A plasmid-encoded class 1 integron carryingsat, a putative phosphoserine phosphatase gene andaadA2from enterotoxigenicEscherichia coliO159 isolated in Japan

Metformin Reverses tmexCD1-toprJ1- and tet(A)-Mediated High-Level Tigecycline Resistance in K. pneumoniae

Tigecycline (TIG) is one of the last effective options against multidrug resistance bacteria. Recently, the RND (resistance–nodulation–division) efflux pump gene cluster, tmexCD1-toprJ1, and the tetracycline-efflux pump tet(A) mutation were reported to mediate high level resistance to TIG in clinically important pathogens, weakening the efficacy of TIG. In this study, we report the potent synergistic effect of the antidiabetic drug metformin in combination with TIG against tet(A) mutant and tmexCD1-toprJ1 positive K. pneumoniae. The fractional inhibitory concentration index (FICI) of TIG and metformin were less than 0.05 for all the tested isolates. The time–kill curve assay showed that the combination of TIG and metformin exhibited much better antimicrobial effect than TIG alone. The synergistic effect was also confirmed in vivo using a well-studied Galleria mellonella larvae model. Mechanistic studies demonstrated that metformin disrupted the important component of proton motive force, the electric potential (Δψ) and the function of efflux pump, thereby increasing the intracellular concentration of TIG. This finding revealed that metformin might be a possible adjuvant of TIG for combating with superbugs carrying the tet(A) mutant and tmexCD1-toprJ1 genes.

Mechanisms of Bacterial Resistance to Antimicrobial Agents

During the past decades resistance to virtually all antimicrobial agents has been observed in bacteria of animal origin. This chapter describes in detail the mechanisms so far encountered for the various classes of antimicrobial agents. The main mechanisms include enzymatic inactivation by either disintegration or chemical modification of antimicrobial agents, reduced intracellular accumulation by either decreased influx or increased efflux of antimicrobial agents, and modifications at the cellular target sites (i.e., mutational changes, chemical modification, protection, or even replacement of the target sites). Often several mechanisms interact to enhance bacterial resistance to antimicrobial agents. This is a completely revised version of the corresponding chapter in the book Antimicrobial Resistance in Bacteria of Animal Origin published in 2006. New sections have been added for oxazolidinones, polypeptides, mupirocin, ansamycins, fosfomycin, fusidic acid, and streptomycins, and the chapters for the remaining classes of antimicrobial agents have been completely updated to cover the advances in knowledge gained since 2006.

Structural diversity of class 1 integrons and their associated gene cassettes in Klebsiella pneumoniae isolates from a hospital in China

Background

Klebsiella pneumoniae strains carrying class 1 integrons are becoming more common worldwide, and their role in the dissemination of drug resistance is significant. The aim of this study was to characterize the structural diversity of class 1 integrons and their associated gene cassettes in K. pneumoniae isolates from hospital settings.

Methodology/Principal Findings

We analyzed a total of 176 K. pneumoniae isolates in a tertiary-care hospital in Beijing, China for the period of November 1, 2010-October 31, 2011. The presence of class 1 integrons and gene cassettes was analyzed by PCR and sequencing. The prevalence of class 1 integrons was 51.1% (90/176). Fourteen different gene cassettes and 10 different gene cassette arrays were detected. dfrA and aadA cassettes were predominant and cassette combination dfrA1-orfC was most frequently found (13.6%, 24/176). Strong association between resistance to a variety of drugs (both phenotypes and the associated genes) and the presence of class 1 integrons was observed. In addition, we also identified an association between some previously identified prevalent sequence types (such as ST11, ST15, ST147, ST562, and ST716) and the presence of class 1 integrons.

Conclusions/Significance

Data from this study demonstrated that class 1 integrons are highly diverse and are associated with a variety of drug resistance phenotypes, drug resistance genes, as well as genotypes among K. pneumoniae isolates. Continuous monitoring of gene cassettes in class 1 integrons is warranted to improve the understanding and control of drug resistance among hospital settings.

