- Characterization of a Salmonella Enteritidis bacteriophage showing broad lytic activity against Gram-negative enteric bacteria
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Shukho Kim , Sung-Hun Kim , Marzia Rahman , Jungmin Kim
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J. Microbiol. 2018;56(12):917-925. Published online October 25, 2018
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DOI: https://doi.org/10.1007/s12275-018-8310-1
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In this study, we sought to isolate Salmonella Enteritidis-specific
lytic bacteriophages (phages), and we found a lytic phage
that could lyse not only S. Enteritidis but also other Gramnegative
foodborne pathogens. This lytic phage, SS3e, could
lyse almost all tested Salmonella enterica serovars as well as
other enteric pathogenic bacteria including Escherichia coli,
Shigella sonnei, Enterobacter cloacae, and Serratia marcescens.
This SS3e phage has an icosahedral head and a long tail, indicating
belong to the Siphoviridae. The genome was 40,793
base pairs, containing 58 theoretically determined open reading
frames (ORFs). Among the 58 ORFs, ORF49, and ORF25
showed high sequence similarity with tail spike protein and
lysozyme-like protein of Salmonella phage SE2, respectively,
which are critical proteins recognizing and lysing host bacteria.
Unlike SE2 phage whose host restricted to Salmonella
enterica serovars Enteritidis and Gallinarum, SS3e showed
broader host specificity against Gram-negative enteric bacteria;
thus, it could be a promising candidate for the phage
utilization against various Gram-negative bacterial infection
including foodborne pathogens.
-
Citations
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Antimicrobial Agents and Chemotherapy.2025;[Epub] CrossRef - Therapeutic potential of novel phages with antibiotic combinations against ESBL-producing and carbapenem-resistant Escherichia Coli
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- Inverse PCR for subtyping of Acinetobacter baumannii carrying ISAba1
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Shukho Kim , Yun-Ju Park , Jungmin Kim
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J. Microbiol. 2016;54(5):376-380. Published online April 20, 2016
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DOI: https://doi.org/10.1007/s12275-016-6038-3
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342
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3
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Abstract
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Acinetobacter baumannii has been prevalent in nosocomial
infections, often causing outbreaks in intensive care units.
ISAba1 is an insertion sequence that has been identified only
in A. baumannii and its copy number varies among strains.
It has been reported that ISAba1 provides a promoter for
blaOXA-51-like, blaOXA-23-like, and blaampC, which are associated
with the resistance of A. baumannii to carbapenems and cephalosporins.
The main purpose of this study was to develop
a novel inverse PCR method capable of typing A. baumannii
strains. The method involves three major steps: cutting of genomic
DNA with a restriction enzyme, ligation, and PCR.
In the first step, bacterial genomic DNA was digested with
DpnI. In the second step, the digested genomic DNAs were
ligated to form intramolecular circular DNAs. In the last step,
the ligated circular DNAs were amplified by PCR with primers
specific for ISAba1 and the amplified PCR products
were electrophoresed. Twenty-two clinical isolates of A. baumannii
were used for the evaluation of the inverse PCR (iPCR)
typing method. Dendrogram analysis revealed two major clusters,
similar to pulsed-field gel electrophoresis (PFGE) results.
Three ISAba1-associated genes – blaampC, blaOXA-66-like, and
csuD – were amplified and detected in the clinical isolates.
This novel iPCR typing method is comparable to PFGE in its
ability to discriminate A. baumannii strains, and is a promising
molecular epidemiological tool for investigating A.
baumannii carrying ISAba1.
-
Citations
Citations to this article as recorded by - DNA sonication inverse PCR for genome scale analysis of uncharacterized flanking sequences
David E. Alquezar‐Planas, Ulrike Löber, Pin Cui, Claudia Quedenau, Wei Chen, Alex D. Greenwood, Susan Johnston
Methods in Ecology and Evolution.2021; 12(1): 182. CrossRef -
Update on the Epidemiological Typing Methods for
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Rayane Rafei, Marwan Osman, Fouad Dabboussi, Monzer Hamze
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Extremophiles.2018; 22(3): 473. CrossRef
- The N3 Subdomain in A Domain of Fibronectin-Binding Protein B Isotype I Is an Independent Risk Determinant Predictive for Biofilm Formation of Staphylococcus aureus Clinical Isolates
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An Sung Kwon , Dong Hoon Lim , Hyo Jung Shin , Geon Park , Jong H. Reu , Hyo Jin Park , Jungmin Kim , Yong Lim
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J. Microbiol. 2013;51(4):499-505. Published online August 30, 2013
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DOI: https://doi.org/10.1007/s12275-013-3319-y
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225
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8
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Abstract
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Fibronectin-binding proteins (FnBP), FnBPA and FnBPB, are purported to be involved in biofilm formation of Staphylococcus aureus. This study was performed to find which of three consecutive N subdomains of the A domain in the FnBP is the key domain in FnBP. A total of 465 clinical isolates of S. aureus were examined for the biofilm forming capacity and the presence of N subdomains of FnBP. In the biofilm-positive strains, N2 and N3 subdomains of FnBPA, and N1 and N3 subdomains of FnBPB were significantly more prevalent. Multivariate logistic regression analysis of 246 biofilm-positive and 123 biofilm-negative strains identified only the FnBPB-N3 subdomain as an independent risk determinant predictive for biofilm-positive strains of S. aureus (Odds ratio [OR], 13.174; P<0.001). We also attempted to delete each of the fnbA-N2 and -N3 and fnbB-N1 and -N3 from S. aureus strain 8325-4 and examined the biofilm forming capacity in the derivative mutants. In agreement with the results of the multivariate regression analysis, deletion of either the fnbA-N2 or -N3, or fnbB-N1 did not significantly diminish the capacity of strain 8325-4 to develop a biofilm, while deletion of the fnbB-N3 did. Therefore, it is suggested that the FnBPB-N3 subdomain of isotype I may be a key domain in FnBP which is responsible for the causing biofilm formation in S. aureus clinical isolates.
