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Kyung SM, Lee JH, Lee ES, Xiang XR, Yoo HS. Emergence and genomic chion of Proteus mirabilis harboring bla NDM-1 in Korean companion dogs. Vet Res 2024; 55:50. [PMID: 38594755 PMCID: PMC11005143 DOI: 10.1186/s13567-024-01306-w] [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: 01/16/2024] [Accepted: 02/26/2024] [Indexed: 04/11/2024] Open
Abstract
Proteus mirabilis is a commensal bacterium dwelling in the gastrointestinal (GI) tract of humans and animals. Although New Delhi metallo-β-lactamase 1 (NDM-1) producing P. mirabilis is emerging as a threat, its epidemiology in our society remains largely unknown. LHPm1, the first P. mirabilis isolate harboring NDM-1, was detected from a companion dog that resides with a human owner. The whole-genome study revealed 20 different antimicrobial resistance (AMR) genes against various classes of antimicrobial agents, which corresponded to the MIC results. Genomic regions, including MDR genes, were identified with multiple variations and visualized in a comparative manner. In the whole-genome epidemiological analysis, multiple phylogroups were identified, revealing the genetic relationship of LHPm1 with other P. mirabilis strains carrying various AMR genes. These genetic findings offer comprehensive insights into NDM-1-producing P. mirabilis, underscoring the need for urgent control measures and surveillance programs using a "one health approach".
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Affiliation(s)
- Su Min Kyung
- Department of Infectious Disease, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
| | - Jun Ho Lee
- Department of Infectious Disease, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
| | - Eun-Seo Lee
- Department of Infectious Disease, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
| | - Xi-Rui Xiang
- Department of Infectious Disease, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
| | - Han Sang Yoo
- Department of Infectious Disease, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea.
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Hafiz TA, Alghamdi GS, Alkudmani ZS, Alyami AS, AlMazyed A, Alhumaidan OS, Mubaraki MA, Alotaibi FE. Multidrug-Resistant Proteus mirabilis Infections and Clinical Outcome at Tertiary Hospital in Riyadh, Saudi Arabia. Infect Drug Resist 2024; 17:571-581. [PMID: 38375102 PMCID: PMC10875173 DOI: 10.2147/idr.s448335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 02/02/2024] [Indexed: 02/21/2024] Open
Abstract
Background Proteus mirabilis (P. mirabilis) is known to cause various infections, most commonly urinary tract infections, and is a threat to hospitalized patients, especially in long-stay departments that utilize invasive devices. This study aims to fill the knowledge gap regarding P. mirabilis epidemiology and antimicrobial resistance in Saudi Arabia. It investigates epidemiological patterns, resistance characteristics, and clinical outcomes among P. mirabilis patients at King Fahad Medical City in Riyadh from 2019 to 2021. Methods A total of 598 P. mirabilis isolated from diverse clinical specimens, including the clinical information of 78 intensive care unit (ICU) patients, were included in the current study. The Phoenix BD instrument was used for complete identification and sensitivity testing of Proteus spp. Demographic, clinical, and outcome data were reported and compared using statistical analysis. Results Pan-drug-resistant isolates were identified in 2019 (n = 6), although multi- and extensively drug-resistant isolate frequencies were greatest among all patients in 2019. The highest susceptibility levels were observed for piperacillin-tazobactam, carbapenems, and cephalosporins antibiotics. In contrast, Cephalothin, trimethoprim-sulfamethoxazole, and ampicillin had the lowest susceptibilities. Urine infections with a positive culture of P. mirabilis were significantly higher in females and non-ICU patients (p <0.001), but respiratory infections were significantly higher in ICU patients (p <0.001). Moreover, ICU patients infected with P. mirabilis and undergoing renal dialysis have a 7.2-fold (P 0.034) higher risk of death than those not receiving dialysis. Conclusion Hospitalized patients are at risk of fatal consequences due to P. mirabilis infection. It is crucial to conduct further investigation to fully understand the severity of this issue and take necessary measures to prevent it.