Detection of extended-spectrum beta-lactamase-producing Escherichia coli isolates in faecal samples of Iberian lynx

AIMS

To characterize the diversity of extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli isolates recovered within the faecal microbiota of Iberian lynx. The identification of other associated resistance genes and the analysis of clonal relationship were also focused in this study.

METHODS AND RESULTS

From 2008 to 2010, 128 faecal samples of Iberian lynx (wild and captive animals) were collected. Eleven tested samples contained cefotaxime-resistant E. coli isolates (all belonging to captive animals) and 10 ESBL-producing isolates were showed. CTX-M-14 and SHV-12 ESBL-types were detected and seven different patterns were identified by pulsed-field gel electrophoresis analysis.

CONCLUSIONS

The occurrence of unrelated multiresistant E. coli in faecal flora of captive specimens of Iberian lynx, including the presence of ESBLs, resistant genes in integrons and virulence determinants was showed in this study.

SIGNIFICANCE AND IMPACT OF THE STUDY

The results obtained in this study highlight the environmental problem as future reintroductions of Iberian lynx could lead to a spread of resistant bacteria. Additionally, ESBL-producing bacteria can represent a health problem for this endangered species.

Use of inverse PCR for analysis of class 1 integrons carrying an unusual 3' conserved segment structure

By using inverse PCR and DNA sequencing, 13 sul3-associated mutational integrons, 2 defective class 1 integrons, and 1 qnrB2-associated complex sul1-type class 1 integrons were identified in Salmonella enterica serovar Choleraesuis, Pseudomonas aeruginosa, and Enterobacter cloacae, respectively. In addition, conjugation and Southern hybridization demonstrated that unusual class 1 integrons were located on plasmids or integrated into chromosomal DNA. Thus, an inverse PCR assay can be a valuable tool for the analysis of unusual structures of the 3' conserved region of class 1 integrons.

Highly variable patterns of antimicrobial resistance in commensal Escherichia coli isolates from pigs, sympatric rodents, and flies

Antimicrobial-resistant Escherichia coli strains from pigs, sympatric rodents, and flies from two large farms in the Czech Republic with different antibiotic exposure histories were characterized based on antimicrobial resistance genes, integrons, and macrorestriction DNA profiles. Isolates of E. coli were tested for susceptibility to 12 antimicrobial agents according to the standard disk diffusion method. In resistant isolates, polymerase chain reaction was used to detect antibiotic resistance genes, integrase genes, and gene cassettes. Pulsed-field gel electrophoresis (PFGE) was used for molecular subtyping of E. coli. In farm A (long-term use of amoxicillin only), 75% (n = 198), 65% (n = 49), 11% (n = 139), and 82% (n = 177) of E. coli isolates from piglets, sows, sympatric rodents, and flies, respectively, were antibiotic resistant. In farm B (various antibiotics commonly used), 53% (n = 154), 69% (n = 98), and 54% (n = 74) of E. coli isolates from piglets, sows, and sympatric rodents, respectively, were antibiotic resistant. In both farms, the highest resistance prevalence was to tetracycline, and resistance patterns of isolates were greatly variable. Isolates with the same resistance phenotype, genes, and PFGE profile were found in pigs and flies. Isolates from rodents showed unique PFGE profiles. Close contact of sympatric rodents and flies with pigs or their products was associated with colonization of rodents and flies with resistant bacteria or transfer of resistance genes found in pig intestinal flora.

Aminoglycosides versus bacteria – a description of the action, resistance mechanism, and nosocomial battleground

Since 1944, we have come a long way using aminoglycosides as antibiotics. Bacteria also have got them selected with hardier resistance mechanisms. Aminoglycosides are aminocyclitols that kill bacteria by inhibiting protein synthesis as they bind to the 16S rRNA and by disrupting the integrity of bacterial cell membrane. Aminoglycoside resistance mechanisms include: (a) the deactivation of aminoglycosides by N-acetylation, adenylylation or O-phosphorylation, (b) the reduction of the intracellular concentration of aminoglycosides by changes in outer membrane permeability, decreased inner membrane transport, active efflux, and drug trapping, (c) the alteration of the 30S ribosomal subunit target by mutation, and (d) methylation of the aminoglycoside binding site. There is an alarming increase in resistance outbreaks in hospital setting. Our review explores the molecular understanding of aminoglycoside action and resistance with an aim to minimize the spread of resistance.

