Molecular characterization of plasmids encoding CTX-M-15 -lactamases from Escherichia coli strains in the United Kingdom

Distribution and expression of the aac(6')-Im (aacA16) aminoglycoside resistance gene

BACKGROUND

The aac(6')-Im (aacA16) amikacin, netilmicin and tobramycin resistance gene cassette had been circulating globally undetected for many years in a sublineage of Acinetobacter baumannii global clone 2.

OBJECTIVES

To identify sources for the aac(6')-Im fragment found in A. baumannii.

METHODS

MinION long-read sequencing and Unicycler hybrid assemblies were used to determine the genetic context of the aac(6')-Im gene. Quantitative reverse transcriptase PCR was used to measure expression.

RESULTS

Among >60 000 non-Acinetobacter draft genomes in the MRSN collection, the aac(6')-Im gene was detected in Pseudomonas putida and Enterobacter hormaechei isolates recovered from patients in Thailand between 2016 and 2019. Genomes of multiply resistant P. putida MRSN365855 and E. hormaechei MRSN791417 were completed. The class 1 integron containing the aac(6')-Im cassette was in the chromosome in MRSN365855, and in an HI2 plasmid in MRSN791417. However, MRSN791417 was amikacin susceptible and the gene was not expressed due to loss of the Pc promoter of the integron. Further examples of aac(6')-Im in plasmids from or the chromosome of various Gram-negative species were found in the GenBank nucleotide database. The aac(6')-Im context in integrons in pMRSN791417-8 and a Klebsiella plasmid pAMR200031 shared similarities with the aac(6')-Im region of AbGRI2-Im islands in A. baumannii. In other cases, the cassette array including the aac(6')-Im cassette was different.

CONCLUSIONS

The aac(6')-Im gene is widespread, being found so far in several different species and in several different gene cassette arrays. The lack of amikacin resistance in E. hormaechei highlights the importance of correlating resistance gene content and antibiotic resistance phenotype.

Extended-Spectrum β-Lactamase-Producing Escherichia coli and Klebsiella pneumoniae: Risk Factors and Economic Burden Among Patients with Bloodstream Infections

Introduction

Although Extended-spectrum β-lactamase-producing Escherichia coli and Klebsiella pneumoniae (ESBL-EK) significantly contribute to bloodstream infections, their economic repercussions remain largely unquantified.

Data Source and Methods

We performed a retrospective analysis of inpatients diagnosed with Escherichia coli or Klebsiella pneumoniae bacteremia in a tertiary hospital from January 2020 to December 2022 in Guangzhou, China. We employed the chi-square test to examine ESBL risk factors and utilized propensity score matching (PSM) to negate baseline confounding factors, assessing economic burden through disability-adjusted life years (DALYs), hospital costs and productivity losses. We employed mediation analysis to eliminate confounding factors and better identify ESBL sources of burden related.

Results

We found 166 ESBL-EC/KP BSI patients (52.2% of the total examined 318 patients). Post-PSM analysis revealed that ESBL-producing EC/KP will reduce the effectiveness of empirical medication by 19.8%, extend the total length of hospitalization by an average of 3 days, and increase the patient's financial burden by US$2047. No significant disparity was found in overall mortality and mean DALYs between the groups. Mediation analysis showed that the link between ESBL and hospital costs is predominantly, if not entirely, influenced by the appropriateness of empirical antibiotic treatment and length of hospital stay.

Conclusion

Patients with BSI due to ESBL-producing ESBL-EK incur higher costs compared to those with non-ESBL-EK BSI. This cost disparity is rooted in varying rates of effective empirical antimicrobial therapy and differences in hospital stay durations. A nuanced approach, incorporating a thorough understanding of regional epidemiological trends and judicious antibiotic use, is crucial for mitigating the financial impact on patients.

Occurrence, Phenotypic and Molecular Characteristics of Extended-Spectrum Beta-Lactamase-Producing Escherichia coli in Healthy Turkeys in Northern Egypt

Poultry is one of the most important reservoirs for zoonotic multidrug-resistant pathogens. The indiscriminate use of antimicrobials in poultry production is a leading factor for development and dissemination of antimicrobial resistance. This study aimed to describe the prevalence and antimicrobial resistance of E. coli isolated from healthy turkey flocks of different ages in Nile delta region, Egypt. In the current investigation, 250 cloacal swabs were collected from 12 turkey farms in five governorates in the northern Egypt. Collected samples were cultivated on Brilliance^TM ESBL agar media supplemented with cefotaxime (100 mg/L). The E. coli isolates were identified using MALDI-TOF-MS and confirmed by a conventional PCR assay targeting 16S rRNA-DNA. The phenotypic antibiogram against 14 antimicrobial agents was determined using the broth micro-dilution method. DNA-microarray-based assay was applied for genotyping and determination of both, virulence and resistance-associated gene markers. Multiplex real-time PCR was additionally applied for all isolates for detection of the actual most relevant Carbapenemase genes. The phenotypic identification of colistin resistance was carried out using E-test. A total of 26 E. coli isolates were recovered from the cloacal samples. All isolates were defined as multidrug-resistant. Interestingly, two different E. coli strains were isolated from one sample. Both strains had different phenotypic and genotypic profiles. All isolates were phenotypically susceptible to imipenem, while resistant to penicillin, rifampicin, streptomycin, and erythromycin. None of the examined carbapenem resistance genes was detected among isolates. At least one beta-lactamase gene was identified in most of isolates, where blaTEM was the most commonly identified determinant (80.8%), in addition to blaCTX-M9 (23.1%), blaSHV (19.2%) and blaOXA-10 (15.4%). Genes associated with chloramphenicol resistance were floR (65.4%) and cmlA1 (46.2%). Tetracycline- and quinolone-resistance-associated genes tetA and qnrS were detected in (57.7%) and (50.0%) of isolates, respectively. The aminoglycoside resistance associated genes aadA1 (65.4%), aadA2 (53.8%), aphA (50.0%), strA (69.2%), and strB (65.4%), were detected among isolates. Macrolide resistance associated genes mph and mrx were also detected in (53.8%) and (34.6%). Moreover, colistin resistance associated gene mcr-9 was identified in one isolate (3.8%). The class 1 integron integrase intI1 (84.6%), transposase for the transposon tnpISEcp1 (34.6%) and OqxB -integral membrane and component of RND-type multidrug efflux pump oqxB (7.7%) were identified among the isolates. The existing high incidence of ESBL/colistin-producing E. coli identified in healthy turkeys is a major concern that demands prompt control; otherwise, such strains and their resistance determinants could be transmitted to other bacteria and, eventually, to people via the food chain.

Veterinary clinic surfaces as reservoirs of multi-drug- and biocide-resistant Gram-negative bacteria

This cross-sectional study was carried out to determine the common Gram-negative bacteria (GNB) contaminating veterinary clinic environments, and to evaluate the susceptibility of the isolates to commonly used antibiotics and biocides. A total of 62 swab samples were collected from different frequently touched surfaces in the 4 veterinary clinics visited. The samples were processed for isolation and identification of GNB using standard microbiological procedures. The susceptibility of the isolates to disinfectants and antibiotics was determined using agar dilution and disc diffusion techniques, respectively. A total of 114 GNB were isolated from the 4 clinics with isolation rates of 21.9, 22.8, 23.7 and 31.6% in clinics A, B, C and D, respectively. The surfaces of treatment tables were more contaminated (16.7 %) than receptionist/clinician desks (15.8%), weighing balances (10.5 %), door handles (7.9 %), drip stands (7.9 %), handwashing basins (7.0 %) and client chairs (7.0%). The surface-contaminating isolates were distributed into 20 genera, with members of Enterobacteriaceae predominating (n=97). Fifty-nine per cent of the isolates were resistant to the disinfectant Septol, while 5.3 and 0.9% were resistant to Purit and Dettol disinfectants, respectively. Multiple drug resistance was observed among 99% of the isolates with approximately 100% resistance to beta-lactams. Phenotypic expression of extended-spectrum (3.5 %) and AmpC beta-lactamase (38.6 %) production was detected. These findings highlight the role of clinic environments in serving as reservoirs for potential pathogens and sources for the spread of multi-drug resistant GNB.