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Affiliation(s)
- Taghreed A Hafiz
- Clinical Laboratory Sciences Department, College of Applied Medical Sciences, King Saud University, Riyadh, 12372, Saudi Arabia
| | - Ghadi S Alghamdi
- Clinical Laboratory Sciences Department, College of Applied Medical Sciences, King Saud University, Riyadh, 12372, Saudi Arabia
| | - Zeina S Alkudmani
- Clinical Laboratory Sciences Department, College of Applied Medical Sciences, King Saud University, Riyadh, 12372, Saudi Arabia
| | - Ahmed S Alyami
- Pathology and Clinical Laboratory Medicine, King Fahad Medical City, Riyadh, 11525, Saudi Arabia
| | - Abeer AlMazyed
- Pathology and Clinical Laboratory Medicine, King Fahad Medical City, Riyadh, 11525, Saudi Arabia
| | - Ohoud S Alhumaidan
- Clinical Laboratory Sciences Department, College of Applied Medical Sciences, King Saud University, Riyadh, 12372, Saudi Arabia
| | - Murad A Mubaraki
- Clinical Laboratory Sciences Department, College of Applied Medical Sciences, King Saud University, Riyadh, 12372, Saudi Arabia
| | - Fawzia E Alotaibi
- Pathology Department, College of Medicine, King Saud University, Riyadh, 12372, Saudi Arabia
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Whole-Genome Analysis of blaNDM-Bearing Proteus mirabilis Isolates and mcr-1-Positive Escherichia coli Isolates Carrying blaNDM from the Same Fresh Vegetables in China. Foods 2023; 12:foods12030492. [PMID: 36766021 PMCID: PMC9913981 DOI: 10.3390/foods12030492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/12/2023] [Accepted: 01/16/2023] [Indexed: 01/24/2023] Open
Abstract
The global spread of colistin or carbapenem-resistant Enterobacteriaceae (CRE) has been a pressing threat to public health. Members of Enterobacteriaceae, especially Proteus mirabilis and Escherichia coli, have been prevalent foodborne pathogens and such pathogens from fresh vegetables have triggered foodborne illness in China. However, reports about CRE, especially P. mirabilis from fresh vegetables, are still lacking. In this study, we identified five blaNDM-positive P. mirabilis and five blaNDM-positive generic E. coli concurrently from five fresh vegetables in two markets from China, and four of the five E. coli also carried mcr-1. The 10 isolates were characterized with methods including antimicrobial susceptibility testing, conjugation, whole-genome sequencing and phylogenetic analysis. All 10 isolates were multidrug-resistant (MDR). blaNDM-5 in five E. coli isolates and one P. mirabilis carrying blaNDM-5 was located on similarly transferable IncX3 plasmids, while transferably untypable plasmids were the carriers of blaNDM-1 in four P. mirabilis isolates from different types of vegetables/markets. mcr-1 in the four blaNDM-5-positive E. coli was located on similarly non-conjugative IncHI2 MDR plasmids lacking transfer region. Notably, ISCR1 complex class 1 integron capable of capturing blaNDM-1 was found on all untypable plasmids from P. mirabilis, and five copies of ISCR1 complex class 1 integron containing blaNDM-1 even occurred in one P. mirabilis, which showed high-level carbapenem resistance. Plasmid and phylogenetic analysis revealed that the blaNDM-positive P. mirabilis and E. coli from fresh vegetables might be derived from animals and transmitted to humans via the food chain. The concurrence of blaNDM-positive P. mirabilis and E. coli carrying both mcr-1 and blaNDM in different types of fresh vegetables eaten raw is alarming and threatens food safety. Sustained surveillance of these foodborne pathogens among fresh vegetables is urgent to ensure the health of food consumers. We report for the first time the concurrence of blaNDM-positive P. mirabilis and mcr-1-bearing E. coli carrying blaNDM from the same fresh vegetables.
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Chen X, Zhang E, Abdulai MK, Tia AB, Ngegba ED, Yin J, Xu S, Wang L, Dong X, Harding D, Kan B, Kan B. Dissemination of Antibiotic Resistance Genes Among Patients with Diarrhea - Freetown, Sierra Leone, 2018. China CDC Wkly 2022; 4:1093-1096. [PMID: 36751663 PMCID: PMC9889225 DOI: 10.46234/ccdcw2022.221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 12/02/2022] [Indexed: 12/14/2022] Open
Abstract
What is already known about this topic? Antibiotic resistance (AR) is a serious public health threat worldwide. However, the AR and antibiotic resistance genes (ARGs) data from West Africa, especially from Sierra Leone, are limited. What is added by this report? The study revealed ARGs' common dissemination, and multiplex antibiotic resistance genes in one sample. Genes bla NDM and bla OXA -48-like were first discovered in Sierra Leone. What are the implications for public health practice? Basic information is provided for AR research and surveillance and highlights that effective AR surveillance among diarrhea patients is necessary for Sierra Leone and West Africa.