- NOTE] Involvement of Curli Fimbriae in the Biofilm Formation of Enterobacter cloacae
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Sung-Min Kim , Hee-Woo Lee , Yeh-Wan Choi , Shuk-Ho Kim , Je-Chul Lee , Yoo-Chul Lee , Sung-Yong Seol , Dong-Taek Cho , Jungmin Kim
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J. Microbiol. 2012;50(1):175-178. Published online February 27, 2012
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DOI: https://doi.org/10.1007/s12275-012-2044-2
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274
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Abstract
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In this study, we examined the biofilm forming ability, the
mRNA expression of curli genes and the morphologies of
curli fimbriae and biofilms in clinical isolates of Enterobacter
cloacae. The csgBA operon was found in 11 (78.6%) of the
14 isolates. The ability of E. cloacae isolates to form biofilms
was significantly correlated with the mRNA expression level
of the csgA and csgD genes. The curli protein fimbriae appeared
as tangled fibers and the curli-proficient strain formed
mature biofilms. Our data suggest that the expression of the
curli fimbriae play an important role in biofilm formation
in E. cloacae.
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Birendra R. Tiwari , Shukho Kim , Marzia Rahman , Jungmin Kim
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DOI: https://doi.org/10.1007/s12275-011-1512-4
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212
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Recently, lytic bacteriophages (phages) have been focused on treating bacterial infectious diseases. We investigated the protective efficacy of a novel Pseudomonas aeruginosa phage, PA1Ø, in normal and neutropenic mice. A lethal dose of P. aeruginosa PAO1 was administered via the intraperitoneal route and a single
dose of PA1Ø with different multiplicities of infection (MOI) was treated into infected mice. Immunocompetent mice infected with P. aeruginosa PAO1 were successfully protected by PA1Ø of 1 MOI, 10 MOI or 100 MOI with 80% to 100% survival rate. No viable bacteria were found in organ samples after 48 h of the phage treatment. Phage clearing patterns were different in the presence or absence of host bacteria but PA1Ø disappeared from all organs after 72 h except spleen in the presence of host bacteria. On the contrary, PA1Ø treatment could not protect neutropenic mice infected with P. aeruginosa PAO1 even though could extend their lives for a short time. In in vitro phage-neutrophil bactericidal test, a stronger bactericidal effect was observed in phage-neutrophil co-treatment than in phage single treatment without neutrophils, suggesting phage-neutrophil co-work is essential for the efficient killing of bacteria in the mouse model. In conclusion, PA1Ø can be possibly utilized in future phage therapy endeavors since it exhibited strong protective effects against virulent P. aeruginosa infection.
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Migma Dorji Tamang , Shukho Kim , Sung-Min Kim , Hyun-Hee Kong , Jungmin Kim
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J. Microbiol. 2011;49(5):841-846. Published online November 9, 2011
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DOI: https://doi.org/10.1007/s12275-011-1063-8
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Acinetobacter baumannii is virtually avirulent for healthy people but maintains a high virulence among critically ill patients or immuno-compromised individuals. The ability of A. baumannii to adhere to cells and persist on surfaces as biofilms could be central to its pathogenicity. In the present study, we compared the virulence of the A. baumannii 1656-2 clinical strain, which is able to form a thick biofilm, with the virulence of the A. baumannii type strain (ATCC 19606T). Acanthamoeba castellanii, a single-celled organism, was used as the host model system to study the virulence of A. baumannii. Compared to A. baumannii ATCC 19606T, A. baumannii 1656-2 exhibited a higher ability to adhere and invade A. castellanii cells and had a higher killing rate of A. castellanii cells. Furthermore, co-incubation of the amoeba cells and the cell-free supernatant of A. baumannii resulted in the cell death of the amoebae. Heat inactivation or proteinase K treatment of the supernatant did not eliminate its cytotoxicity, suggesting heat stable non-protein factors are responsible for its cytotoxicity to A. castellanii cells. In conclusion, this study for the first time has revealed the capacity of the A. baumannii strain and/or its metabolic products to induce cytotoxicity in A. castellanii cells.