Semirapid Detection of Piperacillin/Tazobactam Resistance and Extended-Spectrum Resistance to β-Lactams/β-Lactamase Inhibitors in Clinical Isolates of Escherichia coli

Piperacillin/tazobactam (TZP) is a β-lactam/β-lactamase inhibitor (BL/BLI) recommended for the empirical treatment of severe infections. The excessive and indiscriminate use of TZP has promoted the emergence of TZP-resistant Escherichia coli isolates. Recently, we demonstrated that TZP may contribute to the development of extended-spectrum resistance to BL/BLI (ESRI) in E. coli isolates that are TZP susceptible but have low-level resistance to BL/BLI (resistance to amoxicillin/clavulanic acid [AMC] and/or ampicillin/sulbactam [SAM]). This raises the need for the development of rapid detection systems. Therefore, the objective of this study was to design and validate a method able to detect TZP resistance and ESRI in E. coli. A colorimetric assay based on β-lactam ring hydrolysis by β-lactamases was designed (ESRI test). A total of 114 E. coli isolates from bloodstream and intra-abdominal sources, characterized according to their susceptibility profiles to BL/BLI, were used. Detection of the three most frequent β-lactamases involved in BL/BLI resistance (bla_TEM, bla_OXA-1, and bla_SHV) was performed by PCR. The ESRI test was able to detect all the TZP-intermediate/-resistant isolates, as well as all the TZP-susceptible isolates with a capacity for ESRI development. Their median times to results were 5 and 30 min, respectively. All the isolates without resistance to BL/BLI displayed a negative result in the ESRI test. bla_TEM was the most frequent β-lactamase gene detected, follow by bla_SHV and bla_OXA-1. These results demonstrate the efficacy of the ESRI test, showing great clinical potential which could lead to reductions in health costs, ineffective treatments, and inappropriate use of BL/BLI.

IMPORTANCE TZP is a BL/BLI recommended for the empirical treatment of severe infections. The excessive use of TZP has promoted the emergence of TZP-resistant Escherichia coli isolates. We recently reported that TZP may contribute to the development of ESRI in E. coli isolates that are TZP susceptible but have low-level resistance to BL/BLI. This raises the need for the development of rapid detection systems. Here, we demonstrated that the ESRI test was able to detect the TZP-intermediate or -resistant isolates and the TZP-susceptible isolates with the capacity for ESRI development. All the isolates without BL/BLI resistance were negative for the ESRI test and did not harbor β-lactamase genes. For ESRI developers and TZP-intermediate or -resistant isolates, bla_TEM was the most frequent β-lactamase gene detected, follow by bla_SHV and bla_OXA-1. The sensitivity, specificity, and positive and negative predictive values were all 100%. These data demonstrate the efficacy of the ESRI test and show that it has great clinical potential.

Recent strategies for inhibiting multidrug-resistant and β-lactamase producing bacteria: A review

β-lactam antibiotics are one of the most commonly used drugs for treating bacterial infections, but their clinical effectiveness has been severely affected with bacteria developing resistance against their action. Production of β-lactamase enzymes by bacteria that can degrade β-lactams is the most common mechanism of acquiring such resistance, leading to the emergence of multiple-drug resistance in them. Therefore, the development of efficient approaches to combat infections caused by β-lactamase producing and multidrug-resistant bacteria is the need of the hour. The present review attempts to understand such recent strategies that are in line for development as potential alternatives to conventional antibiotics. We find that apart from efforts being made to develop new antibiotics, several other approaches are being explored, which can help tackle infections caused by resistant bacteria. This includes the development of plant-based drugs, antimicrobial peptides, nano-formulations, bacteriophage therapy, use of CRISPR-Cas9, RNA silencing and antibiotic conjugates with nanoparticles of antimicrobial peptides. The mechanism of action of these novel approaches and potential issues limiting their translation from laboratory to clinics is also discussed. The review is important from an interesting knowledge base which can be useful for researchers working in this domain.

Plasmids shape the diverse accessory resistomes of Escherichia coli ST131

The human gut microbiome includes beneficial, commensal and pathogenic bacteria that possess antimicrobial resistance (AMR) genes and exchange these predominantly through conjugative plasmids. Escherichia coli is a significant component of the gastrointestinal microbiome and is typically non-pathogenic in this niche. In contrast, extra-intestinal pathogenic E. coli (ExPEC) including ST131 may occupy other environments like the urinary tract or bloodstream where they express genes enabling AMR and host cell adhesion like type 1 fimbriae. The extent to which commensal E. coli and uropathogenic ExPEC ST131 share AMR genes remains understudied at a genomic level, and we examined this here using a preterm infant resistome. We found that individual ST131 had small differences in AMR gene content relative to a larger shared resistome. Comparisons with a range of plasmids common in ST131 showed that AMR gene composition was driven by conjugation, recombination and mobile genetic elements. Plasmid pEK499 had extended regions in most ST131 Clade C isolates, and it had evidence of a co-evolutionary signal based on protein-level interactions with chromosomal gene products, as did pEK204 that had a type IV fimbrial pil operon. ST131 possessed extensive diversity of selective type 1, type IV, P and F17-like fimbriae genes that was highest in subclade C2. The structure and composition of AMR genes, plasmids and fimbriae vary widely in ST131 Clade C and this may mediate pathogenicity and infection outcomes.

Successful High-Dosage Monotherapy of Tigecycline in a Multidrug-Resistant Klebsiella pneumoniae Pneumonia-Septicemia Model in Rats

Background: Recent scientific reports on the use of high dose tigecycline monotherapy as a “drug of last resort” warrant further research into the use of this regimen for the treatment of severe multidrug-resistant, Gram-negative bacterial infections. In the current study, the therapeutic efficacy of tigecycline monotherapy was investigated and compared to meropenem monotherapy in a newly developed rat model of fatal lobar pneumonia–septicemia. Methods: A Klebsiella pneumoniae producing extended-spectrum β-lactamase (ESBL) and an isogenic variant producing K. pneumoniae carbapenemase (KPC) were used in the study. Both strains were tested for their in vitro antibiotic susceptibility and used to induce pneumonia–septicemia in rats, which was characterized using disease progression parameters. Therapy with tigecycline or meropenem was initiated at the moment that rats suffered from progressive infection and was administered 12-hourly over 10 days. The pharmacokinetics of meropenem were determined in infected rats. Results: In rats with ESBL pneumonia–septicemia, the minimum dosage of meropenem achieving survival of all rats was 25 mg/kg/day. However, in rats with KPC pneumonia–septicemia, this meropenem dosage was unsuccessful. In contrast, all rats with KPC pneumonia–septicemia were successfully cured by administration of high-dose tigecycline monotherapy of 25 mg/kg/day (i.e., the minimum tigecycline dosage achieving 100% survival of rats with ESBL pneumonia–septicemia in a previous study). Conclusions: The current study supports recent literature recommending high-dose tigecycline as a last resort regimen for the treatment of severe multidrug-resistant bacterial infections. The use of ESBL- and KPC-producing K. pneumoniae strains in the current rat model of pneumonia–septicemia enables further investigation, helping provide supporting data for follow-up clinical trials in patients suffering from severe multidrug-resistant bacterial respiratory infections.

Contrasting patterns of longitudinal population dynamics and antimicrobial resistance mechanisms in two priority bacterial pathogens over 7 years in a single center

BACKGROUND

Two of the most important pathogens contributing to the global rise in antimicrobial resistance (AMR) are Klebsiella pneumoniae and Enterobacter cloacae. Despite this, most of our knowledge about the changing patterns of disease caused by these two pathogens is based on studies with limited timeframes that provide few insights into their population dynamics or the dynamics in AMR elements that they can carry.

RESULTS

We investigate the population dynamics of two priority AMR pathogens over 7 years between 2007 and 2012 in a major UK hospital, spanning changes made to UK national antimicrobial prescribing policy in 2007. Between 2006 and 2012, K. pneumoniae showed epidemiological cycles of multi-drug-resistant (MDR) lineages being replaced approximately every 2 years. This contrasted E. cloacae where there was no temporally changing pattern, but a continuous presence of the mixed population.

CONCLUSIONS

The differing patterns of clonal replacement and acquisition of mobile elements shows that the flux in the K. pneumoniae population was linked to the introduction of globally recognized MDR clones carrying drug resistance markers on mobile elements. However, E. cloacae carries a chromosomally encoded ampC conferring resistance to front-line treatments and shows that MDR plasmid acquisition in E. cloacae was not indicative of success in the hospital. This led to markedly different dynamics in the AMR populations of these two pathogens and shows that the mechanism of the resistance and its location in the genome or mobile elements is crucial to predict population dynamics of opportunistic pathogens in clinical settings.