Characterization of In3Mor, a new integron carrying VIM-1 metallo-β-lactamase and sat1 gene, from Morganella morganii

OBJECTIVES

A carbapenem-resistant Morganella morganii clinical isolate that was phenotypically metallo-beta-lactamase (MBL)-positive was recovered from a Greek patient. The aim of the study was to analyse the structure of the integron containing the MBL gene.

METHODS

MICs were determined by the broth microdilution method. PCR assays and nucleotide sequencing were used for identification of bla gene types and mapping of the integron carrying the MBL gene. The location of the MBL allele was investigated by mating experiments and plasmid analysis as well as by Southern blotting of the plasmid extract and gene-specific hybridization with a bla(VIM-1) probe.

RESULTS

The strain contained In3Mor, a novel class 1 integron carrying a carbapenemase gene (bla(VIM-1)) associated with a trimethoprim (dfrA1), a streptothricin (sat1) and two aminoglycoside resistance genes (aacA7 and aadA1). Conjugation experiments failed to detect a transferable MBL determinant and plasmid DNA was not visualized. The chromosomal location of bla(VIM-1) was confirmed after hybridization of the chromosomal band with the bla(VIM-1) probe.

CONCLUSIONS

Production of a VIM-type MBL in a M. morganii clinical isolate is documented in this study for the first time. Also, the dfrA1-sat1-aadA1 array which is typically described in the variable region of class 2 integrons consistent with that on Tn7 transposons, is originally detected herein in a class 1 integron.

Prevalence of class 1 integrons in commensal Escherichia coli from pigs and pig farmers in Thailand

Escherichia coli isolates (n = 617) from fecal samples of healthy and diarrheal pigs, pig farmers, and nonfarmers were analyzed for class 1 integrons. Three hundred ninety-two isolates (63.5%) were positive for class 1 integrons, based on the presence of intI1, with seventy-one of those isolates (11.5%) harboring all three conserved genes (intI1, qacEdelta1, and sul1) known to be associated with class 1 integrons. The presence of integrons was associated with isolate origin. Integrons were more prevalent in isolates from most pig groups than in isolates from pig farmers and nonfarmers. Selected integron-positive and integron-negative isolates were tested for resistance to 16 antimicrobials. All integron-positive swine isolates were multidrug resistant to at least three antimicrobial agents, demonstrating resistance to 14 different antibiotics that included sulphamethoxazole (100%), tetracycline (97.1%), ampicillin (92.8%), streptomycin (89.9%), trimethoprim-sulphamethoxazole (88.1%), nalidixic acid (60.9%), chloramphenicol (58.0%), kanamycin (55.1%), cephalothin (44.9%), gentamicin (39.1%), ciprofloxacin (33.3%), cefoxitin (8.7%), amoxicillin-clavulanic acid (5.8%), and amikacin (2.9%). All isolates were susceptible to ceftiofur and ceftriaxone. Forty-seven resistance patterns were observed among 69 integron-positive swine and swine farmer isolates. The most frequent pattern was tetracycline-ciprofloxacin-gentamicin-nalidixic acid-sulphamethoxazole-trimethoprim-sulphamethoxazole-kanamycin-ampicillin-streptomycin (10.1%), which was found in diarrheal and healthy pigs. This study shows that integrons and multidrug-resistant commensal bacteria are common and appear to be a significant aspect of microbial communities associated with pigs and humans in southern Thailand.

