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Boueroy P, Chopjitt P, Hatrongjit R, Morita M, Sugawara Y, Akeda Y, Iida T, Hamada S, Kerdsin A. Fluoroquinolone resistance determinants in carbapenem-resistant Escherichia coli isolated from urine clinical samples in Thailand. PeerJ 2023; 11:e16401. [PMID: 37953793 PMCID: PMC10638923 DOI: 10.7717/peerj.16401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 10/12/2023] [Indexed: 11/14/2023] Open
Abstract
Background Escherichia coli is the most common cause of urinary tract infections and has fluoroquinolone (FQ)-resistant strains, which are a worldwide concern. Objectives To characterize FQ-resistant determinants among 103 carbapenem-resistant E. coli (CREc) urinary isolates using WGS. Methods Antimicrobial susceptibility, biofilm formation, and short-read sequencing were applied to these isolates. Complete genome sequencing of five CREcs was conducted using short- and long-read platforms. Results ST410 (50.49%) was the predominant ST, followed by ST405 (12.62%) and ST361 (11.65%). Clermont phylogroup C (54.37%) was the most frequent. The genes NDM-5 (74.76%) and CTX-M-15 (71.84%) were the most identified. Most CREcs were resistant to ciprofloxacin (97.09%) and levofloxacin (94.17%), whereas their resistance rate to nitrofurantoin was 33.98%. Frequently, the gene aac(6')-Ib (57.28%) was found and the coexistence of aac(6')-Ib and blaCTX-M-15 was the most widely predominant. All isolates carried the gyrA mutants of S83L and D87N. In 12.62% of the isolates, the coexistence was detected of gyrA, gyrB, parC, and parE mutations. Furthermore, the five urinary CREc-complete genomes revealed that blaNDM-5 or blaNDM-3 were located on two plasmid Inc types, comprising IncFI (60%, 3/5) and IncFI/IncQ (40%, 2/5). In addition, both plasmid types carried other resistance genes, such as blaOXA-1, blaCTX-M-15, blaTEM-1B, and aac(6')-Ib. Notably, the IncFI plasmid in one isolate carried three copies of the blaNDM-5 gene. Conclusions This study showed FQ-resistant determinants in urinary CREc isolates that could be a warning sign to adopt efficient strategies or new control policies to prevent further spread and to help in monitoring this microorganism.
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Okada K, Roobthaisong A, Hamada S. Flagella-related gene mutations in Vibrio cholerae during extended cultivation in nutrient-limited media impair cell motility and prolong culturability. mSystems 2023; 8:e0010923. [PMID: 37642466 PMCID: PMC10654082 DOI: 10.1128/msystems.00109-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 04/19/2023] [Indexed: 08/31/2023] Open
Abstract
IMPORTANCE Vibrio cholerae undergoes a transition to a viable but non-culturable (VNC) state when subjected to various environmental stresses. We showed here that flagellar motility was involved in the development of the VNC state of V. cholerae. In this study, motility-defective isolates with mutations in various flagella-related genes, but not motile isolates, were predominantly obtained under the stress of long-term batch culture. Other genomic regions were highly conserved, suggesting that the mutations were selective. During the stationary phase of long-term culture, V. cholerae isolates with mutations in the acetate kinase and flagella-related genes were predominant. This study suggests that genes involved in specific functions in V. cholerae undergo mutations under certain environmental conditions.
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Abe R, Akeda Y, Sugawara Y, Matsumoto Y, Motooka D, Iida T, Hamada S. Carbapenem triggers dissemination of chromosomally integrated carbapenemase genes via conjugative plasmids in Escherichia coli. mSystems 2023:e0127522. [PMID: 37272726 DOI: 10.1128/msystems.01275-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023] Open
Abstract
Epidemiological surveys have shown that carbapenem resistance is mainly transmitted across species by carbapenemase genes located on conjugative plasmids. As chromosomal integration of carbapenemase genes has rarely been identified, only a few studies have investigated their advantages to the carbapenem-resistant bacterial community. Here, we confirmed the increased stability of blaIMP-6 on a chromosome-integrated plasmid in an Escherichia coli isolate compared with that on original plasmids in the absence of antibiotic pressure. Although plasmids carrying carbapenemase genes are supposedly lost in successive generations, we found that the complete plasmid backbone was retained in bacterial cells even after the occasional loss of their antibiotic-resistance cassettes. This backbone structure has been observed worldwide to carry various antimicrobial resistance genes. Although the chromosomally integrated plasmid carrying blaIMP-6 could not be transmitted by conjugation, we found that meropenem treatment for 1 wk allowed the plasmid to be released from the chromosome and spread among E. coli strains that were susceptible to meropenem. The copy number of blaIMP-6 on the plasmid was amplified eight times, resulting in enhanced resistance. Although the carbapenemase producers that carry chromosomal carbapenemase genes comprised of small subpopulations, they functioned as stable, long-term reservoirs of carbapenem resistance that could be disseminated via plasmids with amplified resistance upon meropenem stimulation. Although plasmids occasionally lose their resistance cassettes as a scaffold for the acquisition of another resistance gene, chromosomal integration may contribute to the effective sharing of carbapenem resistance within a population, complicating the development of a strategy to avoid the dissemination of antimicrobial resistance.IMPORTANCEAlthough carbapenem antibiotics are the last resort for combating multidrug-resistant organisms, global dissemination of carbapenem-resistant Enterobacteriaceae (CRE) threatens public health. Carbapenemases, which are enzymes responsible for carbapenem resistance, are mainly encoded by genes on plasmids that can be transmitted across bacterial species. Owing to the rarity of chromosomally encoded carbapenemase genes, studies investigating their properties in bacterial communities are lacking. In our study, we revealed the stability of carbapenemase genes on chromosomes compared with those on plasmids, which can be lost through the loss of antimicrobial resistance cassettes despite robust retention of plasmid backbones. Following exposure to meropenem, the carbapenemase gene integrated into the chromosome was released as a plasmid, restarting the dissemination of enhanced carbapenem resistance through amplified copy numbers of carbapenemase genes. Chromosomally encoded carbapenemase genes may function as a reservoir of resistance genes within the bacterial community and challenge infection control against CRE dissemination.