Antimicrobial activity of two novel antimicrobial peptides AA139 and SET-M33 against clinically and genotypically diverse Klebsiella pneumoniae isolates with differing antibiotic resistance profiles

Colistin is an antimicrobial peptide (AMP) used as a drug of last resort, although plasmid-mediated colistin resistance (MCR) has been reported. AA139 and SET-M33 are novel AMPs currently in development for the treatment of multidrug-resistant (MDR) Gram-negative bacterial infections. As many AMPs have a similar mode of action to colistin, potentially leading to cross-resistance, the antimicrobial activity of AA139 and SET-M33 was investigated against a collection of 50 clinically and genotypically diverse Klebsiella pneumoniae isolates with differing antibiotic resistance profiles, including colistin-resistant strains. The collection was genotypically characterised and susceptibility to clinically relevant antibiotics was determined. Susceptibility to AA139 and SET-M33 did not differ among the collection despite differences in underlying mechanisms of resistance or susceptibility to colistin. For three colistin-susceptible and three colistin-resistant strains with distinct MDR profiles as well as an additional MCR-producing strain, the bactericidal activity of AA139, SET-M33 and colistin during 24 h of exposure was examined. Following 24 h of exposure to AA139, SET-M33 or colistin, the seven strains were tested for changes in susceptibility to the respective AMPs. AA139 and SET-M33 showed a concentration-dependent bactericidal effect irrespective of bacterial susceptibility to colistin. Exposure to low colistin concentrations resulted in the development of colistin resistance in colistin-susceptible strains, whereas susceptibility to AA139 and SET-M33 following exposure to the respective AMPs was maintained. The two novel AMPs remained effective against colistin-resistant strains and may be promising novel drugs for the treatment of clinically and genotypically diverse MDR K. pneumoniae infections, including infections associated with colistin-resistant bacteria.

Transmission and persistence of IncF conjugative plasmids in the gut microbiota of full-term infants

Conjugative plasmids represent major reservoirs for horizontal transmission of antibiotic resistance and virulence genes. Our knowledge about the ecology and persistence of these plasmids in the gut microbiota remains limited. The IncF plasmids are the most widespread in clinical samples and in healthy humans and the main aim of this work was to study their ecology and association with the developing gut microbiota. Using a longitudinal (2, 10, 30 and 90 days) cohort of full-term infants, we investigated the transmission and persistence of IncFIA and IncFIB plasmids. The prevalence of IncFIB plasmids was higher than IncFIA in the cohort, while IncFIA always co-occurred with IncFIB. However, the relative gene abundance of IncFIA was significantly higher than IncFIB for all time points, indicating that IncFIA may be a higher copy-number plasmid. Through linear discriminant analysis effect size and operational taxonomic unit-level associations, we observed major differences in the abundance of Enterobacteriaceae in samples positive and negative for IncFIB. This association was significant at 2, 10 and 30 days and showed an association with vaginal delivery. From shot-gun analyses, we assembled de novo multi-replicon shared (IncFIA/IncFIB) and integrated (IncFIA/IB) plasmids that were persistent through the dataset. Overall, the study demonstrates the nature of IncF plasmids in complex microbial communities.

Antimicrobial resistance in Enterobacteriaceae from healthy broilers in Egypt: emergence of colistin-resistant and extended-spectrum β-lactamase-producing Escherichia coli

Background

Poultry remains one of the most important reservoir for zoonotic multidrug resistant pathogens. The global rise of antimicrobial resistance in Gram-negative bacteria is of reasonable concern and demands intensified surveillance.

Methods

In 2016, 576 cloacal swabs were collected from 48 broiler farms located in five governorates in northern Egypt. Isolates of Enterobacteriaceae could be cultivated on different media and were identified by MALDI-TOF MS and PCR. Escherichia coli isolates were genotyped by DNA-microarray-based assays. The antimicrobial susceptibility to 14 antibiotics was determined and resistance-associated genes were detected. The VITEK-2 system was applied for phenotypical confirmation of extended-spectrum β-lactamase-producing isolates. The determination of colistin resistance was carried out phenotypically using E-test and genotypically using PCR for detection of the mcr-1 gene.

Results

Out of 576 samples, 72 representatives of Enterobacteriaceae were isolated and identified as 63 E. coli (87.5%), 5 Enterobacter cloacae (6.9%), 2 Klebsiella pneumoniae (2.8%) and 2 Citrobacter spp. (2.8%). Seven out of 56 cultivated E. coli (12.5%) were confirmed as ESBL-producing E. coli and one isolate (1.8%) as ESBL/carbapenemase-producing E. coli. Five out of 63 E. coli isolates (7.9%) recovered from different poultry flocks were phenotypically resistant to colistin and harboured mcr-1 gene.

Conclusions

This is the first study reporting colistin resistance and emergence of multidrug resistance in Enterobacteriaceae isolated from healthy broilers in the Nile Delta region, Egypt. Colistin-resistant E. coli in poultry is of public health significance. The global rise of ESBL- and carbapenemase-producing Gram-negative bacteria demands intensified surveillance. ESBL-producing E. coli in poultry farms in Egypt are of major concern that emphasizes the possibility of spread of such strains to humans. The results also reinforce the need to develop strategies and to implement specific control procedures to reduce the use of antibiotics.

Escherichia coli: an old friend with new tidings

Escherichia coli is one of the most-studied microorganisms worldwide but its characteristics are continually changing. Extraintestinal E. coli infections, such as urinary tract infections and neonatal sepsis, represent a huge public health problem. They are caused mainly by specialized extraintestinal pathogenic E. coli (ExPEC) strains that can innocuously colonize human hosts but can also cause disease upon entering a normally sterile body site. The virulence capability of such strains is determined by a combination of distinctive accessory traits, called virulence factors, in conjunction with their distinctive phylogenetic background. It is conceivable that by developing interventions against the most successful ExPEC lineages or their key virulence/colonization factors the associated burden of disease and health care costs could foreseeably be reduced in the future. On the other hand, one important problem worldwide is the increase of antimicrobial resistance shown by bacteria. As underscored in the last WHO global report, within a wide range of infectious agents including E. coli, antimicrobial resistance has reached an extremely worrisome situation that ‘threatens the achievements of modern medicine’. In the present review, an update of the knowledge about the pathogenicity, antimicrobial resistance and clinical aspects of this ‘old friend’ was presented.

Genotyping and characterization of CTX-M-15 -producing Klebsiella pneumoniae isolated from an Iranian hospital

The aims were to describe the genetic characterization of blaCTX-M-1 group gene in Klebsiella pneumoniae and to investigate the relationship between isolates by MLVA and PFGE. We analyzed 36 CTX-M group 1-ESBL producing K. pneumoniae. rmpA and wcaG virulence genes were identified by PCR. The genetic environment of blaCTX-M-1 was analyzed by PCR and sequencing. Plasmid replicons were determined using PCR-based replicon typing. The isolates were typed by MLVA and PFGE. All blaCTX-M-1 were blaCTX-M-15. The wcaG and rmpA were detected in 1 and 2 isolates, respectively. IncF were the most frequently detected replicons (63.88%). In all isolates, ISEcp1 was found upstream and orf477 downstream of blaCTX-M-15, IS26 was found in two isolates. MLVA identified 20 MLVA types, whereas PFGE identified 25 different profiles. The dissemination of CTX-M-15 in our isolates was due to the clonal spread of isolates and to the genetic transfer of mobile elements among unrelated strains.

Emerging Perils of Extended Spectrum β-Lactamase Producing Enterobacteriaceae Clinical Isolates in a Teaching Hospital of Nepal

Introduction. Infections due to extended spectrum β-lactamase producing Enterobacteriaceae are on the rise. They pose serious public health problems due to their resistance to large number of antibiotics. However, little is known about the genotypes of ESBL from Nepal. Therefore, the study presents results of phenotypic and molecular characterization of ESBL producing Escherichia coli and Klebsiella spp. isolated from various clinical specimens in a tertiary care teaching hospital of Nepal. Methods. A total of 172 Enterobacteriaceae clinical isolates recovered from various clinical specimens were analyzed for their antibiotic susceptibility test. Detection of ESBLs was carried out using combination disk test and multiplex PCR for their genotypes (CTX-M, SHV, and TEM). Results. Out of 172 clinical isolates, 70 (40.6%) of them were found ESBL producers. The major source of ESBL producers was urinary tract samples and the highest ESBL production was observed in Escherichia coli (46.5%). Among ESBL genotypes, CTX-M (91.4%) was most predominant, followed by TEM (65.7%) and SHV (11.4%) in both of the isolates. Conclusions. High level of drug resistance and ESBL production was observed among the clinical isolates. There is a need for longitudinal and nationwide surveillance for drug resistance in clinical isolates and antimicrobial stewardship is necessary to guide the appropriate and judicious antibiotic use.