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Affiliation(s)
- Xia Chen
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing Municipality, China,Sierra Leone-China Friendship Biological Safety Laboratory, Chinese Center for Disease Control and Prevention, Freetown, Sierra Leone and Beijing Municipality, China
| | - Enmin Zhang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing Municipality, China,Sierra Leone-China Friendship Biological Safety Laboratory, Chinese Center for Disease Control and Prevention, Freetown, Sierra Leone and Beijing Municipality, China
| | - Michael K Abdulai
- Sierra Leone-China Friendship Biological Safety Laboratory, Chinese Center for Disease Control and Prevention, Freetown, Sierra Leone and Beijing Municipality, China
| | - Alie Brima Tia
- Sierra Leone-China Friendship Biological Safety Laboratory, Chinese Center for Disease Control and Prevention, Freetown, Sierra Leone and Beijing Municipality, China
| | - Esther Debora Ngegba
- Sierra Leone-China Friendship Biological Safety Laboratory, Chinese Center for Disease Control and Prevention, Freetown, Sierra Leone and Beijing Municipality, China
| | - Jianhai Yin
- Sierra Leone-China Friendship Biological Safety Laboratory, Chinese Center for Disease Control and Prevention, Freetown, Sierra Leone and Beijing Municipality, China,National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention; Chinese Center for Tropical Diseases Research, Shanghai Municipality, China
| | - Songtao Xu
- Sierra Leone-China Friendship Biological Safety Laboratory, Chinese Center for Disease Control and Prevention, Freetown, Sierra Leone and Beijing Municipality, China,National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing Municipality, China
| | - Lili Wang
- Center for Global Public Health, Chinese Center for Disease Control and Prevention, Beijing Municipality, China
| | - Xiaoping Dong
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing Municipality, China,Center for Global Public Health, Chinese Center for Disease Control and Prevention, Beijing Municipality, China,Biao Kan,
| | - Doris Harding
- Ministry of Health and Sanitation, Freetown, Sierra Leone,Doris Harding,
| | - Biao Kan
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing Municipality, China,Sierra Leone-China Friendship Biological Safety Laboratory, Chinese Center for Disease Control and Prevention, Freetown, Sierra Leone and Beijing Municipality, China,Xiaoping Dong,
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Shaaban M, Elshaer SL, Abd El-Rahman OA. Prevalence of extended-spectrum β-lactamases, AmpC, and carbapenemases in Proteus mirabilis clinical isolates. BMC Microbiol 2022; 22:247. [PMID: 36221063 PMCID: PMC9552493 DOI: 10.1186/s12866-022-02662-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 09/29/2022] [Indexed: 11/10/2022] Open
Abstract
Background Proteus mirabilis is an opportunistic pathogen, causing a variety of community-acquired and nosocomial illnesses. It poses a potential threat to patients via the production of β-lactamases, which decrease the efficacy of antimicrobial treatment and impair the management of its pathogenicity. Hence, this study was established to determine the prevalence of extended-spectrum β-lactamases (ESBLs), AmpC, and carbapenemases of P. mirabilis isolated from various clinical specimens. Results Proteus mirabilis was identified in 20.7% (58/280) of specimens. ESBL producers were present at a rate of 51.7% (30/58). All AmpC-positive isolates (n = 20) produced ESBLs as well, so 66.7% of ESBL-producing isolates coproduced AmpC enzymes. The modified Hodge test confirmed carbapenemase production in six out of seven imipenem nonsusceptible isolates. Of these, only two (5.7%) isolates were also ESBL-and AmpC-positive. Antibiotic resistance reached the highest level for cotrimoxazole (62.1%, n = 36/58 isolates) and the lowest for imipenem (12.1%, n = 7/58 isolates). The levels of multidrug-resistant (MDR) was 41.4% among the tested isolates. The blaSHV (83.3%), blaAmpC (80%), and blaVIM-1 (50%) were the most detected genes in phenotypically confirmed ESBL-, AmpC-, and carbapenemase-producing isolates, respectively. Besides, more than a half of the tested P. mirabilis strains (53%) coproduced ESBLs and AmpC. Moreover, two isolates coproduced ESBLs and AmpC together with carbapenemases. Furthermore, dendrogram analysis showed great genetic divergence based on the 21 different enterobacterial repetitive intergenic consensus (ERIC) patterns (P1–P21) through the 34 β-lactamase producers. ERIC analysis distinguished clonal similarities between isolates 21 and 22 in P2 and 9 and 10 in P4, which were isolated from the same clinical source and possessed similar patterns of β-lactamase-encoding genes. Conclusion Hence, there is an urgent need to monitor hospitalized patients and improve healthcare in order to reduce the incidence of infection and outbreaks of infection with antibiotic-resistant Proteus. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-022-02662-3.