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Abstract
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Multidrug-resistant clinical isolates of Providencia carrying blaPER-1 and blaVIM-2 were evaluated for the abilities to form biofilm and high biofilm forming capacity was demonstrated in them. Minimum biofilm inhibitory concentrations (MBICs), minimum biofilm eradication concentrations (MBECs), and minimum inhibitory concentrations (MICs) for imipenem and meropenem were also determined. In all tested strains, the MBICs were higher than the MICs for both drugs. Interestingly, the MBICs and the MBEC50 for meropenem were lower than those for imipenem in the isolates producing high amounts of biofilm, suggesting that meropenem is superior to imipenem in the growth inhibition and eradication of biofilm forming Providencia strains.
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This study introduces a simple colorimetric method which can measure the antimicrobial susceptibility of bacteria in biofilms using trimethyl tetrazolium chloride (TTC) as an indicator of viable bacteria. The new method was utilized for the evaluation of antibiotic susceptibility of Escherichia coli, Klebsiella pneumoniae, and Staphylococcus aureus biofilms.
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Pseudomonas aeruginosa is an opportunistic human pathogen of clinical importance that causes airway infections in immunocompromised patients. Here, we report the virulence-associated characteristics of strains of P. aeruginosa, isolated from the sputa of 25 Korean pneumonia patients. A high degree of genomic plasticity was observed by random amplified polymorphic DNA genotype analysis, suggesting that the infections were caused by strains with diverse genomic backgrounds. Biofilm formation of each isolate was heterogeneous in terms of their relative motilities. In addition, 48% of isolates were defective in the production of 3-oxo-C12-HSL (PAI-1), a quorum sensing signal molecule. In these strains, PAI-1-dependent elastase production was correspondingly decreased, suggesting that a large number of strains were presumed to be quorum sensing deficient. Multidrug resistance (MDR) was seen in 56% of the isolates tested, and 44% of the MDR strains were resistant to five or more antibiotics. Taken together, our results provide additional insights into the virulence traits of P. aeruginosa clinical isolates, which will aid in treating P. aeruginosa infections in pneumonia patients.
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Ji-Hyun Shin , Hee-Woo Lee , Sung-Min Kim , Jungmin Kim
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J. Microbiol. 2009;47(6):728-735. Published online February 4, 2010
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DOI: https://doi.org/10.1007/s12275-009-0158-y
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Recently, multidrug-resistant clinical isolates of Acinetobacter baumannii have been found to have a high capacity to form biofilm. It is well known that bacterial cells within biofilms are highly resistant to antibiotics, UV light, acid exposure, dehydration, and phagocytosis in comparison to their planktonic counterparts, which suggests that the cells in a biofilm have altered metabolic activity. To determine which proteins are up-regulated in A. baumannii biofilm cells, we performed a proteomic analysis. A clinical isolate of A. baumannii 1656-2, which was characterized to have a high biofilm forming ability, was cultivated under biofilm and planktonic conditions. Outer membrane enriched A. baumannii 1656-2 proteins were separated by two-dimensional (2-D) gel electrophoresis and the differentially expressed proteins were identified by MALDI-TOF mass spectrometry. The proteins up-regulated or expressed only in biofilm cells of A. baumannii are categorized as follows: (i) proteins processing environmental information such as the outer membrane receptor protein involved in mostly Fe transport, a sensor histidine kinase/response regulator, and diguanylate cyclase (PAS-GGEDF-EAL domain); (ii) proteins involved in metabolism such as NAD- linked malate dehydrogenase, nucleoside-diphosphate sugar epimerase, putative GalE, ProFAR isomerase, and N-acetylmuramoyl-L-alanine amidase; (iii) bacterial antibiotic resistance related proteins; and (iv) proteins related to gene repair such as exodeoxyribonuclease III and GidA. This proteomic analysis provides a fundamental platform for further studies to reveal the role of biofilm in the persistence and tolerance of A. baumannii.