Complete Sequence of the FII Plasmid p42-2, Carrying blaCTX-M-55, oqxAB, fosA3, and floR from Escherichia coli

We sequenced a novel conjugative multidrug resistance IncF plasmid, p42-2, isolated from Escherichia coli strain 42-2, previously identified in China. p42-2 is 106,886 bp long, composed of a typical IncFII-type backbone (∼54 kb) and one distinct acquired DNA region spanning ∼53 kb, harboring 12 antibiotic resistance genes [blaCTX-M-55, oqxA, oqxB, fosA3, floR, tetA(A), tetA(R), strA, strB, sul2, aph(3')-II, and ΔblaTEM-1]. The spread of these multidrug resistance determinants on the same plasmid is of great concern and, because of coresistance to antibiotics from different classes, is therapeutically challenging.

Plasmid-mediated quinolone resistance

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

Prevalence and characterization of extended-spectrum beta-lactamases producing Enterobacteriaceae in healthy children and associated risk factors

Background

Community acquired infections due to extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-PE) had been increased. The fecal flora of children in the community represents a huge potential reservoir for ESBLs which are located on highly transmissible plasmids. This study examined the prevalence of ESBL-PE fecal carriage, antimicrobial susceptibility pattern, possible risk factors, and characterized the genes encoding these ESBL enzymes in Lebanese children community.

Methods

A total of 125 rectal swabs were taken from healthy children aged from 1 to 5 years. Detection of ESBLs was carried out using combination-disc method test and multiplex PCR. A questionnaire concerning child’s lifestyle and risk factors for ESBL carriage was illustrated.

Results

Thirty-one of 125 participants (24.8 %) carried ESBL-PE. Regular consumption of meat, and chicken were significantly associated with high carriage rate of ESBL-PE, while dairy products (milk, yogurt, cheese) association was non-significant. Intimate hygiene habits were found also affecting the carriage rate. Multiple bla genes were the most common, 48.4 % (15/31) of ESBL-PE carried both bla_CTX-M and bla_TEM, and 22.6 % (7/31) carried bla_CTX-M, bla_SHV, and bla_TEM, 29 % (9) carried bla_CTX-M only. Concerning CTX-M-types, CTX-M-9 was the most predominant (24/31) and mostly in combination with CTX-M-15 type.

Conclusion

High rate of colonization in healthy children with ESBL-PE was observed, regular consumption of dietary products from animal source (meat or chicken) were associated with this colonization in the community in non-hospitalized children. To our best knowledge it is the first study about regular consumption of dairy product as a risk factor for ESBL-PE community carriage, the first data about the carriage rate of ESBL-PE in community children in Lebanon and Middle East, and for the wide dissemination of CTX-M-9 type in this population.

The emergence of plasmid mediated quinolone resistance qnrA2 in extended spectrum β-lactamase producing Klebsiella pneumoniae in the Middle East

Background

Klebsiella pneumoniae is one of the most important opportunistic pathogens causing serious complications in patients in hospitals and community. The clinical significance of K. pneumoniae is mainly due to its ability to acquire multiple antibiotic resistance genes. In this study we report the findings of a survey of plasmid mediated quinolone resistance in Extended-Spectrum β-lactamase (ESBL)-producing K. pneumoniae in Kuwait.

Methods

Clinical samples were collected from the microbiology laboratories of three major hospitals. Isolates were confirmed as ESBL-producers by disc diffusion method and PCR for the presence of bla genes. Antimicrobial susceptibility testing and genetic analysis were performed to detect the presence of a number of genes conferring resistance to β-lactam and fluoroquinolone antimicrobial agents including bla_SHV, bla_TEM, aac (6')-Ib-cr, qnrA, qnrB and qnrS. Pulsed-field gel electrophoresis (PFGE) was used for typing the isolates.

Results

In total 173 ESBL-producing K. pneumoniae were detected. qnr genes were identified in 27 (15.6 %) isolates and aac(6′)-Ib Ib-cr gene in 26 (96 %). One (3.7 %) contained qnrA2, 21 harbored qnrB1 (78 %) and 5 (18.5 %) contained qnrS. Twenty one (78 %) isolates contained all three bla genes. PFGE showed diverse profiles.

Conclusion

We identified for the first time the emergence of the mobile fluoroquinolone resistance qnrA2 in a clinical isolate in the middle east and also showed the dissemination of aac (6')-Ib-cr, qnrB, and qnrS genes among ESBL-producing K. pneumoniae in Kuwait. The abundance of plasmid mediated resistance to fluoroquinolones among ESBL-producing K. pneumoniae is alarming as it facilitates therapy failure. Preventing the spread of these isolates is crucial if we are to sustain the effectiveness of the limited choices we have left in antimicrobial therapy.

Molecular identification of aminoglycoside-modifying enzymes in clinical isolates of Escherichia coli resistant to amoxicillin/clavulanic acid isolated in Spain

The activity of eight aminoglycosides (amikacin, apramycin, arbekacin, gentamicin, kanamycin, neomycin, netilmicin and tobramycin) against a collection of 257 amoxicillin/clavulanic acid (AMC)-resistant Escherichia coli isolates was determined by microdilution. Aminoglycoside resistance rates, the prevalence of aminoglycoside-modifying enzyme (AME) genes, the relationship between AME gene detection and resistance phenotype to aminoglycosides, and the association of AME genes with mechanisms of AMC resistance in E. coli isolates in Spain were investigated. Aminoglycoside-resistant isolates were screened for the presence of genes encoding common AMEs [aac(3)-Ia, aac(3)-IIa, aac(3)-IVa, aac(6')-Ib, ant(2″)-Ia, ant(4')-IIa and aph(3')-Ia] or 16S rRNA methylases (armA, rmtB, rmtC and npmA). In total, 105 isolates (40.9%) were resistant to at least one of the aminoglycosides tested. Amikacin, apramycin and arbekacin showed better activity, with MIC90 values of 2mg/L (arbekacin) and 8mg/L (amikacin and apramycin). Kanamycin presented the highest MIC90 (128mg/L). The most common AME gene was aac(6')-Ib (36 strains; 34.3%), followed by aph(3')-Ia (31 strains; 29.5%), ant(2″)-Ia (29 strains; 27.6%) and aac(3)-IIa (23 strains; 21.9%). aac(3)-Ia, aac(3)-IVa, ant(4')-IIa and the four methylases were not detected. The ant(2″)-Ia gene was usually associated with OXA-1 [21/30; 70%], whilst 23/25 (92%) strains producing CTX-M-15 had the aac(6')-Ib gene. The most prevalent AME gene was aac(6')-Ib (18/41; 44%) in nosocomial isolates, whilst ant(2″)-Ia and aph(3')-Ia genes (20/64; 31%) were more frequent in strains of community origin. In 64.6% isolates the phenotypic profile correlated with the presence of commonly encountered AMEs.

Escherichia coli ST131, an intriguing clonal group

In 2008, a previously unknown Escherichia coli clonal group, sequence type 131 (ST131), was identified on three continents. Today, ST131 is the predominant E. coli lineage among extraintestinal pathogenic E. coli (ExPEC) isolates worldwide. Retrospective studies have suggested that it may originally have risen to prominence as early as 2003. Unlike other classical group B2 ExPEC isolates, ST131 isolates are commonly reported to produce extended-spectrum β-lactamases, such as CTX-M-15, and almost all are resistant to fluoroquinolones. Moreover, ST131 E. coli isolates are considered to be truly pathogenic, due to the spectrum of infections they cause in both community and hospital settings and the large number of virulence-associated genes they contain. ST131 isolates therefore seem to contradict the widely held view that high levels of antimicrobial resistance are necessarily associated with a fitness cost leading to a decrease in pathogenesis. Six years after the first description of E. coli ST131, this review outlines the principal traits of ST131 clonal group isolates, based on the growing body of published data, and highlights what is currently known and what we need to find out to provide public health authorities with better information to help combat ST131.

Dissemination of IncF-type plasmids in multiresistant CTX-M-15-producing Enterobacteriaceae isolates from surgical-site infections in Bangui, Central African Republic

Background

Surgical-site infection is the most frequent health care-associated infection in the developing world, with a strikingly higher prevalence than in developed countries We studied the prevalence of resistance to antibiotics in Enterobacteriaceae isolates from surgical-site infections collected in three major tertiary care centres in Bangui, Central African Republic. We also studied the genetic basis for antibiotic resistance and the genetic background of third-generation cephalosporin-resistant (3GC-R) Enterobacteriaceae.