Genetic characterization of multidrug resistance in Shigella spp. from Japan

This study characterized the genetic basis of antimicrobial resistance of a number of Shigella spp. isolated from humans from 2000 to 2004 in Hiroshima prefecture, Japan. A total of 26 isolates of Shigella spp. were included in this study. Antimicrobial susceptibility tests revealed high levels of resistance, especially to ampicillin, streptomycin, trimethoprim, tetracycline, nalidixic acid and ciprofloxacin. PCR and DNA sequencing were used for screening and characterization of antibiotic-resistance determinants. PCR sequencing analysis revealed the presence of only one type of class 1 integron in one isolate of Shigella sonnei. This class 1 integron was 1904 bp and contained two gene cassettes: a probable esterase/lipase (estX) and aadA1, which confers resistance to streptomycin and spectinomycin. Two types of class 2 integron were identified in this study. One was the classic type (2158 bp) and carried the three conserved resistance gene cassettes of the class 2 integron, dfrA1, sat1 and aadA1, which confer resistance to trimethoprim, streptothricin and streptomycin/spectinomycin, respectively. This type was detected in both Shigella sonnei (14 isolates) and Shigella flexneri (five isolates). The other type was shorter (1313 bp) and carried only two gene cassettes, dfrA1 and sat1. This integron was detected in a single isolate of Shigella sonnei. PFGE patterns showed limited diversity within clusters of the same species. Furthermore, an extended-spectrum beta-lactamase gene, bla(OXA-30), which confers resistance to ampicillin, was characterized in all isolates of Shigella flexneri except the oldest strain, which was isolated in 2000. Southern blot hybridization and conjugation experiments showed that bla(OXA-30) was located in the chromosome.

Insertion sequence ISEcp1-like element connected with a novel aph(2'') allele [aph(2'')-Ie] conferring high-level gentamicin resistance and a novel streptomycin adenylyltransferase gene in Enterococcus

Enterococcus casseliflavus HZ95 is an enterococcus with high-level resistance to aminoglycosides. Nine genes responsible for high-level aminoglycoside resistance, including aac(6')-Ie-aph(2'')-Ia, aph(2'')-Ib, aph(2'')-Ic, aph(2'')-Id, aph(3')-IIIa, aac(6')-Ii, ant(3')-Ia, ant(4')-Ia and ant(6')-Ia, were not detected in HZ95. An 8 kb fragment from unconjugative plasmids of HZ95 was cloned, and expressed gentamicin resistance in Escherichia coli DH5alpha. The genetic structures ( approximately 8 kb DNA fragment) containing these aminoglycoside-modifying enzyme genes in Ent. casseliflavus HZ95 were determined. The deduced amino acid sequence of the novel aph(2'') allele, aph(2'')-Ie, had 93.7 % amino acid identity with APH(2'')-Id. The aph(2'')-Ie gene was bracketed upstream by an insertion sequence (IS)Ecp1-like element and downstream by a streptomycin adenylyltransferase gene (str). The streptomycin adenylyltransferase encoded by the str gene had 80.3 % amino acid identity with the protein encoded by aadE. The plasmid of approximately 16 kb could hybridize with a PCR-generated aph(2'')-Ie intragenic probe. The ISEcp1-like element had 91 % identity with ISEcp1. ISEcp1, which commonly acts as a key factor in the dissemination of CTX-M-type beta-lactamase genes in Gram-negative bacteria, has not been reported in Enterococcus.

paa, originally identified in attaching and effacing Escherichia coli, is also associated with enterotoxigenic E. coli

Previous studies on virotypes and antimicrobial resistance in a collection of porcine enterotoxigenic Escherichia coli (ETEC) O149 strains from Quebec revealed an increase in the number of multiresistant strains (in particular to tetracycline) and the appearance of new virulence factors with time. Among these factors is paa (for porcine attaching- and effacing-associated), originally identified in a porcine enteropathogenic strain, but also present in enterohemorrhagic E. coli O157:H7. In the present study, the association of paa with other ETEC virulence genes, its conservation and expression were investigated in the O149 ETEC collection. All 37 paa-positive strains possessed estB, elt, astA and faeG, and more than half also carried the estA gene, defining two main virotypes, estA(+) and estA(-). Most strains were tetA- or tetB-positive, or both. paa is carried on high molecular weight plasmids. On tetA plasmids, paa is mostly found with enterotoxin gene estA and autotransporter gene sepA. Paa, a 30 kDa protein, is highly conserved and expressed in these strains. Moreover, paaETEC and porcine EPEC/EHEC contain IS signatures, suggesting that paa could be derived from a common ancestor. All these observations suggest a broader role than previously assessed in virulence for paa.