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Affiliation(s)
- Mona Shaaban
- Department of Microbiology and Immunology, Faculty of Pharmacy, Mansoura University, Mansoura, 35516, Egypt.
| | - Soha Lotfy Elshaer
- Department of Microbiology and Immunology, Faculty of Pharmacy, Mansoura University, Mansoura, 35516, Egypt.
| | - Ola A Abd El-Rahman
- Department of Microbiology and Immunology, Faculty of Pharmacy (Girls), Al-Azhar University, Cairo, 11651, Egypt
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Yi L, Chen S, Li G, Ren J, Zhou R, Zeng K. Prevalence of antibiotic resistance pathogens in online fresh-cut fruit from Chongqing, China and controlling Enterococcus faecalis by bacteriocin GF-15. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.113678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Taechowisan T, Klomluam K, Chuen-Im T, S Phutdhawong W. Synergistic Antibacterial Activity of 1-Methyl Ester-Nigericin and Methyl 5-(Hydroxymethyl) Furan-2-Carboxylate Against Proteus spp. Pak J Biol Sci 2022; 25:304-312. [PMID: 35638524 DOI: 10.3923/pjbs.2022.304.312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
<b>Background and Objective:</b> Synergistic combinations of antimicrobial agents with different mechanisms of action are successful approaches for combating bacterial infections. This study aimed to evaluate the synergistic effect of 1-methyl ester-nigericin <b>(1)</b> and methyl 5-(hydroxymethyl) furan-2-carboxylate <b>(2)</b> against <i>Proteus</i> spp., isolates. <b>Materials and Methods:</b> The synergistic antimicrobial activity of the compounds was tested by the checkerboard method and time-kill curves. To estimate the interaction between the compounds, the Fractional Inhibitory Concentration Index (FICI) of the combination was calculated. The cytotoxic activity of the compounds in combination was determined by the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT) assay on LLC-MK2 cell lines. The reduction percentage of biofilms was obtained using the colourimetric method. <b>Results:</b> The MIC values for compounds <b>1</b> and <b>2</b> against test bacteria ranged from 39.06-78.12 μg mL<sup>1</sup> and from 78.12-156.25 μg mL<sup>1</sup>, respectively. The MIC was reduced to 1-8th as a result of the combination of compounds <b>1</b> and <b>2</b>. After 4-24 hrs of treatment with ½ MIC of compounds <b>1</b> and <b>2</b>, the killing rate (in CFU mL<sup>1</sup>) increased to a greater degree than observed with either test compound alone. The combination of compounds <b>1</b> and <b>2</b> showed a synergistic effect with FICI of 0.50 and 0.28. The synergistic combination of compounds <b>1</b> and <b>2</b> was effective on the biofilm reduction of <i>Proteus</i> <i>vulgaris</i> NP16 (85.72%) and NP47 (89.14%). <b>Conclusion:</b> This study recommends compounds <b>1</b> and <b>2</b> in combination as a potential alternative treatment agent for <i>Proteus</i> spp. infections.