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Sakamoto N, Laolerd W, Akeda Y, Sugawara Y, Motooka D, Yamamoto N, Takeuchi D, Shanmugakani RK, Nishi I, Suzuki M, Shibayama K, Iida T, Santanirand P, Tomono K, Hamada S. Temporal shifts in the predominant carbapenemase gene types among carbapenemase-producing Klebsiella pneumoniae isolated in Bangkok, Thailand, during 2013-2016. J Med Microbiol 2023; 72. [PMID: 37294294 DOI: 10.1099/jmm.0.001711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023] Open
Abstract
Introduction. Carbapenemase-producing Enterobacteriaceae (CPE) have emerged as a global threat to public health and clinical practice.Hypothesis/Gap Statement. In Thailand, reports describing CPEs carrying bla NDM and bla OXA-48-like genes have been increasing recently; however, data on detailed plasmid analysis and temporal shift of sequence type and carbapenemase type are limited.Aim. In this study, we analysed whole-genome sequencing (WGS) data of clinically isolated carbapenemase-producing Klebsiella pneumoniae (CPKP) to reveal the molecular epidemiology of CPKP in a tertiary-care hospital in Bangkok, Thailand.Methodology. Seventy-seven non-duplicated CPKP isolates collected during 2013-2016 were examined for their drug-resistance genes, sequence types and phylogenetic relationships.Results. All the tested isolates possessed carbapenemase gene(s), and the major type of carbapenemase gene in 2014-2015 was bla NDM-1, whereas isolates in 2016 harboured more bla OXA-232 than bla NDM-1. Other carbapenemase gene variants, such as bla NDM-4, bla NDM-5, bla OXA-48, bla OXA-181 and bla IMP-14 were detected in some CPKP isolates. Furthermore, this study revealed that CPKP co-harbouring two genes, bla NDM-1 and bla OXA-232 or bla OXA-181, emerged during this period. Notably, such isolates co-carrying the two carbapenemase genes emerged in three different sequence types, even in a single hospital, and then spread clonally. The WGS of CPKP revealed a temporal shift of the predominant carbapenemase genes from bla NDM-1 to bla OXA-232 along with a variation in other carbapenemase gene types within a span of 4 years.Conclusion. Our findings suggest that a substantial change in CPE types occurred in Thailand and potentially in Southeast Asian countries.
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Rudeeaneksin J, Phetsuksiri B, Nakajima C, Fukushima Y, Suthachai W, Tipkrua N, Suthum K, Jekloh N, Bunchoo S, Srisungngam S, Klayut W, Hamada S, Suzuki Y. Molecular Characterization of Mutations in Isoniazid- and Rifampicin-Resistant Mycobacterium tuberculosis Isolated in Thailand. Jpn J Infect Dis 2023; 76:39-45. [PMID: 36047179 DOI: 10.7883/yoken.jjid.2022.055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The control of drug-resistant tuberculosis (TB) is a major challenge. The frequency and mutation characteristics indicate the efficiency of molecular tests for the rapid detection of TB drug resistance. This study examined the existence of katG and inhA mutations for isoniazid (INH) resistance and rpoB mutations for rifampicin (RFP) resistance. In total, 178 drug-resistant Mycobacterium tuberculosis (MTB) isolates were analyzed. Mutations in katG encoding and inhA regulatory regions were detected in 136/168 (81.0%) and 29/168 (17.3%), respectively, with the most prominent mutation of Ser315Thr substitution in katG in 126/168 (75.0%), and -15 C to T substitution in the regulatory region of the inhA (26/168; 15.5%). Two distinct katG mutations (Tyr337Cys, 1003InsG) were identified. Of 125 RFP-resistant isolates, 118 (94.4%) carried mutations affecting the 81-bp RFP resistance-determining region, with the most commonly affected codons 450, 445, and 435 identified in 74 (59.2%), 26 (20.8%), and 12 (9.6%) isolates, respectively. Genetic mutations were highly associated with phenotypic INH and RFP resistance, and the majority shared similarities with those reported in previous studies in Thailand and other Asian countries. These data are useful for guiding the use and improvement of molecular tests for TB drug resistance.
