| 1. |
- Gumpert, H., et al.
(författare)
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Transfer and Persistence of a Multi-Drug Resistance Plasmid in situ of the Infant Gut Microbiotain the Absence of Antibiotic Treatment
- 2017
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Ingår i: Frontiers in Microbiology. - : Frontiers Media SA. - 1664-302X. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- The microbial ecosystem residing in the human gut is believed to play an important role in horizontal exchange of virulence and antibiotic resistance genes that threatens human health. While the diversity of gut-microorganisms and their genetic content has been studied extensively, high-resolution insight into the plasticity, and selective forces shaping individual genomes is scarce. In a longitudinal study, we followed the dynamics of co-existing Escherichia coli lineages in an infant not receiving antibiotics. Using whole genome sequencing, we observed large genomic deletions, bacteriophage infections, as well as the loss and acquisition of plasmids in these lineages during their colonization of the human gut. In particular, we captured the exchange of multidrug resistance genes, and identified a clinically relevant conjugative plasmid mediating the transfer. This resistant transconjugant lineage was maintained for months, demonstrating that antibiotic resistance genes can disseminate and persist in the gut microbiome; even in absence of antibiotic selection. Furthermore, through in vivo competition assays, we suggest that the resistant transconjugant can persist through a fitness advantage in the mouse gut in spite of a fitness cost in vitro. Our findings highlight the dynamic nature of the human gut microbiota and provide the first genomic description of antibiotic resistance gene transfer between bacteria in the unperturbed human gut. These results exemplify that conjugative plasmids, harboring resistance determinants, can transfer and persists in the gut in the absence of antibiotic treatment.
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| 2. |
- Helldal, Lisa, et al.
(författare)
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Evaluation of MLVA for epidemiological typing and outbreak detection of ESBL-producing Escherichia coli in Sweden
- 2017
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Ingår i: Bmc Microbiology. - : Springer Science and Business Media LLC. - 1471-2180. ; 17
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Tidskriftsartikel (refereegranskat)abstract
- Background: To identify the spread of nosocomial infections and halt outbreak development caused by Escherichia coli that carry multiple antibiotic resistance factors, such as extended-spectrum beta-lactamases (ESBLs) and carbapenemases, is becoming demanding challenges due to the rapid global increase and constant and increasing influx of these bacteria from the community to the hospital setting. Our aim was to assess a reliable and rapid typing protocol for ESBL-E. coli, with the primary focus to screen for possible clonal relatedness between isolates. All clinical ESBL-E. coli isolates, collected from hospitals (n = 63) and the community (n = 41), within a single geographical region over a 6 months period, were included, as well as clinical isolates from a polyclonal outbreak (ST131, n = 9, and ST1444, n = 3). The sporadic cases represented 36 STs, of which eight STs dominated i.e. ST131 (n = 33 isolates), ST648 (n = 10), ST38 (n = 9), ST12 and 69 (each n = 4), ST 167, 405 and 372 (each n = 3). The efficacy of multiple-locus variable number tandem repeat analysis (MLVA) was evaluated using three, seven or ten loci, in comparison with that of pulsed-field gel electrophoresis (PFGE) and multi locus sequence typing (MLST). Results: MLVA detected 39, 55 and 60 distinct types, respectively, using three (GECM-3), seven (GECM-7) or ten (GECM-10) loci. For GECM-7 and -10, 26 STs included one type and eleven STs each included several types, the corresponding numbers for GECM-3 were 29 and 8. The highest numbers were seen for ST131 (7,7 and 8 types, respectively), ST38 (5,5,8) and ST648 (4,5,5). Good concordance was observed with PFGE and GECM-7 and -10, despite fewer types being identified with MLVA; 78 as compared to 55 and 60 types. The lower discriminatory power of MLVA was primarily seen within the O25b-ST131 lineage (n = 34) and its H30-Rx subclone (n = 21). Epidemiologically unrelated O25b-ST131 isolates were clustered with O25b-ST131 outbreak isolates by MLVA, whereas the ST1444 outbreak isolates were accurately distinguished from unrelated isolates. Conclusion: MLVA, even when using only three loci, represents an easy initial typing tool for epidemiological screening of ESBL-E. coli. For the ST131-O25b linage, complementary methods may be needed to obtain sufficient resolution.
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| 3. |
- Helldal, Lisa, et al.
(författare)
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Increasing prevalence of ESBL but not AmpC in Escherichia coli and Klebsiella pneumoniae, in Göteborg, 2004-2008
- 2009
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Ingår i: Scandinavian Society for Antimicrobial Chemotherapy - 2009, September 3, Tromsø, Norway.