Enterobacter cloacae outbreak and emergence of quinolone resistance gene in Dutch hospital

Plasmid-mediated qnrA1 is an emerging resistance trait.

An outbreak of Enterobacter cloacae infections with variable susceptibility to fluoroquinolones occurred in the University Medical Center Utrecht in the Netherlands in 2002. Our investigation showed that a qnrA1 gene was present in 78 (94%) of 83 outbreak isolates and that a qnrA1-encoding plasmid transferred to other strains of the same species and other species. The earliest isolate carrying this same plasmid was isolated in 1999. qnrA1 was located in a complex integron consisting of the intI1, aadB, qacEΔ1, sul1, orf513, qnrA1, ampR, qacEΔ1, and sul1 genes that were not described previously. On the same plasmid, 2 other class 1 integrons were present. One was a new integron associated with the bla_CTX-M-9 extended-spectrum β-lactamase.

Antimicrobial resistance in Irish isolates of verocytotoxigenic Escherichia coli (E. coli)—VTEC

This study compared the antimicrobial resistance profiles of Escherichia coli O157:H7 isolates (n=257) recovered from bovine hides, minced beef and human clinical samples in Ireland, to those profiles of a range of Irish non-O157 E. coli (O111 and O26) isolates (n=31) from a variety of clinical and veterinary sources. Four multi-drug resistant (MDR) E. coli O157:H7 food isolates were identified, with resistance to 10 (1 isolate), 6 (1 isolate) and 4 (2 isolates) antimicrobial agents, respectively. Two of these isolates (resistant to 7 and 4 antimicrobial classes) were characterised further by molecular methods and found to contain class 1 integrons along with a beta-lactamase-encoding tem-1 gene. Transfer of antimicrobial resistance (ampicillin, streptomycin and sulphonamides), the tem-1 gene and markers (int1, qacEDelta1, sul1) characteristic of class 1 integrons were evident in one MDR isolate (resistant to 4 antimicrobial classes) when conjugation and transformation experiments were performed. A clinical isolate and a veterinary isolate of the O111 serotype were MDR and resistant to 4 and 3 antimicrobial classes, respectively. These data suggest that the prevalence of antimicrobial resistance among the three VTEC serotypes examined in this study is low. However, these organisms may become a public health risk should they enter the food chain.

Molecular understanding of aminoglycoside action and resistance

Aminoglycosides are potent bactericidal antibiotics targeting the bacterial ribosome, where they bind to the A-site and disrupt protein synthesis. They are particularly active against aerobic, Gram-negative bacteria and act synergistically against certain Gram-positive organisms. Aminoglycosides are used in the treatment of severe infections of the abdomen and urinary tract, bacteremia, and endocarditis. They are also used for prophylaxis, especially against endocarditis. Bacterial resistance to aminoglycosides continues to escalate and is widely recognized as a serious health threat. This might be the reason for the interest in understanding the mechanisms of resistance. It is now clear that the resistance occurs by different mechanisms such as prevention of drug entry, active extrusion of drugs, alteration of the drug target (mutational modification of 16S rRNA and mutational modification of ribosomal proteins), and enzymatic inactivation through the expression of enzymes, which covalently modify these antibiotics. Enzymatic inactivation is normally due to acetyltransferases, nucleotidyltransferases, and phosphotransferases. In this review, we focus on the recent concept of molecular understanding of aminoglycoside action and resistance.