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Hamada S, Mathias V, Barba T, Dubois V, Rabeyrin M, Morelon E, Thaunat O. L’inhibition de la calcineurine et de mTOR prévient de façon synergique le rejet NK induit par « missing self ». Nephrol Ther 2022. [DOI: 10.1016/j.nephro.2022.07.271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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Abe R, Akeda Y, Iida T, Hamada S. Population Analysis Profiling: Is It Still the Gold Standard for the Determination of Heteroresistance in Carbapenemase-Producing Enterobacteriaceae? Int J Antimicrob Agents 2022; 60:106644. [PMID: 35907596 DOI: 10.1016/j.ijantimicag.2022.106644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Revised: 04/18/2022] [Accepted: 07/18/2022] [Indexed: 11/05/2022]
Abstract
Heteroresistance is the phenomenon wherein subpopulations of presumed isogenic bacteria show varied antibiotic susceptibilities, and the current gold standard for heteroresistance determination is population analysis profiling (PAP). However, when we conducted PAP to confirm carbapenem-heteroresistance in Enterobacteriaceae, we found some isolates that did not seem heteroresistant despite meeting PAP criteria. Here, we elaborate on the validity of PAP for heteroresistance determination, especially among carbapenemase-producing Enterobacteriaceae (CPE). We revealed that the bacterial cells that were originally inviable on the selective agar supplemented with a high concentration of meropenem were occasionally viable, likely owing to the hydrolysis of carbapenems by carbapenemases produced by dying cells, mimicking the emergence of subpopulations with enhanced resistance. PAP for CPE is highly affected by carbapenemases produced by the dying populations, and may not appropriately detect heterogeneity in carbapenem resistance among seemingly isogenic clones.
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Abe R, Akeda Y, Takeuchi D, Sakamoto N, Sugawara Y, Yamamoto N, Kerdsin A, Matsumoto Y, Motooka D, Leolerd W, Santanirand P, Suzuki M, Shibayama K, Tomono K, Iida T, Hamada S. Clonal dissemination of carbapenem-resistant Klebsiella pneumoniae ST16 co-producing NDM-1 and OXA-232 in Thailand. JAC Antimicrob Resist 2022; 4:dlac084. [PMID: 35983103 PMCID: PMC9380991 DOI: 10.1093/jacamr/dlac084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 07/22/2022] [Indexed: 11/12/2022] Open
Abstract
Abstract
Background
Klebsiella pneumoniae ST258 and ST11 carrying blaKPC are among the most widespread carbapenem-resistant K. pneumoniae strains worldwide. Our carbapenem-resistant Enterobacteriaceae surveillance in Thailand revealed a nationwide dissemination of K. pneumoniae ST16 isolates carrying blaNDM-1 and blaOXA-232.
Objectives
To analyse the genomic details of this nationwide dissemination by focusing on plasmids and virulence factors.
Methods
Using WGS data of 119 K. pneumoniae ST16 isolates carrying blaNDM-1 obtained in our previous surveillance study, clonality of chromosomes and plasmids of the isolates with carriage of virulence factors was evaluated.
Results
Of the 119 isolates, 111 carried plasmid pKP151_NDM1, and all 104 isolates harbouring blaOXA-232 carried plasmid pKP151_OXA232. These 104 K. pneumoniae ST16 isolates showing chromosomal clonality possessed both pKP151_NDM1 and pKP151_OXA232, demonstrating clonal dissemination of K. pneumoniae ST16 with these plasmids. The isolates had essentially similar virulence factors as those of K. pneumoniae ST16 clones carrying blaKPC, which were recently reported as highly invasive clones in Brazil.
Conclusions
The potential global dissemination of these invasive clones with resistance to several antibiotics highlights the importance of appropriate monitoring and strict standard precautions.
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Takeuchi D, Kerdsin A, Akeda Y, Sugawara Y, Sakamoto N, Matsumoto Y, Motooka D, Ishihara T, Nishi I, Laolerd W, Santanirand P, Yamamoto N, Tomono K, Hamada S. Nationwide surveillance in Thailand revealed genotype-dependent dissemination of carbapenem-resistant Enterobacterales. Microb Genom 2022; 8. [PMID: 35438076 PMCID: PMC9453063 DOI: 10.1099/mgen.0.000797] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Carbapenem-resistant
Enterobacterales
(CRE) are a serious public health threat because of their rapid dissemination. To determine the epidemiological and genetic characteristics of CRE infections in Thailand, we performed whole-genome sequencing of 577 carbapenem-resistant
Klebsiella pneumoniae
isolates and 170 carbapenem-resistant
Escherichia coli
isolates from hospitals across the nation. The four most prevalent carbapenemase genes harboured by these bacteria were bla
NDM-1, bla
NDM-5, bla
OXA-181 and bla
OXA-232. The gene bla
NDM-1 was identified in diverse sequence types. The gene bla
NDM-5 was identified almost exclusively in
E. coli
. The genes bla
OXA-181, bla
OXA-232, and co-carriage of bla
NDM-1 and bla
OXA-232 were found in specific sequence types from certain provinces. Replicon typing revealed the diverse backbones of bla
NDM-1- and bla
NDM-5-harbouring plasmids and successful expansion of bla
NDM-1-harbouring IncN2-type plasmids. Core-genome single-nucleotide polymorphism analysis suggested that bla
OXA-181-, bla
OXA-232-, bla
NDM-5-, and co-carriage of bla
NDM-1 and bla
OXA-232-associated sub-clonal lineages have recently predominated in the provinces from where these isolates were isolated. Thus, we demonstrate genotype-dependent dissemination of CRE in Thailand, which is helpful for establishing infection-control strategies in CRE-endemic areas.