Results

Between April 2011 and April 2012, 195 patients with nosocomial surgical-site infections were consecutively recruited into the study at five surgical departments in three major tertiary care centres. Of the 165 bacterial isolates collected, most were Enterobacteriaceae (102/165, 61.8%). Of these, 65/102 (63.7%) were 3GC-R, which were characterized for resistance gene determinants and genetic background. The bla_CTX-M-15 and aac(6′)-Ib-cr genes were detected in all strains, usually associated with qnr genes (98.5%). Escherichia coli, the most commonly recovered species (33/65, 50.8%), occurred in six different sequence types, including the pandemic B2-O25b-ST131 group (12/33, 36.4%). Resistance transfer was studied in one representative strain of the resistance gene content in each repetitive extragenic palindromic and enterobacterial repetitive intergenic consensus sequence-PCR banding pattern. Plasmids were characterized by PCR-based replicon typing and sub-typing schemes. In most isolates (18/27, 66.7%), bla_CTX-M-15 genes were found in incompatibility groups F/F31:A4:B1 and F/F36:A4:B1 conjugative plasmids. Horizontal transfer of both plasmids is probably an important mechanism for the spread of bla_CTX-M-15 among Enterobacteriaceae species and hospitals. The presence of sets of antibiotic resistance genes in these two plasmids indicates their capacity for gene rearrangement and their evolution into new variants.

Conclusions

Diverse modes are involved in transmission of resistance, plasmid dissemination probably playing a major role.

Determination of antimicrobial resistance in Salmonella spp

Infections with Salmonella are an important public health problem worldwide. Salmonella are one of the most common causes of food-borne illness in humans. There are many types of Salmonella but they can be divided into two broad categories: those that cause typhoid and those that do not. The typhoidal Salmonella (TS), such as S. enterica subsp. enterica serovars Typhi and S. Paratyphi only colonize humans and are usually acquired by the consumption of food or water contaminated with human fecal material. The much broader group of non-typhoidal Salmonella (NTS) usually results from improperly handled food that has been contaminated by animal or human fecal material. Antimicrobials are critical to the successful outcome of invasive Salmonella infections and enteric fever. Due to resistance to the older antimicrobials, ciprofloxacin [fluoroquinolone (FQ)] has become the first-line drug for treatment. Nevertheless, switch to FQ has led to a subsequent increase in the occurrence of salmonellae resistant to this antimicrobial agent. The exact mechanism of this FQ resistance is not fully understood. FQ resistance has driven the use of third-generation cephalosporins and azithromycin. However, there are sporadic worldwide reports of high level resistance to expanded-spectrum cephalosporins (such as ceftriaxone) in TS and in NTS it has been recognized since 1988 and are increasing in prevalence worldwide. Already there are rare reports of azithromycin resistance leading to treatment failure. Spread of such resistance would further greatly limit the available therapeutic options, and leave us with only the reserve antimicrobials such as carbapenem and tigecycline as possible treatment options. Here, we describe the methods involved in the genotypic characterization of antimicrobial resistance in clinical isolates of salmonellae.

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.

Quinolone Susceptibility and Detection of qnr and aac(6')-Ib-cr Genes in Community Isolates of Klebsiella pneumoniae

Background:

Plasmid-mediated quinolone resistance genes (PMQR) have been shown to play not only an important role in quinolone resistance, but also resistance to other antibiotics, particularly β-lactams and aminoglycosides. These genes are mainly associated with clinical isolates of Enterobacteriaceae. However, detection of PMQR genes in the community isolates can increase the dissemination rate of resistance determinants among bacteria.

Objectives:

This study aimed to investigate quinolone resistance and distribution of qnr and aac (6’)-Ib-cr genes among the community isolates of Klebsiella pneumoniae.

Materials and Methods:

Fifty-two K. pneumoniae isolates were collected from the Central Laboratory in Karaj between July 2010 and January 2011. Antibacterial susceptibility was determined by the disc diffusion method. Quinolone and/or cephalosporin-resistant isolates were screened for the presence of qnrA, qnrB, qnrS and aac (6’)-Ib-cr genes by polymerase chain reaction (PCR).

Results:

Of the 52 K. pneumoniae isolates, 23 were resistant to cephalosporins and/or quinolones. Overall, 7 out of the 23 resistant isolates harbored qnr and/or aac (6’)-Ib-cr genes (30.4%). Among these, 5 isolates were resistant to both classes of antibiotics of which; 3 carried the aac (6’)-Ib-cr gene, one had the qnrS, and one harbored both aac (6’)-Ib-cr and qnrB genes. None of the isolates contained qnrA. Two isolates were sensitive to quinolones and resistant to cephalosporins of which; one had qnrS and the other carried the aac (6’)-Ib-cr gene.

Conclusions:

Our study showed that 30.4% of the quinolone and/or cephalosporin resistant community isolates of K. pneumoniae carried PMQR genes. These results confirm that community isolates can be an important source for spreading antibiotic resistance determinants among Gram negative pathogens. This is the first report from Iran on detection of PMQR in the community isolates of K. pneumoniae.

Cefotaxime resistant Escherichia coli collected from a healthy volunteer; characterisation and the effect of plasmid loss

In this study 6 CTX-M positive E. coli isolates collected during a clinical study examining the effect of antibiotic use in a human trial were analysed. The aim of the study was to analyse these isolates and assess the effect of full or partial loss of plasmid genes on bacterial fitness and pathogenicity. A DNA array was utilised to assess resistance and virulence gene carriage. Plasmids were characterised by PCR-based replicon typing and addiction system multiplex PCR. A phenotypic array and insect virulence model were utilised to assess the effect of plasmid-loss in E. coli of a large multi-resistance plasmid. All six E. coli carrying bla_CTX-M-14 were detected from a single participant and were identical by pulse field gel electrophoresis and MLST. Plasmid profiling and arrays indicated absence of a large multi-drug resistance (MDR) F-replicon plasmid carrying blaTEM, aadA4, strA, strB, dfrA17/19, sul1, and tetB from one isolate. Although this isolate partially retained the plasmid it showed altered fitness characteristics e.g. inability to respire in presence of antiseptics, similar to a plasmid-cured strain. However, unlike the plasmid-cured or plasmid harbouring strains, the survival rate for Galleria mellonella infected by the former strain was approximately 5-times lower, indicating other possible changes accompanying partial plasmid loss. In conclusion, our results demonstrated that an apparently healthy individual can harbour bla_CTX-M-14E. coli strains. In one such strain, isolated from the same individual, partial absence of a large MDR plasmid resulted in altered fitness and virulence characteristics, which may have implications in the ability of this strain to infect and any subsequent treatment.

Pathotyping bla CTX-M Escherichia coli from Nigeria

BACKGROUND

Escherichia coli have become the enterobacteriaceae species most affected by extended-spectrum β-lactamases (ESBLs) in view of the emergence of CTX-M-type ESBLs. These CTX-M-positive E. coli have been reported in numerous regions worldwide. Virulence determinants of already reported CTX-M-positive E. coli were investigated.

METHODOLOGY

To gain insights into the mechanism underlying this phenomenon, we assessed serogroup, susceptibility pattern and diversity of virulence profiles within a collection of nine bla CTX-M-positive E. coli strains and their virulent determinant using miniaturized DNA microarray techniques. The nine ESBL-positive E. coli isolates were from eight male and one female patient(s) selected for study based on previous work. Virulence potential was inferred by detection of 63 virulence factor (VF) genes.

RESULTS

Four (44.4%) of the 9 E. coli isolates exhibited the same set of core characteristics: serotype O8:Hnt, while all were positive for OXA-1, ciprofloxacin resistance. Five of the isolates exhibited highly similar (91% to 100%) VF profiles.

CONCLUSION

The findings describe a broadly disseminated, bla CTX-M-positive and virulent E. coli serogroup with highly homogeneous virulence genotypes, suggesting recent emergence in this zone. Understanding how this clone has emerged and successfully disseminated within the hospital and community, including across national boundaries, should be a public health priority.

Predominance of Klebsiella pneumoniae ST14 carrying CTX-M-15 causing neonatal sepsis in Tanzania

Background

Klebsiella pneumoniae strains expressing ESBLs are a predominant cause of hospital acquired infections. Here we describe the molecular epidemiology of these isolates in a tertiary hospital in Tanzania, as potential pathogens for neonatal infections.