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Characterization of NDM-1-Producing Carbapenemase in Proteus mirabilis among Broilers in China. Microorganisms 2021; 9:microorganisms9122443. [PMID: 34946044 PMCID: PMC8707091 DOI: 10.3390/microorganisms9122443] [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: 10/09/2021] [Revised: 11/14/2021] [Accepted: 11/23/2021] [Indexed: 11/28/2022] Open
Abstract
Carbapenem-resistant pathogens mediated by metallo-beta-lactamases (MBLs) have spread worldwide, where NDM-1 is a typical and key MBL. Here, we firstly discussed the distribution characterization of NDM-1, which produces multidrug-resistant Proteus mirabilis among broilers in China. From January to April 2019, 40 (18.1%, 40/221) blaNDM-1-carrying P. mirabilis strains were recovered from commercial broilers in slaughterhouse B in China. All the isolates were resistant to imipenem, meropenem and other β-lactams. These isolates belong to five clusters identified via pulsed field gel electrophoresis (PFGE). Further studies on twenty representative strains revealed that seven blaNDM-1 genes were located on plasmids with sizes of 104.5–138.9 kb. Notably, only three strains (PB72, PB96 and PB109) were successfully transferred to Escherichia coli J53, while the other four isolates were located in nontransferable plasmids. The rest were harbored in chromosomes. Ulteriorly, based on whole genome sequencing (WGS), these twenty isolates showed four typical phylogenetic clades according to single nucleotide polymorphisms (SNPs) of a core genome and presented four main genomic backbone profiles, in which type II/III strains shared a similar genetic context. All of the above is evidence of blaNDM-1 transmission and evolution in P. mirabilis, suggesting that the prevalence may be more diverse in broiler farms. Accordingly, as intestinal and environmental symbiotic pathogens, blaNDM-1-positive P. mirabilis will pose greater threats to the environment and public health.
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Ragheb SM, Govinden U, Osei Sekyere J. Genetic support of carbapenemases: a One Health systematic review and meta-analysis of current trends in Africa. Ann N Y Acad Sci 2021; 1509:50-73. [PMID: 34753206 DOI: 10.1111/nyas.14703] [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: 05/21/2020] [Revised: 09/06/2021] [Accepted: 09/26/2021] [Indexed: 11/28/2022]
Abstract
Antimicrobial resistance (AMR) is a public health threat globally. Carbapenems are β-lactam antibiotics used as last-resort agents for treating antibiotic-resistant infections. Mobile genetic elements (MGEs) play an important role in the dissemination and expression of antimicrobial resistance genes (ARGs), including the mobilization of ARGs within and between species. The presence of MGEs around carbapenem-hydrolyzing enzymes, called carbapenemases, in bacterial isolates in Africa is concerning. The association between MGEs and carbapenemases is described herein. Specific plasmid replicons, integrons, transposons, and insertion sequences were found flanking specific and different carbapenemases across the same and different clones and species isolated from humans, animals, and the environment. Notably, similar genetic contexts have been reported in non-African countries, supporting the importance of MGEs in driving the intra- and interclonal and species transmission of carbapenemases in Africa and globally. Technical and budgetary limitations remain challenges for epidemiological analysis of carbapenemases in Africa, as studies undertaken with whole-genome sequencing remained relatively few. Characterization of MGEs in antibiotic-resistant infections can deepen our understanding of carbapenemase epidemiology and facilitate the control of AMR in Africa. Investment in genomic epidemiology will facilitate faster clinical interventions and containment of outbreaks.
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Affiliation(s)
- Suzan Mohammed Ragheb
- Department of Microbiology and Immunology, Faculty of Pharmacy, Modern University for Technology and Information (MTI), Cairo, Egypt
| | - Usha Govinden
- Discipline of Pharmaceutical Sciences, College of Health Sciences, University of KwaZulu-Natal, KwaZulu-Natal, South Africa
| | - John Osei Sekyere
- Department of Microbiology & Immunology, Indiana University School of Medicine-Northwest, Gary, Indiana.,Department of Dermatology, School of Medicine, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