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Introduction: The increasing prevalence of transferable broad-spectrum resistance to beta-lactams, such as Extended Spectrum Beta Lactamases (ESBL) and AmpC, is troublesome, since they confer resistance to cephalosporins and penicillins, and often also are associated with additional resistance. Materials and methods: Resistance for E. coli and Klebsiella pneumoniae isolated from urine (~10.000 isolates/year) and blood (~xxx isolates/year), during 2004-2008 were determined. Cephalosporin resistant isolates were examined for presence of ESBL with a double-disk-assay using clavulanic acid as inhibitory substance. Cefoxitine-resistant strains were analyzed for presence of AmpC with a second double-disk-assay using cloxacillin as inhibitory substance. Positive strains where further tested with PCR assays for ESBL and plasmid AmpC. Results: During 2004-2008 presence of ESBL increased from 0,3–1,5% in urinary and 0,0–1,4 % in blood E. coli. For Klebsiella the corresponding figures were 0,08–0,68% and 0%, respectively. For ESBL-producing E. coli, 60–80% were resistant also to quinolones and trimetoprime. In 2008, the vast a majority of the ESBL-isolates carried CTX-M subtype 1. Approximately 50 % is community-acquired isolates. 0,15-0,23% of the urinary E. coli-strains had phenotypical characteristics indicating AmpC-production. Presence of plasmid-mediated AmpC will be tested. Approximately 50% of these were multidrug resistant. In blood E coli isolates as well as in Klebsiella from urine and blood AmpC was rarely detected (0-2 isolates/year). Discussion and Conclusion: There is a steady increase in ESBL-producing bacteria in our region. However, the frequency of isolates with AmpC is still low. In addition, a majority of these strains are multidrug resistant which is particularly alarming.
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| 4. |
- Helldal, Lisa, et al.
(författare)
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Shift of CTX-M genotypes has determined the increased prevalence of extended-spectrum beta-lactamase-producing Escherichia coli in south-western Sweden
- 2013
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Ingår i: Clinical Microbiology and Infection. - : Elsevier BV. - 1198-743X .- 1469-0691. ; 19:2
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Tidskriftsartikel (refereegranskat)abstract
- The prevalence of Escherichia coli producing extended-spectrum β-lactamases (ESBLs) markedly increased during 2004-2008 in south-western Sweden, with a greater increase in urinary isolates in hospitals (0.2-2.5%) than in the community (0.2-1.6%). ESBLs of genotype CTX-M predominated, with a significant (p<0.02) shift from the CTX-M-9 to CTX-M-1 phylogroup occurring among urinary ESBL-producing E.coli isolated early (n=41) as compared with late (n=221) in the study period. The increase in ESBL-producing E.coli was polyclonal, and only partly attributable to an increase (0-24%) in the number of O25b-ST131 isolates carrying CTX-M-15. The increase was prominent in men and in elderly patients, and warrants continued surveillance.
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| 5. |
- Helldal, Lisa, et al.
(författare)
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Shifts in Extended-Spectrum Beta-Lactamase types with increasing prevalence of Escherichia coli producing ESBL
- 2010
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Ingår i: 20th European Congress of Clinical Microbiology and Infectious Diseases (ECCMID), Vienna, Austria.