Methods

Between April 2009 and March 2010 all Klebsiella pneumoniae isolates with phenotypic expression Extended Spectrum Beta Lactamase (ESBL) were collected and characterized. Identification was done using in house biochemical tests in case of ambiguous results confirmation was done using API 20E. Susceptibility testing was determined using the disc diffusion method followed by specific PCR and sequencing to determine ESBL genes. Phylogenetic analysis, Pulse field gel electrophoresis (PFGE) and Multi-Locus sequence typing (MLST) to PFGE clusters representative isolates were performed to determine clones of the isolates. Conjugation and hybridization were performed to determine the location of blaCTX-M-15 gene.

Results

A total of 92 non- repetitive ESBL producing K. pneumoniae representing 50.3% of Klebsiella pneumoniae isolates were characterized. These isolates were from blood 61 (66%), wound swab 13 (14%), urine 12 (13%) and pus 6 (7%) were analyzed. Most blood culture strains originated from neonatal unit 39/61(64%) and 22 (36%) of the blood culture isolates were from neonatal ICU. All isolates were resistant to gentamicin and 54% were resistant to ciprofloxacin. Using a similarity index of 80%, the isolates were assigned to thirteen clusters based on PFGE patterns and contained sub-clusters with identical strains indicating clonal outbreaks. Cluster X5, X7 and X8, and X9 were grouped into ST48, ST14 and ST348 respectively. Based on gyrA PCR- RFLP phylogenetic analysis all isolates were grouped as KpI. The predominant ESBL allele detected was bla_CTX-M-15 which was found in 76% of isolates, followed by bla_TEM-104 (19%), bla_SHV-11 (3.2%) and bla_TEM-176 (2%). The bla_CTX-M-15 gene was located in multiple conjugative IncF plasmids ranging from 25 kb-485 kb in size.

Conclusion

The high prevalence of bla_CTX-M-15 observed among ESBL producing K. pneumoniae in Tanzania, is possibly due to the spread of a common IncFII 145 kb plasmid and of certain clones such as ST14 and ST48. Furthermore the 485 kb plasmid detected is the largest plasmid reported to carry bla_CTX-M-15 todate.

Antibiotic trapping by plasmid-encoded CMY-2 β-lactamase combined with reduced outer membrane permeability as a mechanism of carbapenem resistance in Escherichia coli

A liver transplant patient was admitted with cholangitis, for which meropenem therapy was started. Initial cultures showed a carbapenem-susceptible (CS) Escherichia coli strain, but during admission, a carbapenem-resistant (CR) E. coli strain was isolated. Analysis of the outer membrane protein profiles showed that both CS and CR E. coli lacked the porins OmpF and OmpC. Furthermore, PCR and sequence analysis revealed that both CS and CR E. coli possessed bla(CTX-M-15) and bla(OXA-1). The CR E. coli strain additionally harbored bla(CMY-2) and demonstrated a >15-fold increase in β-lactamase activity against nitrocefin, but no hydrolysis of meropenem was detected. However, nitrocefin hydrolysis appeared strongly inhibited by meropenem. Furthermore, the CMY-2 enzyme demonstrated lower electrophoretic mobility after its incubation either in vitro or in vivo with meropenem, indicative of its covalent modification with meropenem. The presence of the acyl-enzyme complex was confirmed by mass spectrometry. By transformation of the CMY-2-encoding plasmid into various E. coli strains, it was established that both porin deficiency and high-level expression of the enzyme were needed to confer meropenem resistance. In conclusion, carbapenem resistance emerged by a combination of elevated β-lactamase production and lack of porin expression. Due to the reduced outer membrane permeability, only small amounts of meropenem can enter the periplasm, where they are trapped but not degraded by the large amount of the β-lactamase. This study, therefore, provides evidence that the mechanism of "trapping" by CMY-2 β-lactamase plays a role in carbapenem resistance.

Molecular characteristics of extended-spectrum β-lactamases in clinical isolates from Escherichia coli at a Japanese tertiary hospital

The prevalence of ESBL has been increasing worldwide. In this study, we investigated the molecular characteristics of ESBL among clinical isolates of Escherichia coli from a Japanese tertiary hospital. A total of 71 consecutive and nonduplicate clinical isolates of ESBL-positive E. coli collected at Tohoku University Hospital between January 2008 and March 2011 were studied. The antimicrobial susceptibility profile of these strains was determined. PCR and sequencing were performed to identify genes for β-lactamase (bla(TEM), bla(SHV), bla(OXA-1-like), and bla(CTX-M)) and plasmid-mediated quinolone resistance determinants (PMQR). The isolates were also analyzed by pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). Of the 71 strains, 68 were positive for CTX-M, 28 were positive for TEM, four were positive for OXA-1, and one was positive for SHV. Sequencing revealed that CTX-M-14 was the most prevalent (31/71), followed by CTX-M-27 (21/71) and then CTX-M-15 (9/71). Of the 28 TEM-positive strains, one was TEM-10 and the rest were TEM-1. One SHV-positive strain was SHV-12. The 21 CTX-M-27-producing isolates were divided into 14 unique PFGE types, while the 9 CTX-M-15 producers were divided into 8 types. Based on MLST, 9 CTX-M-14 procedures, 19 CTX-M-27 procedures, and 8 CTX-M-15 producers belonged to ST131. Thirty-five (94.6%) of the 37 ST131 E. coli strains showed resistance to levofloxacin, which was a higher rate than among non-ST131 strains (63.6%). Among ESBL-producing isolates, one, two, and six possessed qnrB, qnrS, qepA, and aac(6')-Ib-cr, respectively. Of the 6 isolates with aac(6')-Ib-cr, 4 carried the CTX-M-15 gene. Our data suggest that CTX-M-15-producing E. coli ST131 has emerged as a worldwide pandemic clone, while CTX-M-27 (a variant of CTX-M-14) is also spreading among E. coli ST131 in Japan.

Antimicrobial resistance and virulence: a successful or deleterious association in the bacterial world?

Hosts and bacteria have coevolved over millions of years, during which pathogenic bacteria have modified their virulence mechanisms to adapt to host defense systems. Although the spread of pathogens has been hindered by the discovery and widespread use of antimicrobial agents, antimicrobial resistance has increased globally. The emergence of resistant bacteria has accelerated in recent years, mainly as a result of increased selective pressure. However, although antimicrobial resistance and bacterial virulence have developed on different timescales, they share some common characteristics. This review considers how bacterial virulence and fitness are affected by antibiotic resistance and also how the relationship between virulence and resistance is affected by different genetic mechanisms (e.g., coselection and compensatory mutations) and by the most prevalent global responses. The interplay between these factors and the associated biological costs depend on four main factors: the bacterial species involved, virulence and resistance mechanisms, the ecological niche, and the host. The development of new strategies involving new antimicrobials or nonantimicrobial compounds and of novel diagnostic methods that focus on high-risk clones and rapid tests to detect virulence markers may help to resolve the increasing problem of the association between virulence and resistance, which is becoming more beneficial for pathogenic bacteria.

Multidrug-resistant gram-negative bacteria colonization of healthy US military personnel in the US and Afghanistan

Background

The US military has seen steady increases in multidrug-resistant (MDR) gram-negative bacteria (GNB) infections in casualties from Iraq and Afghanistan. This study evaluates the prevalence of MDR GNB colonization in US military personnel.

Methods

GNB colonization surveillance of healthy, asymptomatic military personnel (101 in the US and 100 in Afghanistan) was performed by swabbing 7 anatomical sites. US-based personnel had received no antibiotics within 30 days of specimen collection, and Afghanistan-based personnel were receiving doxycycline for malaria chemoprophylaxis at time of specimen collection. Isolates underwent genotypic and phenotypic characterization.

Results

The only colonizing MDR GNB recovered in both populations was Escherichia coli (p=0.01), which was seen in 2% of US-based personnel (all perirectal) and 11% of Afghanistan-based personnel (10 perirectal, 1 foot+groin). Individuals with higher off-base exposures in Afghanistan did not show a difference in overall GNB colonization or MDR E. coli colonization, compared with those with limited off-base exposures.

Conclusion

Healthy US- and Afghanistan-based military personnel have community onset-MDR E. coli colonization, with Afghanistan-based personnel showing a 5.5-fold higher prevalence. The association of doxycycline prophylaxis or other exposures with antimicrobial resistance and increased rates of MDR E. coli colonization needs further evaluation.