Genomic analysis of a multidrug-resistant strain of enterohaemorrhagic Escherichia coli O157 : H7 causing a family outbreak in Japan

A family outbreak of enterohaemorrhagic Escherichia coli (EHEC) O157:H7 infection occurred in October 2003 in the Hiroshima prefecture, Japan. Four isolates of EHEC O157:H7, 03064, 03065, 03066 and 03067, were recovered from a 1-year-old daughter, mother, father and 3-year-old daughter, respectively. All EHEC O157:H7 isolates were positive for Stx1 and Stx2 Shiga toxins. Surprisingly, DNA fingerprinting profiles obtained by PFGE showed that the first isolate, 03064, had unique XbaI and BlnI profiles that differed from the other three isolates. Also, plasmid analysis results revealed that isolate 03064 contained an extra plasmid larger than the classic large plasmid of EHEC O157, pO157 (93.6 kb). This new plasmid was named pMDR157. Furthermore, isolate 03064 showed a multidrug-resistance (MDR) phenotype against streptomycin, spectinomycin, co-trimoxazole (trimethoprim/sulfamethoxazole), ampicillin and tetracycline; the other isolates were completely sensitive to these antibiotics. Molecular analysis of the MDR phenotype in this unique strain revealed the presence of a class 1 integron containing two gene cassettes: a dihydrofolate reductase type 1 gene (dfrI), which confers resistance to trimethoprim, and an aminoglycoside adenyltransferase gene (aadA1), which confers resistance to streptomycin and spectinomycin. Southern blot hybridization showed that the class 1 integron was located in the extra plasmid, pMDR157. The ampicillin resistance was found to be due to the presence of the TEM-1-type beta-lactamase gene. The MDR phenotype was transferred successfully to E. coli HB101 by conjugation, indicating that both the class 1 integron and the TEM-1 beta-lactamase were located on the conjugative transferable plasmid, pMDR157. To the authors' knowledge, this is the first report of the identification of a beta-lactamase gene in EHEC O157.

Molecular characterization of a multidrug-resistant strain of enteroinvasive Escherichia coli O164 isolated in Japan

Enteroinvasive Escherichia coli (EIEC) O164 strain RIMD05091045 was isolated from a travelling patient suffering from diarrhoea at the Osaka airport quarantine facility in Japan. The strain showed multidrug resistance against streptomycin, spectinomycin, co-trimoxazole (trimethoprim/sulfamethoxazole) and ampicillin, and reduced susceptibility to ciprofloxacin. Molecular characterization of the multidrug-resistance phenotype revealed the presence of a class 1 integron containing three genes, a dihydrofolate reductase type XII gene, dfrXII, which confers resistance to trimethoprim, an aminoglycoside adenyltransferase gene, aadA2, which confers resistance to streptomycin and spectinomycin, and an ORF of unknown function. Southern blot hybridization and conjugation experiments showed that the class 1 integron was located on a transferable plasmid that was less than 90 kb in size. The resistance of EIEC O164 to ampicillin was found to be due to the presence of TEM-1 β-lactamase. On the other hand, a single mutation that has not previously been described, P158-to-S, was detected downstream of the quinolone-resistance-determining region of parC of topoisomerase IV and may be responsible for the reduced susceptibility to ciprofloxacin in this strain.

The chloramphenicol resistance genecmlAis disseminated on transferable plasmids that confer multiple-drug resistance in swineEscherichia coli

A recent study of beta-hemolytic Escherichia coli isolated from diarrheic swine found that 53% were resistant to chloramphenicol, a drug that has been prohibited from use in food animals in the US since the mid-1980s. To identify the factors governing the persistence of chloramphenicol resistance in the absence of specific selection pressure, the location of the chloramphenicol resistance gene cmlA and its linkage to other resistance determinants were investigated. Southern blot analysis of plasmid DNA from 46 swine E. coli isolates indicated that cmlA was present on large plasmids greater than 100 kbp. Fifty-two percent of the isolates were able to transfer chloramphenicol resistance to an E. coli recipient at conjugation frequencies ranging from 10(-3) to 10(-8) per recipient. Antimicrobial susceptibility tests on transconjugant strains demonstrated that resistance to sulfamethoxazole, tetracycline, and kanamycin frequently transferred along with chloramphenicol resistance. The transconjugant strains possessed at least two distinct class 1 integrons that linked cmlA to both aminoglycoside resistance genes aadA1 and aadA2 and either to sul1 or to sul3 sulphonamide resistance genes. These results suggest that in the absence of specific chloramphenicol selection pressure, the cmlA gene is maintained by virtue of gene linkage to genes encoding resistance to antimicrobials that are currently approved for use in food animals.