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Morita M, Okada K, Yamashiro T, Sekizuka T, Roobthaisong A, Wongboot W, Chantaroj S, Tu ND, Xangsayarath P, Sithivong N, Noilath K, Vongdouangchanh A, Kuroda M, Hamada S, Izumiya H, Ohnishi M. Corrigendum to: Phylogenetic Analysis Revealed the Dissemination of Closely Related Epidemic Vibrio cholerae O1 Isolates in Laos, Thailand, and Vietnam. Open Forum Infect Dis 2021; 8:ofab355. [PMID: 34901298 PMCID: PMC8661072 DOI: 10.1093/ofid/ofab355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
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Hamada S, Ogino E, Yasuba H. Cycling biologic therapy for severe asthma. Pulmonology 2021; 28:65-67. [PMID: 34627771 DOI: 10.1016/j.pulmoe.2021.07.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 07/28/2021] [Accepted: 07/29/2021] [Indexed: 11/28/2022] Open
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Abe R, Oyama F, Akeda Y, Nozaki M, Hatachi T, Okamoto Y, Yoshida H, Hamaguchi S, Tomono K, Matsumoto Y, Motooka D, Iida T, Hamada S. Hospital-wide outbreaks of carbapenem-resistant Enterobacteriaceae horizontally spread through a clonal plasmid harbouring blaIMP-1 in children's hospitals in Japan. J Antimicrob Chemother 2021; 76:3314-3317. [PMID: 34477841 DOI: 10.1093/jac/dkab303] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 07/26/2021] [Indexed: 12/22/2022] Open
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Poomchuchit S, Kerdsin A, Chopjitt P, Boueroy P, Hatrongjit R, Akeda Y, Tomono K, Nuanualsuwan S, Hamada S. Fluoroquinolone resistance in non-typhoidal Salmonella enterica isolated from slaughtered pigs in Thailand. J Med Microbiol 2021; 70. [PMID: 34319224 DOI: 10.1099/jmm.0.001386] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Introduction. The emergence and spread of non-typhoidal Salmonella enterica (NTS) serovars resistant to fluoroquinolones and third- and higher-generation cephalosporins is a matter of great concern. Antimicrobial-resistant NTS is increasingly being discovered in humans, animals, food animals, food products, and agricultural environments. Pigs are considered a major reservoir of antimicrobial-resistant Salmonella spp.Hypothesis/Gap Statement. Fluoroquinolone-resistant Salmonella spp. warrant further surveillance and characterization for a better understanding of the bacteria isolated from animals.Aim. NTS isolated from pork from slaughterhouses across Thailand were characterized in terms of their serovars; resistance to fluoroquinolones, third-generation cephalosporins, and carbapenems; and antimicrobial resistance genes.Methodology. A total of 387 NTS isolates, collected from slaughtered pigs in ten provinces across Thailand between 2014 and 2015, were characterized based on their serovars, antimicrobial resistance genes, and susceptibility to fluoroquinolones, third-generation cephalosporins, and carbapenems.Results. Among all NTS isolates, S. enterica serovar Rissen was predominant. Antimicrobial resistance was exhibited in 93/387 isolates (24 %). Although 24 (6.2 %) isolates were susceptible to all the tested antimicrobials, they were found to possess β-lactamase genes, such as bla TEM, bla SHV, or bla CTX-M. Mobilized colistin-resistant genes (mcr) and resistance to colistin were not observed in any tested isolate. Carbapenem resistance was detected in ten isolates (10.7 %); however, bla KPC, bla NDM, bla OXA-48-like, and bla IMP were not present. Among the 93 antimicrobial-resistant isolates, 87.1 % showed fluoroquinolone resistance with the quinolone resistance gene (qnrS) combined with topoisomerase genes parC (T57S) or gyrA (S83E/Y and D124E/G) substitutions, or topoisomerase gene substitutions alone.Conclusion. We found high fluoroquinolone resistance rates among the NTS isolates from pigs from slaughterhouses. The fluoroquinolone resistance mechanism in NTS was associated with the combination of qnrS and substitutions in gyrA, parC, or both. To prevent the transmission of antimicrobial-resistant NTS between animals and humans, continuous monitoring, surveillance, and regulation of Salmonella in the pork supply chain are pivotal.