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Objectives: Contrary to other multidrug-resistant pathogens, the prevalence of bacteria producing extended-spectrum beta-lactamase (ESBL) is increasing rapidly in Sweden. In Europe, ESBL of CTX-M-, TEM-, OXA- and SHV-types are generally associated with E. coli infections, CTX-M being the most predominant. We have investigated how the prevalence of these types has changed during the last five years in the low endemic setting of western Sweden. Methods: Yearly resistance in urinary (approximately 10,000 isolates/year) and blood (approximately 250 isolates/year) E. coli during 2004-2008 were determined. Cephalosporin-resistant isolates were screened for ESBL, using a double-disk assay with clavulanic acid as the inhibitory agent. All ESBL-E. coli isolated in the region during the periods Sept 2003-April 2005 (n=46) and April 2008-March 2009 (n=256) were typed by multiplex-PCR, detecting CTX-M, TEM, OXA and SHV. CTX-M-positive isolates were sub-typed by real time Q-PCR for CTX-M-1, CTX-M-2 and CTXM-9 groups. Results: During 2004-2008, ESBL-producing E. coli strains increased from 0.3-1.5% in urinary and 0-1.4% in blood isolates. Resistance to quinolones and trimethoprim was observed in 60-80% of strains, as compared to less than 8% in non-ESBL-producing E. coli. The majority of the ESBL-E. coli strains possessed the CTX-M gene-type, increasing from 78% (36/46) in 2003-2005 to 93% (238/256) in 2008-2009. Between these time-periods, a marked shift occurred in the distribution of CTX-M types, in that strains with the CTX-M-9 group decreased from 42% (15/36) of isolates to 21% (51/238, p=0.01) and, simultaneously, strains with the CTX-M-1 group increased from 58% (21/36) to 78% (185/238, p= 0.02). Furthermore, strains of CTX-M-type exhibiting also TEM- and/or OXA increased to comprise 86% of cases, as compared to 75% previously. Similar trends were seen for community and hospital detected isolates and with no differences associated with age in affected patients. Conclusion: A steady increase in multidrug-resistant ESBL-E. coli, possessing the genes for multiple ESBL-types, was observed in western Sweden, contrary to the patterns of other multidrug-resistant bacteria. As ESBL has increased during the five-year study period, we detected a shift in the prevalence of ESBL-types, currently dominated by the CTX-M-1 group. These observations suggest that a novel ESBL-producing E. coli clone may have emerged in the area, which will be further investigated and presented.
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| 6. |
- Johnning, Anna, 1985, et al.
(författare)
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The resistomes of six carbapenem-resistant pathogens - a critical genotype-phenotype analysis
- 2018
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Ingår i: Microbial Genomics. - : Microbiology Society. - 2057-5858. ; 4:11
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Tidskriftsartikel (refereegranskat)abstract
- Carbapenem resistance is a rapidly growing threat to our ability to treat refractory bacterial infections. To understand how carbapenem resistance is mobilized and spread between pathogens, it is important to study the genetic context of the underlying resistance mechanisms. In this study, the resistomes of six clinical carbapenem-resistant isolates of five different species - Acinetobacter baumannii, Escherichia colt, two Klebsiella pneumoniae, Proteus mirabilis and Pseudomonas aeruginosa - were characterized using whole genome sequencing. All Enterobacteriaceae isolates and the A. baumannii isolate had acquired a large number of antimicrobial resistance genes (7-18 different genes per isolate), including the following encoding carbapenemases: bla(KPC-2), bla(OXA-48), bla(OXA-72), bla(NDM-1), bla(NDm-7) and bla(VIM-1). In addition, a novel version of bla(SHv) was discovered. Four new resistance plasmids were identified and their fully assembled sequences were verified using optical DNA mapping. Most of the resistance genes were colocalized on these and other plasmids, suggesting a risk for coselection. In contrast, five out of six carbapenemase genes were present on plasmids with no or few other resistance genes. The expected level of resistance - based on acquired resistance determinants - was concordant with measured levels in most cases. There were, however, several important discrepancies for four of the six isolates concerning multiple classes of antibiotics. In conclusion, our results further elucidate the diversity of carbapenemases, their mechanisms of horizontal transfer and possible patterns of co-selection. The study also emphasizes the difficulty of using whole genome sequencing for antimicrobial susceptibility testing of pathogens with complex genotypes.
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| 7. |
- Karami, Nahid, 1959, et al.
(författare)
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Antibiotic resistance is linked to carriage of papC and iutA virulence genes and phylogenetic group D background in commensal and uropathogenic Escherichia coli from infants and young children.
- 2017
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Ingår i: European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology. - : Springer Science and Business Media LLC. - 1435-4373. ; 36:4, s. 721-729
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Tidskriftsartikel (refereegranskat)abstract
- P fimbriae, enabling adherence to colonic and urinary epithelium, and aerobactin, an iron sequestering system, are both colonization factors in the human colon and virulence factors for urinary tract infection. The colonic microbiota is suggested to be a site suitable for the transfer of antibiotic resistance genes. We investigated whether phenotypic resistance to antibiotics in commensal and uropathogenic Escherichia coli from infants and young children is associated with carriage of virulence genes and to phylogenetic group origin and, in the case of fecal strains, to persistence in the gut and fecal population levels. The commensal strains (n=272) were derived from a birth cohort study, while the urinary isolates (n=205) were derived from outpatient clinics. Each strain was assessed for phenotypic antibiotic resistance and for carriage of virulence genes (fimA, papC, sfaD/E, hlyA, iutA, kfiC, and neuB), phylogenetic group (A, B1, B2, or D), and markers of particular virulent clones (CGA-D-ST69, O15:H1-D-ST393, and O25b:H4-B2-ST131). Resistance to ampicillin, tetracycline, and trimethoprim was most prevalent. Multivariate analysis showed that resistance to any antibiotic was significantly associated with carriage of genes encoding P fimbriae (papC) and aerobactin (iutA), and a phylogenetic group D origin. Neither fecal population numbers nor the capacity for long-term persistence in the gut were related to antibiotic resistance among fecal strains. Our study confirms the importance of phylogenetic group D origin for antibiotic resistance in E. coli and identifies the virulence genes papC and iutA as determinants of antibiotic resistance. The reason for the latter association is currently unclear.