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Hee Young Kang , Jungmin Kim , Sung Yong Seol , Yoo Chul Lee , Je Chul Lee , Dong Taek Cho
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J. Microbiol. 2009;47(1):68-75. Published online February 20, 2009
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DOI: https://doi.org/10.1007/s12275-008-0158-3
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In this study, we identified extended-spectrum ß-lactamase (ESBL) and plasmid-mediated AmpC ß-lactamase which were associated with 16S rRNA methylase gene on the conjugative plasmid. Among 82 clinical isolates of Enterobacteriaceae that carry 16S rRNA methylase gene (64 strains, armA, and 18 strains, rmtB), blaSHV-12 was detected either alone or combined with blaDHA-1, blaCTX-M-3, and blaCTX-M-14 in 30 strains carrying armA and 6 strains carrying rmtB. The blaCTX-M-3 was detected in 13 of 64 strains carrying armA but no strains carrying rmtB. Whereas blaCTX-M-14 was detected in 15 of 18 strains carrying rmtB but only 2 of 64 strains carrying armA. Overall, blaSHV-12 and blaCTX-M-14 was the most common ESBL gene which was associated with armA and rmtB, respectively. In addition, we found that blaCTX-M-3 localized with armA on the same IncL/M plasmid and blaCTX-M-14 localized with rmtB on the same IncA/C plasmid. Restriction fragment length polymorphism of conjugative plasmids and pulsed-field gel electrophoresis of genomic DNAs revealed that intercellular horizontal transfer of conjugative plasmid and clonal transmission have been occurred at the same time.
- The Identification of CTX-M-14, TEM-52, and CMY-1 Enzymes in Escherichia coli Isolated from the Han River in Korea
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Jungmin Kim , Hee Young Kang , Yeonhee Lee
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J. Microbiol. 2008;46(5):478-481. Published online October 31, 2008
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DOI: https://doi.org/10.1007/s12275-008-0150-y
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361
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From water samples collected monthly between 2000 and 2001 from the Han River in Seoul, sixteen strains of Escherichia coli which confer resistance to at least 10 kinds of antimicrobial agents were isolated. From these isolates, 2 kinds of extended-spectrum β-lactamases (ESBLs) and one plasmid-mediated AmpC β-lactamase were detected; CTX-M-14 from 10 isolates, TEM-52 from 5 isolates, and CMY-1 from one isolate. Class 1 integron gene cassettes, such as aadA1, dfr12-orfF-aadA2, and dfr17-aadA5, were also detected and the integrons are the same as those found in E. coli isolated from swine, poultry, and humans in Korea. The result of this study indicated the importance of river water as a reservoir for antimicrobial resistance genes and resistant bacteria.
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- A Comparison of Adult and Pediatric Methicillin-Resistant Staphylococcus aureus Isolates Collected from Patients at a University Hospital in Korea
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Jin Yeol Park , Jong Sook Jin , Hee Young Kang , Eun Hee Jeong , Je Chul Lee , Yoo Chul Lee , Sung Yong Seol , Dong Taek Cho , Jungmin Kim
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J. Microbiol. 2007;45(5):447-452.
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DOI: https://doi.org/2591 [pii]
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Abstract
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In this study, we compared the phenotypic and genotypic characteristics of 138 MRSA isolates obtained from adult and pediatric patients (adult, 50; children, 88). The resistance rates against gentamicin, clindamycin, and ciprofloxacin were much higher in the adult MRSA isolates than in the pediatric MRSA isolates. The ermC gene, which is responsible for inducible clindamycin resistance, was detected in 52(59.1%) of the 88 pediatric MRSA isolates but in only 5(10.0%) of the 50 adult MRSA isolates. MRSA isolates of clonal type ST5 with an integration of SCCmec type II/II variants was the most predominant clone among the adult isolates, while clonal type ST72 with an integration of SCCmec IV/IVA was the most predominant clone among the pediatric MRSA isolates. Staphylococcal enterotoxin A and toxic shock syndrome toxin-1 were prevalent among the adult MRSA isolates but not among the pediatric MRSA isolates. The results of this study demonstrated remarkable differences between adult and pediatric MRSA isolates in terms of their antimicrobial susceptibility profiles, SCCmec type, multilocus sequence type, staphylococcal toxin genes, and erythromycin resistance genes.
- Multidrug-Resistant Providencia Isolates Carrying blaPER-1, blaVIM-2, and armA
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Hee-Woo Lee , Hee-Young Kang , Kyeong-Seob Shin , Jungmin Kim
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J. Microbiol. 2007;45(3):272-274.
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DOI: https://doi.org/2531 [pii]
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Abstract
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During May to July 2004, three strains of Providencia spp. with multidrug-resistance (MDR) were isolated from urinary specimen of three patients hospitalized with a same hospital room. By PCR analysis, all three strains have been found to carry both VIM-2 type metallo-β-lactamase gene and PER-1 type extendedspectrum β-lactamase gene. One out of three strains carried additional resistance gene, armA, 16S rRNA methylase gene responsible for high level resistance to aminoglycosides. To our knowledge, this is the first report on the identification of Providencia spp. simultaneously carrying blaVIM-2, blaPER-1, and armA genes.
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