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Sugawara Y, Akeda Y, Hagiya H, Zin KN, Aye MM, Takeuchi D, Matsumoto Y, Motooka D, Nishi I, Tomono K, Hamada S. Characterization of bla NDM-5-harbouring Klebsiella pneumoniae sequence type 11 international high-risk clones isolated from clinical samples in Yangon General Hospital, a tertiary-care hospital in Myanmar. J Med Microbiol 2021; 70. [PMID: 34038339 DOI: 10.1099/jmm.0.001348] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Fifteen Klebsiella pneumoniae isolates harbouring bla NDM genes were identified from blood and sputum specimens of patients at a tertiary-care facility (Yangon General Hospital, Yangon, Myanmar) in 2018. Two of the isolates belonged to sequence type (ST) 11, an international high-risk clone. Whole-genome sequencing and phylogenetic analyses revealed that these two isolates were clustered together with other ST11 isolates originating from other countries. The isolates harboured the bla NDM-5 gene on an IncFII-type plasmid that is prevalent among carbapenemase-producing Enterobacteriaceae in Yangon but has rarely been found in other ST11 isolates. Our data suggests the regional presence of the ST11 international high-risk clone and its acquisition of an endemic bla NDM-5-carrying plasmid.
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Sugawara Y, Hagiya H, Akeda Y, Takeuchi D, Sakamoto N, Matsumoto Y, Motooka D, Nishi I, Tomono K, Hamada S. Community spread and acquisition of clinically relevant Escherichia coli harbouring blaNDM among healthy Japanese residents of Yangon, Myanmar. J Antimicrob Chemother 2021; 76:1448-1454. [PMID: 33758942 DOI: 10.1093/jac/dkab070] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Accepted: 02/18/2021] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Carbapenemase-producing Enterobacterales (CPE) are spreading in hospitals, environment and retail foods in Yangon, Myanmar. OBJECTIVES To investigate whether CPE colonize healthy individuals living in Yangon and whether clinical-related strains are spreading in the community. METHODS CPE was isolated from faecal samples obtained from healthy Japanese residents of Yangon with no history of hospitalization. Isolates were subjected to WGS using short- and long-read sequencers and compared with those previously isolated in Yangon. RESULTS Six Escherichia coli strains harbouring blaNDM-1 or blaNDM-5 belonging to five different STs-ST10, ST38, ST48, ST410 and ST8453-were isolated from 69 volunteers. The ST38 isolates were related to those previously isolated from retail food in Yangon. The ST410 and ST8453 isolates were highly related to previous Yangon isolates including those of clinical and food origins. CONCLUSIONS The analysis suggested the acquisition of blaNDM-positive E. coli, which are disseminating in a clinical setting and through retail foods, by healthy residents in Yangon.
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Kumwenda GP, Sugawara Y, Akeda Y, Matsumoto Y, Motooka D, Tomono K, Hamada S. Genomic features of plasmids coding for KPC-2, NDM-5 or OXA-48 carbapenemases in Enterobacteriaceae from Malawi. J Antimicrob Chemother 2021; 76:267-270. [PMID: 32929493 DOI: 10.1093/jac/dkaa387] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
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17
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Khanawapee A, Kerdsin A, Chopjitt P, Boueroy P, Hatrongjit R, Akeda Y, Tomono K, Nuanualsuwan S, Hamada S. Distribution and Molecular Characterization of Escherichia coli Harboring mcr Genes Isolated from Slaughtered Pigs in Thailand. Microb Drug Resist 2020; 27:971-979. [PMID: 33325796 DOI: 10.1089/mdr.2020.0242] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The resistance of Enterobacteriaceae to colistin mediated by plasmid-borne mobile mcr genes is an emerging public health concern. This study aimed to explore the distribution and characteristics of Escherichia coli isolates harboring mcr genes from slaughtered pigs in Thailand from 2014 to 2015. A total of 779 E. coli isolates were assessed, of which 61 (7.8%) were found to carry mcr genes, including mcr-1, mcr-3, mcr-6, mcr-7, mcr-8, and mcr-9, together with co-occurrences of mcr-1+mcr-3, mcr-1+mcr-9, and mcr-3+mcr-6+mcr-7. In these mcr-harboring E. coli isolates, mcr-1 (40.9%) and mcr-9 (32.8%) were predominant. Colistin resistance was mainly mediated by the mcr-1 gene, whereas intermediate resistance was noted in isolates that harbored mcr-9, mcr-6, mcr-7, and mcr-8 genes. Most E. coli isolates harboring mcr genes were susceptible to third-generation cephalosporins and all of these isolates were susceptible to carbapenems. Clermont phylotyping demonstrated that mcr-harboring isolates mainly belonged to phylogroup A (44.3%), followed by phylogroups B1 (34.4%), D (14.8%), and B2 (6.6%). Multilocus sequence typing revealed that 25 sequence types (STs) were assigned to 45 mcr-harboring E. coli isolates, whereas the remaining 16 isolates were novel STs. The mcr-1 and mcr-9 genes were mostly predominant in ST101 and ST8900, respectively. This study provides a comprehensive insight into the prevalence and diversity of mcr-harboring E. coli isolates obtained from slaughtered pigs across Thailand. Strengthening of surveillance systems by the government for controlling and preventing mcr dissemination from animals to humans or vice versa is urgently needed. No clinical trial registration number.