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| 8. |
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| 9. |
- Karami, Nahid, 1959, et al.
(författare)
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Sub-Typing of Extended-Spectrum-beta-Lactamase-Producing Isolates from a Nosocomial Outbreak: Application of a 10-Loci Generic Escherichia coli Multi-Locus Variable Number Tandem Repeat Analysis
- 2013
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Ingår i: Plos One. - : Public Library of Science (PLoS). - 1932-6203. ; 8:12
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Tidskriftsartikel (refereegranskat)abstract
- Extended-spectrum beta-lactamase producing Escherichia coli (ESBL-E. coli) were isolated from infants hospitalized in a neonatal, post-surgery ward during a four-month-long nosocomial outbreak and six-month follow-up period. A multi-locus variable number tandem repeat analysis (MLVA), using 10 loci (GECM-10), for 'generic' (i.e., non-STEC) E. coli was applied for sub-species-level (i.e., sub-typing) delineation and characterization of the bacterial isolates. Ten distinct GECM-10 types were detected among 50 isolates, correlating with the types defined by pulsed-field gel electrophoresis (PFGE), which is recognized to be the 'gold-standard' method for clinical epidemiological analyses. Multi-locus sequence typing (MLST), multiplex PCR genotyping of bla(CTX-M), bla(TEM), bla(OXA) and bla(SHV) genes and antibiotic resistance profiling, as well as a PCR assay specific for detecting isolates of the pandemic O25b-ST131 strain, further characterized the outbreak isolates. Two clusters of isolates with distinct GECM-10 types (G06-04 and G07-02), corresponding to two major PFGE types and the MLST-based sequence types (STs) 131 and 1444, respectively, were confirmed to be responsible for the outbreak. The application of GECM-10 sub-typing provided reliable, rapid and cost-effective epidemiological characterizations of the ESBL-producing isolates from a nosocomial outbreak that correlated with and may be used to replace the laborious PFGE protocol for analyzing generic E. coli.
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| 10. |
- Karami, Nahid, 1959, et al.
(författare)
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Tetracycline resistance in Escherichia coli and persistence in the infantile colonic microbiota.
- 2006
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Ingår i: Antimicrobial agents and chemotherapy. - 0066-4804. ; 50:1, s. 156-61
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Tidskriftsartikel (refereegranskat)abstract
- The ecological impact of antibiotic resistance in the absence of selective pressure has been poorly studied. We assessed the carriage of tetracycline resistance genes, persistence in the microbiota, fecal population counts and virulence factor genes in 309 commensal, intestinal Escherichia coli strains obtained from 128 Swedish infants followed during the first year of life with regular quantitative fecal cultures. No infant was given tetracycline, but 25% received other antibiotics. Tetracycline resistance was identified in 12% of strains, all of which carried either tet(A) (49%) or tet(B) (51%) genes. Resistance to other antibiotics occurred in 50% of tet(A)-positive strains, 42% of tet(B)-positive strains and 13% of tetracycline-sensitive strains. However, colonization with tetracycline-resistant strains was unrelated to treatment with antibiotics. Strains that were tet(B)- or tet(A)-positive carried the genes for P fimbriae and aerobactin, respectively, more often than susceptible strains. Tetracycline-resistant and -susceptible strains were equally likely to persist among the intestinal microbiota for > or = 3 weeks and had similar population numbers. However, when a resistant strain and a susceptible strain colonized a child simultaneously, the resistant variety showed lower counts (P = 0.03). In cases of long-term colonization by initially tetracycline-resistant E. coli strains, loss of tet genes occurred in 3 of 13 cases with variable effects on population counts. The results indicate that there is limited pressure against the carriage of tet genes in the infantile gut microbiota even in the absence of antibiotics. Resistant strains may possess colonization factors that balance the cost of producing resistance elements.
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