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A Novel SXT/R391 Integrative and Conjugative Element Carries Two Copies of the blaNDM-1 Gene in Proteus mirabilis. mSphere 2021; 6:e0058821. [PMID: 34378988 PMCID: PMC8386438 DOI: 10.1128/msphere.00588-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The rapid spread of the blaNDM-1 gene is a major public health concern. Here, we describe the multidrug-resistant Proteus mirabilis strain XH1653, which contains a novel SXT/R391 integrative and conjugative element (ICE), harboring two tandem copies of blaNDM-1 and 21 other resistance genes. XH1653 was resistant to all antibiotics tested, apart from aztreonam. Whole-genome data revealed that two copies of blaNDM-1 embedded in the ISCR1 element are located in HS4 of the novel ICE, which we named ICEPmiChnXH1653. A circular intermediate of ICEPmiChnXH1653 was detected by PCR, and conjugation experiments showed that the ICE can be transferred to the Escherichia coli strain EC600 with frequencies of 1.5 × 10-7. In the recipient strain, the ICE exhibited a higher excision frequency and extrachromosomal copy number than the ICE in the donor strain. We also observed that the presence of ICEPmiChnXH1653 has a negative impact on bacterial fitness and leads to changes in the transcriptome of the host. In vitro evolution experiments under nonselective conditions showed that the two tandem copies of the ISCR1 element and the ISVsa3 element can be lost during repeated laboratory passage. This is the first report of a novel SXT/R391 ICE carrying two tandem copies of blaNDM-1, which also illustrates the role that ICEs may play as platforms for the accumulation and transmission of antibiotic resistance genes. IMPORTANCE The occurrence of carbapenemase-producing Proteus mirabilis, especially those strains producing NDM-1 and its variants, is a major public health concern worldwide. The integrative conjugative element (ICE) plays an important role in horizontal acquisition of resistance genes. In this study, we characterized a novel SXT/R391 ICE from a clinical P. mirabilis isolate that we named ICEPmiChnXH1653, which contains two tandem copies of the carbapenemase gene blaNDM-1. We performed an integrative approach to gain insights into different aspects of ICEPmiChnXH1653 evolution and biology and observed that ICEPmiChnXH1653 obtained the carbapenemase gene blaNDM-1 by ISCR1-mediated homologous recombination. Our study reveals that the transmission of blaNDM-1 by ISCR1 elements or ICEs may be an important contributor to the carbapenem resistance development across species, which could improve our understanding of horizontal gene transfer in clinical environments.
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Dziri O, Dziri R, Ali El Salabi A, Chouchani C. Carbapenemase Producing Gram-Negative Bacteria in Tunisia: History of Thirteen Years of Challenge. Infect Drug Resist 2020; 13:4177-4191. [PMID: 33262613 PMCID: PMC7699306 DOI: 10.2147/idr.s259562] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 06/11/2020] [Indexed: 11/23/2022] Open
Abstract
The wide spread of multidrug-resistant bacteria, particularly carbapenem-resistant Gram-negative bacteria (CR-GNB), constitutes a major public health threat worldwide, owing to the limited therapeutic options. This review will describe and uncover the Tunisian experience in the challenge against carbapenem resistance. Indeed, we illuminate on the dissemination of CR-GNB in different hospitals, animals, and other natural environments in this country. We resumed the different carbapenemase variants detected from various bacterial species and mapped their regional distribution, basing on Tunisian published data during a period extended from 2006, the date of its first description in Tunisia, to February 2019. We also resumed the different mobile genetic elements implicated in their dissemination. This review shows that the majority of the research reports focused in the north and the coastal cities in spite of the fact that KPC and IMP carbapenemases were uncommonly detected in our country. However, VIM, NDM-1, and OXA-48 enzymes were usually reported with the predominance of OXA-48 among Enterobacteriaceae. Furthermore, OXA-23, OXA-51, and OXA-58 carbapenemases constituted the main mechanism conferring carbapenem resistance among Acinetobacter baumannii in Tunisia. Collaborative efforts and raising awareness of the threat of antibiotic resistance are required in order to minimize the spread of multidrug-resistant bacteria.