Molecular diversity associated with the dissemination of CTX-M-15 beta-lactamase gene in blood culture isolates of Escherichia coli from Edinburgh

BACKGROUND

Escherichia coli producing the CTX-M-15 β-lactamase are a major cause of infection. We present the characterization of plasmids encoding the CTX-M-15 β-lactamase gene, the genetic environment, and the mode of spread of this gene in blood culture isolates from a single hospital.

METHODS

Blood culture E. coli isolates with extended spectrum β-lactamase (ESBL) phenotype were screened for the presence of the bla(CTX-M) gene, other ESBLs, and aac(6')-Ib-cr genes. The genetic environment of bla(CTX-M) was determined by DNA sequencing. Plasmids were classified by their incompatibility group from polymerase chain reaction (PCR) replicon typing. Plasmid numbers and sizing were assessed by alkaline lysis and S1 nuclease digestion. Genotyping of the strains was determined by pulsed-field gel electrophoresis (PFGE) and ST131 by allele-specific PCR.

RESULTS

Seven isolates had bla(CTX-M-15), with these isolates additionally having bla(TEM) (n = 5), bla(OXA) (n = 6), and aac(6')-Ib-cr (n = 6). Insertion sequence ISEcp1 was found upstream of the bla(CTX-M) gene, and in 2 isolates, ISEcp1 was found to be truncated with insertion sequence IS26. Plasmid replicon typing showed bla(CTX-M-15) genes were carried on the IncFII plasmid. All 7 isolates were associated with the O25b-ST131 clone. The PFGE banding pattern showed only 3 isolates were able to demonstrate clonality.

CONCLUSIONS

This study shows the molecular diversity associated with the dissemination of bla(CTX-M-15) in a single Scottish hospital, which is largely due to horizontal transfer of multi- resistance IncF plasmids rather than clonal spread. It demonstrates that more detailed information is needed to monitor these bacteria to control them appropriately.

Analysis of β-lactamase phenotypes and carriage of selected β-lactamase genes among Escherichia coli strains obtained from Kenyan patients during an 18-year period

Background

Although β-lactam antibiotics are heavily used in many developing countries, the diversity of β-lactamase genes (bla) is poorly understood. We screened for major β-lactamase phenotypes and diversity of bla genes among 912 E. coli strains isolated from clinical samples obtained between 1992 and 2010 from hospitalized and non-hospitalized patients.

Results

None of the isolates was resistant to carbapenems but 30% of all isolates were susceptible to cefepime, cephamycins and piperacillin-tazobactam. Narrow spectrum β-lactamase (NSBL) phenotype was observed in 278 (30%) isolates that contained bla_TEM-1 (54%) or bla_SHV-1 (35%) or both (11%). Extended Spectrum β-lactamase (ESBL) phenotype was detected in 247 (27%) isolates which carried bla_CTX-M-14 (29%), bla_CTX-M-15 (24%), bla_CTX-M-9 (2%), bla_CTX-M-8 (4%), bla_CTX-M-3 (11%), bla_CTX-M-1 (6%), bla_SHV-5 (3%), bla_SHV-12 (5%), and bla_TEM-52 (16%). Complex Mutant TEM-like (CMT) phenotype was detected in 220 (24%) isolates which carried bla_TEM-125 (29%), while bla_TEM-50, bla_TEM-78, bla_TEM-109, bla_{TEM −152} and bla_TEM-158 were detected in lower frequencies of between 7% and 11%. Majority of isolates producing a combination of CTX-M-15 + OXA-1 + TEM-1 exhibited resistance phenotypes barely indistinguishable from those of CMT-producers. Although 73 (8%) isolates exhibited Inhibitor Resistant TEM-like (IRT) phenotype, bla_TEM-103 was the only true IRT-encoding gene identified in 18 (25%) of strains with this phenotype while the rest produced a combination of TEM-1 + OXA-1. The pAmpCs-like phenotype was observed in 94 (10%) isolates of which 77 (82%) carried bla_CMY-2 while 18% contained bla_CMY-1.

Isolates from urine accounted for 53%, 53%, 74% and 72% of strains exhibiting complex phenotypes such as IRT, ESBL, CMT or pAmpC respectively. On the contrary, 55% isolates from stool exhibited the relatively more susceptible NSBL-like phenotype. All the phenotypes, and majority of the bla genes, were detected both in isolates from hospitalized and non-hospitalized patients but complex phenotypes were particularly common among strains obtained between 2000 and 2010 from urine of hospitalized patients.

Conclusions

The phenotypes and diversity of bla genes in E. coli strains implicated in clinical infections in non-hospitalized and hospitalized patients in Kenya is worryingly high. In order to preserve the efficacy of β-lactam antibiotics, culture and susceptibility data should guide therapy and surveillance studies for β-lactamase-producers in developing countries should be launched.

First description of Escherichia coli producing CTX-M-15- extended spectrum beta lactamase (ESBL) in out-patients from south eastern Nigeria

We studied the presence of extended spectrum beta lactamases (ESBLs) in 44 clinical isolates of Escherichia coli collected from out-patients in two university teaching hospitals in South-Eastern Nigeria. Species identification was performed by standard microbiology methods and re-confirmed by MALDI-TOF technology. Phenotypic characterization of ESBL enzymes was done by double disc synergy test and presence of ESBL genes was determined by specific PCR followed by sequencing. Transfer of plasmid DNA was carried out by transformation using E. coli DH5 as recipient strain. Phenotypic characterization identified all isolates to be ESBL positive. 77% of strains were from urine, 13.6% from vaginal swabs and 9.0% from wound swabs. 63.6% were from female patients, 68% were from outpatients and 95.5% from patients younger than 30 years. All ESBL producers were positive in a PCR for bla_CTX-M-1 cluster, in exemplary strains bla_CTX-M-15 was found by sequencing. In all strains ISEcp1 was found upstream and ORF477 downstream of bla_CTX-M. PCR for bla_TEM and bla_OXA-1 was positive in 93.1% of strains, whereas bla_SHV was not detected, aac(6′)-Ib-cr was found in 97.7% of strains. RAPD analysis revealed seven different clonal groups named A through G with the majority of the strains (65.9%) belonging to clone A. Transfer of an ESBL plasmid with co-resistance to gentamicin, kanamycin, tobramycin, doxycycline and trimethropim-sulfamethoxazole was successful in 19 (43.2%) strains. This study showed a high rate of CTX-M-1 cluster - ESBLs in South-Eastern Nigeria and further confirms the worldwide spread of CTX-M ESBL in clinical isolates.

Current epidemiology and growing resistance of gram-negative pathogens

In the 1980s, gram-negative pathogens appeared to have been beaten by oxyimino-cephalosporins, carbapenems, and fluoroquinolones. Yet these pathogens have fought back, aided by their membrane organization, which promotes the exclusion and efflux of antibiotics, and by a remarkable propensity to recruit, transfer, and modify the expression of resistance genes, including those for extended-spectrum β-lactamases (ESBLs), carbapenemases, aminoglycoside-blocking 16S rRNA methylases, and even a quinolone-modifying variant of an aminoglycoside-modifying enzyme. Gram-negative isolates--both fermenters and non-fermenters--susceptible only to colistin and, more variably, fosfomycin and tigecycline, are encountered with increasing frequency, including in Korea. Some ESBLs and carbapenemases have become associated with strains that have great epidemic potential, spreading across countries and continents; examples include Escherichia coli sequence type (ST)131 with CTX-M-15 ESBL and Klebsiella pneumoniae ST258 with KPC carbapenemases. Both of these high-risk lineages have reached Korea. In other cases, notably New Delhi Metallo carbapenemase, the relevant gene is carried by promiscuous plasmids that readily transfer among strains and species. Unless antibiotic stewardship is reinforced, microbiological diagnosis accelerated, and antibiotic development reinvigorated, there is a real prospect that the antibiotic revolution of the 20th century will crumble.

[Antimicrobial resistance and virulence: a beneficial relationship for the microbial world?]

While bacterial virulence has experienced a long host/pathogen-dependent evolutionary process, antimicrobial resistance has had a very different, shorting and changing evolution due to the biological pressure caused by the introduction of the antimicrobials in human medicine. This strong pressure has forced the microorganisms to adapt to these changing conditions, continuously acquiring or developing new resistance mechanisms, causing major changes in cellular functions and finally influencing the virulence and bacterial fitness. Multiple factors may mediate in the relationship between virulence and resistance. The genes often involved in both phenomena have the same transport and dispersion mediums. Islands, integrons, transposons and other genetic elements could also facilitate the combined selection of virulence and resistance genes. The increase in resistance can affect virulence in different ways, mainly depending on the bacterial species, the environment, and the mechanism of resistance. This review presents the different phenomena in which the genetic mechanism that provides an advantage over the antimicrobials directly affects the virulence and fitness, such as changes in the structure of the cellular wall, efflux pumps, porins or two-component regulatory systems. The co-selection of virulence and antimicrobial resistance factors and the relative ease of bacteria to develop compensatory mutations can favour, particularly in environments with high antibiotic pressure, the emergence of prevalent clones. These can be virulent and with few treatment options, and could be a major health problem in the near future.