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Chopjitt P, Kerdsin A, Takeuchi D, Hatrongjit R, Boueroy P, Akeda Y, Tomono K, Hamada S. Whole genome analysis of extensively drug-resistant Acinetobacter bau-mannii clinical isolates in Thailand. Infect Disord Drug Targets 2020; 21:e270421188042. [PMID: 33200701 DOI: 10.2174/1871526520999201116201911] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 09/10/2020] [Accepted: 09/29/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Acinetobacter baumannii is recognized as a majority opportunistic nosocomial pathogen and caus-ing hospital-acquired infection worldwide. The increasing prevalence of extensively drug-resistant Acinetobacter baumannii (XDRAB) has become a rising concern in healthcare facilities and has impeded public health due to limitation of therapeutic options and are associated with high morbidity and mortality as well as longer hospitalization. Whole-genome sequencing of highly multidrug resistant A. baumannii will increase understanding of resistant mechanisms, the emergence of novel re-sistance, genetic relationships among the isolates, source tracking, and treatment decisions in selected patients. OBJECTIVE This study revealed the genomic analysis to explore blaOXA-23 harboring XDRAB isolates in Thailand. METHODS Whole-genome sequencing of the two XDRAB isolates was carried out on a HiSeq2000 Illumina platform and susceptibility on antimicrobials was conducted. RESULTS Both isolates revealed sequence types of international, clone II-carrying, multiple antimicrobial-resistant genes-ST195 and ST451. They were resistant to antimicrobial agents in all drug classes tested for Acinetobacter spp. They carried 18 antimicrobial-resistant genes comprising of 4 -lactamase genes (blaOXA-23, blaOXA-66, blaTEM-1D, blaADC-25), 4 aminogly-coside-resistant genes (armA, aph(3')-Ia, aph(3')-Ib, aph(6)-Id), 3 macrolide-resistant genes (amvA, mphE, msrE), 1 sulfon-amide-resistant gene (sul-2), 2 tetracycline-resistant genes (tetB, tetR), 1 resistant-nodulation-cell division (RND) antibiotic efflux pump gene cluster, 2 major facilitator superfamily (MFS) antibiotic efflux pump genes (abaF, abaQ), and 1 small multidrug-resistant (SMR) antibiotic efflux pump gene (abeS). Mutation of gyrA (S81L) occurred in both isolates. CONCLUSIONS Whole-genome sequencing revealed both blaOXA-23 harboring XDRAB isolates were clustered under interna-tional clone II with difference STs and carrying multiple antimicrobial-resistant genes conferred their resistance to antimi-crobial agents. Inactivation of antimicrobials and target modification by enzymes, and pumping antibiotics by efflux pump are mainly resistance mechanism of the XDRAB in this study.
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Frick M, Bauermann K, Kirschfink A, Hamada S, Weber O, Marx N, Altiok E. High sensitive troponin T as gatekeeper for cardiac magnetic resonance imaging in patients with suspected acute myocarditis. Eur Heart J 2020. [DOI: 10.1093/ehjci/ehaa946.2058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Background
The diagnosis of acute (AM) is difficult because of the variable, unspecific clinical presentation. Cardiac magnetic resonance (CMR) is the noninvasive gold standard diagnostic tool, but limited availability and high costs make a quick and inexpensive test necessary to clarify the need for CMR. Quantification of high sensitive Troponin T (hsTNT) is a broadly available, specific blood test for cardiomyocyte damage.
Aim
The aim of this study was to evaluate hsTNT as a gatekeeper for CMR with a lower cut off-value for exclusion and an upper cut-off value for confirmation of acute myocarditis as defined by CMR.
Methods
This retrospective analysis included 244 patients (age 39±17 years, 71% male) who received CMR for clinically suspected AM and quantification of hsTNT within 28 days (Median: 2 days) of CMR. CMR (1.5 Tesla) consisted of cine-sequences, edema-sensitive T2 and late gadolinium enhancement (LGE) imaging. AM was diagnosed in presence of both, myocardial edema and LGE consistent with acute myocarditis.
Results
Of 244 patients, 78 (32%) were CMR-positive (CMR+) for AM. 166 (68%) were CMR negative (CMR−). Mean hsTNT was 206±454 pg/ml.
HsTNT was significantly higher in CMR+ than in CMR− (604±639 pg/ml vs 20±56 pg/ml, p<0.001, see figure A). 8 CMR+ patients (10%) had hsTNT in the normal range (<14 ng/ml).
HsTNT showed good discriminatory performance in the Receiver Operator Characteristic (ROC) analysis (AUC 0.91, see figure B).
A lower cut-off value of 4 pg/ml had a sensitivity of 98.7% for diagnosis of AM (hsTNT ≥4 pg/ml) and a negative predictive value of 98.2% for rule out of AM (hsTNT<4 pg/ml) as defined by CMR, leading to a reduction of 23.4% of CMR exams. An upper cut-off value of >343 pg/ml had a specificity of 99.4% and positive predictive value of 97.8% for diagnosis of AM, leading to a reduction of 18.4% of CMR exams (see table).
