control strategies.