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Affiliation(s)
- Olfa Dziri
- Laboratory of Microorganisms and Active Biomolecules, Faculty of Sciences of Tunis, University of Tunis El Manar, Tunis, Tunisia.,Laboratory of Research in Sciences and Technology of Environment, High Institute of Science and Technology of Environment, University of Carthage, Hammam-Lif, Tunisia
| | - Raoudha Dziri
- Laboratory of Microorganisms and Active Biomolecules, Faculty of Sciences of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Allaaeddin Ali El Salabi
- Department of Environmental Health, Faculty of Public Health, University of Benghazi, Benghazi, Libya.,Infection Control and Patient Safety Office, New Marwa Hospital, Benghazi, Libya
| | - Chedly Chouchani
- Laboratory of Microorganisms and Active Biomolecules, Faculty of Sciences of Tunis, University of Tunis El Manar, Tunis, Tunisia.,Laboratory of Research in Sciences and Technology of Environment, High Institute of Science and Technology of Environment, University of Carthage, Hammam-Lif, Tunisia
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Multidrug-Resistant Proteus mirabilis Strain with Cointegrate Plasmid. Microorganisms 2020; 8:microorganisms8111775. [PMID: 33198099 PMCID: PMC7696407 DOI: 10.3390/microorganisms8111775] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 11/02/2020] [Accepted: 11/10/2020] [Indexed: 12/11/2022] Open
Abstract
Proteus mirabilis is a component of the normal intestinal microflora of humans and animals, but can cause urinary tract infections and even sepsis in hospital settings. In recent years, the number of multidrug-resistant P. mirabilis isolates, including the ones producing extended-spectrum β-lactamases (ESBLs), is increasing worldwide. However, the number of investigations dedicated to this species, especially, whole-genome sequencing, is much lower in comparison to the members of the ESKAPE pathogens group. This study presents a detailed analysis of clinical multidrug-resistant ESBL-producing P. mirabilis isolate using short- and long-read whole-genome sequencing, which allowed us to reveal possible horizontal gene transfer between Klebsiella pneumoniae and P. mirabilis plasmids and to locate the CRISPR-Cas system in the genome together with its probable phage targets, as well as multiple virulence genes. We believe that the data presented will contribute to the understanding of antibiotic resistance acquisition and virulence mechanisms for this important pathogen.
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Hoard A, Montaña S, Moriano A, Fernandez JS, Traglia GM, Quiroga C, Franchi A, Cohen E, Corigliano C, Almuzara M, Ramirez MS. Genomic Analysis of two NDM-1 Providencia stuartii Strains Recovered from a Single Patient. Curr Microbiol 2020; 77:4029-4036. [PMID: 33048176 DOI: 10.1007/s00284-020-02242-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 10/01/2020] [Indexed: 12/18/2022]
Abstract
In the last years, an increasing number of untreatable infections caused by drug-resistant microbes have impacted the health care system. Worldwide, infections caused by carbapenem-resistant (CR) Gram-negative bacilli have dramatically increased. Among the CR-Gram-negative bacilli, those producing carbapenemases, such as NDM-1, are the main concern. Different Enterobacterales harboring NDM-1 have been reported lately. Providencia stuartii, a member of the Morganellaceae family, is ubiquitous in the environment, but is also known to cause nosocomial infections. Here we describe the genomic analysis of two NDM-1- producing P. stuartii strains recovered from the same patient as well as other carbapenem resistant strains recovered from the same hospital. As a result of the genomic analysis thirteen resistance genes, including three to β-lactams (blaOXA-1, blaTEM-1, blaNDM-1), four to aminoglycosides (aphA6, aac(3)-IId, aac(2')-Ia, aac(6')-Ib-cr5), one to sulfonamides (sul1), two to chloramphenicol (catB3, catA3), one to rifampicin, one to bleomycin (ble), and one to tetracycline (tet(B)) were found. Moreover, a variety of mobile genetic elements, such as insertion sequences, plasmids and phage- related sequences, were found within P. stuartii genomes. The spread of carbapenem-resistant isolates remains a significant clinical and public health concern. Therefore, we considered that the detection of CR isolates is an essential step in addressing this problem.
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Affiliation(s)
- Amparo Hoard
- Center for Applied Biotechnology Studies, Department of Biological Science, California State University Fullerton, Fullerton, CA, USA
| | - Sabrina Montaña
- Laboratorio de Bacteriología Clínica, Departamento de Bioquímica Clínica, Facultad de Farmacia Y Bioquímica, Hospital de Clínicas José de San Martín, Buenos Aires, Argentina
| | - Alessandro Moriano
- Center for Applied Biotechnology Studies, Department of Biological Science, California State University Fullerton, Fullerton, CA, USA
| | - Jennifer S Fernandez
- Center for Applied Biotechnology Studies, Department of Biological Science, California State University Fullerton, Fullerton, CA, USA
| | - German M Traglia
- Laboratorio de Bacteriología Clínica, Departamento de Bioquímica Clínica, Facultad de Farmacia Y Bioquímica, Hospital de Clínicas José de San Martín, Buenos Aires, Argentina
| | - Cecilia Quiroga
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas Y Tecnológicas, Instituto de Investigaciones en Microbiología Y Parasitología Médica (IMPAM), Facultad de Medicina, Paraguay 2155- C1121ABG, Buenos Aires, Argentina
| | - Agustina Franchi
- Laboratorio de Bacteriologia, Hospital Interzonal de Agudos Eva Perón, Provincia de Buenos Aires, San Martín, Argentina
| | - Emilia Cohen
- Laboratorio de Bacteriologia, Hospital Interzonal de Agudos Eva Perón, Provincia de Buenos Aires, San Martín, Argentina
| | - Cecilia Corigliano
- Laboratorio de Bacteriologia, Hospital Interzonal de Agudos Eva Perón, Provincia de Buenos Aires, San Martín, Argentina
| | - Marisa Almuzara
- Laboratorio de Bacteriologia, Hospital Interzonal de Agudos Eva Perón, Provincia de Buenos Aires, San Martín, Argentina
| | - Maria Soledad Ramirez
- Center for Applied Biotechnology Studies, Department of Biological Science, California State University Fullerton, Fullerton, CA, USA.