Conclusions
hsTNT showed good discriminatory capacity for acute myocarditis (AM) as defined by CMR. However, 10% of patients had hsTNT in the normal range (<14 pg/ml). A lower cut-off value of <4 pg/ml ruled out AM with very high negative predictive value, whereas an upper cut-off of >343 pg/ml had a very high positive predictive value for confirmation of AM as defined by CMR. Performing CMR only in patients with hsTNT between 4 and 343 pg/ml would have led to a reduction of 41.8% of CMR exams.
Funding Acknowledgement
Type of funding source: None
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Morita M, Okada K, Yamashiro T, Sekizuka T, Roobthaisong A, Wongboot W, Chantaroj S, Tu ND, Xangsayarath P, Sithivong N, Noilath K, Vongdouangchanh A, Kuroda M, Hamada S, Izumiya H, Ohnssishi M. Phylogenetic Analysis Revealed the Dissemination of Closely Related Epidemic Vibrio cholerae O1 Isolates in Laos, Thailand, and Vietnam. Open Forum Infect Dis 2020; 7:ofaa492. [PMID: 33244479 PMCID: PMC7679066 DOI: 10.1093/ofid/ofaa492] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 10/13/2020] [Indexed: 11/24/2022] Open
Abstract
We performed whole-genome sequencing of Vibrio cholerae O1 isolates from Laos, Thailand, and Vietnam, where cholera outbreaks occurred, to determine their genetic lineages. Core genome phylogenetic analysis revealed that the isolates located in same lineage without regional clusters, which suggests that closely related strains circulated in Southeast Asia.
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Shanmugakani RK, Sugawara Y, Akeda Y, Hagiya H, Sakamoto N, Aye MM, Myint T, Hamada S, Tomono K. bla OXA -731 , a new chromosome-encoded bla OXA -48 -like variant in Shewanella sp. from the aquatic environment in Myanmar. ENVIRONMENTAL MICROBIOLOGY REPORTS 2020; 12:548-554. [PMID: 32776437 DOI: 10.1111/1758-2229.12875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 08/06/2020] [Indexed: 06/11/2023]
Abstract
Shewanella sp., the progenitors of blaOXA-48 -like genes are increasingly reported with the possession of different blaOXA-48 -like variants. This study aims to characterize blaOXA-731 , a new variant of a blaOXA-48 -like gene identified in Shewanella sp. isolated from the aquatic environment in Myanmar. Phylogenetic analysis of the blaOXA-731 sequence with other blaOXA-48 -like variants showed that it has the highest nucleotide identity of 86.09% with blaOXA-48 . However, the active site motifs in OXA-731 were 100% identical to that in OXA-48. Whole-genome sequencing analysis showed that blaOXA-731 is not surrounded by any mobile genetic elements. The genetic context of blaOXA-731 was found as similar to other blaOXA-48 -like genes previously identified in Shewanella sp. S1 nuclease pulsed-field gel electrophoresis followed by Southern blotting confirmed the location of blaOXA-731 in the chromosome of the Shewanella genome. Cloning and expression studies showed that OXA-731 has β-lactamase activity similar to OXA-48 and OXA-181, but it has no significant carbapenemase activity. Our results showed the significance of blaOXA-48 -like-carrying Shewanella sp. in the spreading of blaOXA-48 -like genes in the community.
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Enomoto A, Shimoide T, Kinoshita Y, Sukedai M, Hamada S. Application of an oral appliance for endotracheal tube fixation in facial burn patients. Br J Oral Maxillofac Surg 2020; 59:127-128. [PMID: 32861471 DOI: 10.1016/j.bjoms.2020.08.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 08/03/2020] [Indexed: 11/24/2022]
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Abe R, Akeda Y, Sakamoto N, Kumwenda G, Sugawara Y, Yamamoto N, Kawahara R, Tomono K, Fujino Y, Hamada S. Genomic characterisation of a novel plasmid carrying bla IMP-6 of carbapenem-resistant Klebsiella pneumoniae isolated in Osaka, Japan. J Glob Antimicrob Resist 2020; 21:195-199. [PMID: 31627024 DOI: 10.1016/j.jgar.2019.10.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 10/04/2019] [Accepted: 10/04/2019] [Indexed: 12/31/2022] Open
Abstract
OBJECTIVES To analyse plasmids carrying blaIMP-6 in Klebsiella pneumoniae isolates obtained from multicentre carbapenem-resistant Enterobacteriaceae surveillance. METHODS Plasmids harbouring blaIMP-6 were characterised by the whole-genome sequencing of four Klebsiella pneumoniae isolates carrying blaIMP-6, and compared with the pKPI-6 plasmid, which is widespread in western Japan, through pulsed-field gel electrophoresis, Southern blotting, bacterial conjugation, and qPCR. RESULTS Whole-genome sequencing analysis revealed that three of the four isolates carried approximately 50 kbp plasmids similar to the pKPI-6 plasmid; however, one isolate carried a 250 kbp plasmid harbouring blaIMP-6 (pE196_IMP6). So far, all of the reported plasmids carrying blaIMP-6 were similar to the pKPI-6 plasmid, and this plasmid was a novel blaIMP6-carrier. The size and transferability of this plasmid was confirmed by Southern hybridisation and conjugation experiments. It was demonstrated that the generation of plasmid pE196_IMP6 was due to an intramolecular transposition mediated by IS26, and a homologous recombination between plasmids pKPI-6 and pE013 that was obtained from another carbapenem-resistant Enterobacteriaceae isolate in this analysis. As a result of co-integration with pE013, pE196_IMP6 acquired six additional pairs of type II toxin-antitoxin systems that pKPI-6 does not carry. Transcription of all of the toxin-antitoxin systems were confirmed in an isolate carrying pE196_IMP6 by qPCR. CONCLUSIONS This study detected a novel plasmid carrying blaIMP-6, and revealed the origin of this plasmid. Toxin-antitoxin system acquisition could enable pE196_IMP6 maintenance persistently through successions, even without selection pressure by the clinical usage of antimicrobials, generating broad dissemination and longer carbapenem-resistant Enterobacteriaceae colonisation duration in patients.