Faecal carriage of extended-spectrum β-lactamase-producing Enterobacteriaceae among humans in Java, Indonesia, in 2001-2002

OBJECTIVE

To characterise commensal Escherichia coli and other Enterobacteriaceae with reduced susceptibility to cefotaxime that were collected in a large survey carried out among 3995 patients and healthy persons in two urban regions on Java, Indonesia, in 2001-2002.

METHODS

The putative extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae were analysed using double-disk synergy tests, isoelectric focusing, PCR assays, DNA sequencing, and pulsed-field gel electrophoresis (PFGE).

RESULTS

On the day of discharge after five or more days of hospitalisation, at least 95 of 999 (9.5%) patients carried ESBL-positive Enterobacteriaceae as dominant faecal flora. Six patients were simultaneously colonised with E. coli and Klebsiella pneumoniae isolates with ESBL activity. On admission, only 6 of 998 (0.6%) patients were colonised. Faecal carriage of ESBL-producing Enterobacteriaceae among healthy persons or persons visiting a public health centre was not detected. The 107 ESBL-positive strains included 68 E. coli, 35 K. pneumoniae, and four other Enterobacteriaceae. bla(CTX-M-15) was the most prevalent ESBL in both E. coli (47.1%) and K. pneumoniae (45.7%), but the E. coli O25b-ST131 clone was virtually absent. Other ESBL types found were: SHV-2, -2a, -5, -12, CTX-M-3, -9, -14, and TEM-19. PFGE revealed extensive genetic diversity among the isolates.

CONCLUSIONS

In 2001-2002, faecal carriage of ESBL-producing Enterobacteriaceae as dominant flora in Indonesia was almost exclusively hospital-associated. The presence of various bla(ESBL) genes and the extensive genetic diversity among isolates argue against a single/dominant strain outbreak.

Mechanisms of reduced susceptibility to ciprofloxacin in Escherichia coli isolates from Canadian hospitals

OBJECTIVE

To determine whether plasmid-mediated quinolone resistance (PMQR) determinants play a role in the increasing resistance to fluoroquinolones among Escherichia coli isolates in Canadian hospitals, and to determine the mechanisms of reduced susceptibility to ciprofloxacin in a recent collection of 190 clinical E coli isolates.

METHODS

E coli isolates (n=1702) were collected as part of the 2007 Canadian Hospital Ward Antibiotic Resistance Surveillance (CANWARD) study. Antimicrobial susceptibility testing was performed by Clinical and Laboratory Standards Institute (CLSI) broth microdilution. Using a representative subset of isolates (n=190), the mechanisms of reduced susceptibility to ciprofloxacin were detected by polymerase chain reaction and sequencing of the quinolone resistance-determining regions (QRDR) of chromosomal gyrA and parC genes, and by polymerase chain reaction for the PMQR genes: qnr, aac(6') Ib-cr and qepA.

RESULTS

2.1% and 1.1% of E coli harboured aac(6')Ib-cr and qnrB, respectively. Single amino acid substitutions in the QRDR of gyrA were observed among isolates with ciprofloxacin minimum inhibitory concentrations as low as 0.12 μg/mL. As the ciprofloxacin minimum inhibitory concentration increased to 1 μg/mL (which is still considered to be susceptible by the CLSI), the vast majority of isolates demonstrated both gyrA and parC mutations.

CONCLUSION

PMQR determinants and QRDR mutants among clinical E coli isolates with reduced susceptibility to ciprofloxacin demonstrates the need for increased surveillance and the need to re-evaluate the current CLSI breakpoints to prevent further development of fluoroquinolone resistance.

Characterization of plasmids encoding extended-spectrum β-lactamases and their addiction systems circulating among Escherichia coli clinical isolates in the UK

OBJECTIVES

To characterize plasmids encoding extended-spectrum β-lactamases (ESBLs) from a recent UK collection of clinical Escherichia coli isolates.

METHODS

The isolates comprised 118 ESBL producers referred from 54 laboratories. Plasmids were transferred by electroporation, and their incompatibility groups, associated addiction systems and resistance genes with the flanking genetic environments were identified by PCR or sequencing.

RESULTS

Seventy isolates had plasmids encoding CTX-M-15 (n = 53), CTX-M-14 (n =9), CTX-M-27 (n = 1), CTX-M-3 (n = 2) and SHV-12 (n = 5) ESBLs that were transformable; non-transformable ESBLs were mainly CTX-M enzymes (42/48). Most transformable bla(CTX-M-15) genes (43/53) were harboured on single replicon or multireplicon IncF plasmids, with IncFIA4-FIB1-FII31 (n = 11) and IncFIA1-FII2 (n = 15) being most frequent; the latter included eight pEK499 plasmids, typical of UK epidemic strain A. Plasmids harbouring bla(CTX-M-14) belonged variously to IncF, IncI1 and IncHI2 types, and 16 encoding CTX-M or SHV enzymes were non-typeable. Only IncF plasmid types carried the addiction systems sought and those with bla(CTX-M-15) frequently harboured bla(OXA-1) and aac(6')-Ib-cr, and often transferred trimethoprim and tetracycline resistance; those with bla(CTX-M-14) encoded trimethoprim, sulphonamide, streptomycin and tetracycline resistance. Most ESBL genes were associated with the well-known mobile elements ISEcp1 and IS26, but nearly half (23/55) of the ISEcp1 sequences upstream of bla(CTX-M-15) were interrupted by an IS26 at various positions.

CONCLUSIONS

Most ESBLs (70/118) were encoded by transformable plasmids, although a sizable minority could not be transformed. The majority of transformable plasmids (51/70; 72.9%) were diverse multiresistant IncF types possessing multiple addiction systems. The spread of bla(CTX-M-15) can be attributed not just to clonal expansion, but also to the horizontal dissemination of related plasmids.

Transfer of an Escherichia coli ST131 multiresistance cassette has created a Klebsiella pneumoniae-specific plasmid associated with a major nosocomial outbreak

OBJECTIVES

To characterize the complete sequence, horizontal spread and stability of the CTX-M-15-encoding multiresistance plasmid of a Klebsiella pneumoniae strain involved in a large nosocomial outbreak.

METHODS

The 220 kbp plasmid pUUH239.2 was completely sequenced using 454 technology. The conjugational host range, conjugation frequencies, plasmid stability and fitness cost of plasmid carriage were studied in vitro. Conjugational spread during the outbreak was assessed retrospectively by multiplex PCR screening, restriction fragment length polymorphism and PFGE.

RESULTS

Plasmid pUUH239.2 encodes resistance to β-lactams (bla(CTX-M-15), bla(TEM-1) and bla(OXA-1)), aminoglycosides [aac-(6')-1b-cr and aadA2], tetracyclines [tet(A) and tetR], trimethoprim (dhfrXII), sulphonamides (sul1), quaternary ammonium compounds (qacEΔ1), macrolides [mph(A)-mxr-mphR(A)] and heavy metal ions (silver, copper and arsenic). The plasmid consists of a backbone, highly similar to the K. pneumoniae plasmid pKPN3, and a 41 kbp resistance region, highly similar to the resistance regions of plasmids pEK499 and pC15-1a previously isolated from Escherichia coli strains belonging to the outbreak lineage ST131 (where ST stands for sequence type). The pUUH239.2 plasmid is stable in K. pneumoniae but unstable in E. coli and confers a fitness cost when introduced into a naive host cell. Transfer of pUUH239.2 from the outbreak K. pneumoniae clone to the E. coli of the patients' intestinal floras has occurred on multiple occasions during the outbreak.

CONCLUSIONS

The plasmid pUUH239.2 is a composite of the pKPN3 K. pneumoniae plasmid backbone and the bla(CTX-M-15)-encoding multiresistance cassette associated with the internationally recognized outbreak strain E. coli ST131. The resulting plasmid differs in stability between K. pneumoniae and E. coli, and this has probably limited the spread of this plasmid during the outbreak.