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Okada K, Wongboot W, Kamjumphol W, Suebwongsa N, Wangroongsarb P, Kluabwang P, Chuenchom N, Swaddiwudhipong W, Wongchai T, Manosuthi W, Assawapatchara N, Khum-On P, Udompat P, Thanee C, Kitsaran S, Jirapong L, Jaiwong C, Nedsuwan S, Siripipattanamongkol C, Okada PA, Chantaroj S, Komukai S, Hamada S. Etiologic features of diarrheagenic microbes in stool specimens from patients with acute diarrhea in Thailand. Sci Rep 2020; 10:4009. [PMID: 32132604 PMCID: PMC7055299 DOI: 10.1038/s41598-020-60711-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 02/13/2020] [Indexed: 12/13/2022] Open
Abstract
Many microbial species have been recognized as enteropathogens for humans. Here, we predicted the causative agents of acute diarrhea using data from multiplex quantitative PCR (qPCR) assays targeting 19 enteropathogens. For this, a case-control study was conducted at eight hospitals in Thailand. Stool samples and clinical data were collected from 370 hospitalized patients with acute diarrhea and 370 non-diarrheal controls. Multiple enteropathogens were detected in 75.7% and 13.0% of diarrheal stool samples using multiplex qPCR and bacterial culture methods, respectively. Asymptomatic carriers of enteropathogens were found among 87.8% and 45.7% of individuals by qPCR and culture methods, respectively. These results suggested the complexity of identifying causative agents of diarrhea. An analysis using the quantification cut-off values for clinical relevance drastically reduced pathogen-positive stool samples in control subjects from 87.8% to 0.5%, whereas 48.9% of the diarrheal stool samples were positive for any of the 11 pathogens. Among others, rotavirus, norovirus GII, Shigella/EIEC, and Campylobacter were strongly associated with acute diarrhea (P-value < 0.001). Characteristic clinical symptoms, epidemic periods, and age-related susceptibility to infection were observed for some enteropathogens. Investigations based on qPCR approaches covering a broad array of enteropathogens might thus improve our understanding of diarrheal disease etiology and epidemiological trends.
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Phetsuksiri B, Rudeeaneksin J, Srisungngam S, Bunchoo S, Klayut W, Nakajima C, Hamada S, Suzuki Y. Comparison of Loop-Mediated Isothermal Amplification, Microscopy, Culture, and PCR for Diagnosis of Pulmonary Tuberculosis. Jpn J Infect Dis 2020; 73:272-277. [PMID: 32115540 DOI: 10.7883/yoken.jjid.2019.335] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The diagnosis of tuberculosis (TB) in endemic countries is challenging due to high caseloads and limited resources. A simple and cost-effective diagnostic test for the rapid detection of Mycobacterium tuberculosis (M. tuberculosis) in clinical specimens is crucially needed. We evaluated the performance of an in-house assay based on loop-mediated isothermal amplification (LAMP) targeting the M. tuberculosis 16S ribosomal RNA (rRNA) gene for the diagnosis of TB in Thailand. A total of 252 sputum samples from suspected cases of pulmonary TB were analyzed. The sensitivity of LAMP was 99.04% (103/104; 95% confidence interval [CI]: 94.76-9.98%) and 72.73% (16/22; 95% CI: 49.78-89.27%) for smear-positive and smear-negative samples with TB-culture positivity, respectively. LAMP detected 20.69% (24/116) of TB culture negative samples but all those were positive by conventional polymerase chain reaction (PCR). The sensitivity of LAMP was higher than that of sputum microscopy while the performance of LAMP was similar to PCR. None of the samples positive for non-tuberculous mycobacteria by culture and PCR were positive by LAMP. Compared to TB culture, the positive predictive value (PPV), negative predictive value (NPV), and kappa coefficient of LAMP were 83.22%, 88.33%, and 0.75 respectively. Based on the diagnostic performance, we propose that LAMP would be suitable as a potential diagnostic test for rapid TB diagnosis in resource-limited laboratory settings.
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