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Complete Genome and Plasmids Sequences of a Clinical Proteus mirabilis Isolate Producing Plasmid Mediated NDM-1 from Italy. Microorganisms 2020; 8:microorganisms8030339. [PMID: 32121207 PMCID: PMC7142865 DOI: 10.3390/microorganisms8030339] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 02/10/2020] [Accepted: 02/26/2020] [Indexed: 11/16/2022] Open
Abstract
Background: The spread of carbapenemase genes, such as blaNDM-1, in Proteus mirabilis poses a public health threat. The aim of the study was to characterize the genome and plasmids sequences of an NDM-1-positive strain (IBCRE14), which was isolated in 2019 from a catheterized patient hospitalized in Italy. Methods: Whole genome sequencing (WGS) of IBCRE14 was performed on extracted genomic DNA using Sequel I platform. Genome assembly was performed using "Microbial Assembly". Genomic analysis was conducted by uploading the contigs to ResFinder and PlasmidFinder databases from the Center for Genomic Epidemiology. Results: IBCRE14 had a genome size of 4,018,329 bp and harboured genes coding for resistance to aminoglycosides (aadA1), phenicol (cat), tetracycline (tetJ), and trimethoprim (dfrA1). A large plasmid (pIB_NDM_1) harboured antibiotic resistance genes against sulphonamide (sul1), trimethoprim (dfrA14), tetracycline (tetB), rifampicin (arr-2), aminoglycosides (aadA1, aph3-VI), and beta-lactams (blaOXA-10, blaNDM-1). Furthermore, a small plasmid (pIB_COL3M) harboured a qnrD1 gene coding for quinolone resistance. Conclusion: The ability to conjugate and the presence of a composite antibiotic resistance island suggests that pIB_NDM_1 could both acquire more resistance genes and easily disseminate. To our knowledge, this is the first report on an untypable plasmid harbouring blaNDM-1 in P. mirabilis, in Italy.
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Kopotsa K, Osei Sekyere J, Mbelle NM. Plasmid evolution in carbapenemase-producing Enterobacteriaceae: a review. Ann N Y Acad Sci 2019; 1457:61-91. [PMID: 31469443 DOI: 10.1111/nyas.14223] [Citation(s) in RCA: 109] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 07/22/2019] [Accepted: 07/26/2019] [Indexed: 12/17/2022]
Abstract
Carbapenem-resistant Enterobacteriaceae (CRE) have been listed by the WHO as high-priority pathogens owing to their high association with mortalities and morbidities. Resistance to multiple β-lactams complicates effective clinical management of CRE infections. Using plasmid typing methods, a wide distribution of plasmid replicon groups has been reported in CREs around the world, including IncF, N, X, A/C, L/M, R, P, H, I, and W. We performed a literature search for English research papers, published between 2013 and 2018, reporting on plasmid-mediated carbapenem resistance. A rise in both carbapenemase types and associated plasmid replicon groups was seen, with China, Canada, and the United States recording a higher increase than other countries. blaKPC was the most prevalent, except in Angola and the Czech Republic, where OXA-181 (n = 50, 88%) and OXA-48-like (n = 24, 44%) carbapenemases were most prevalent, respectively; blaKPC-2/3 accounted for 70% (n = 956) of all reported carbapenemases. IncF plasmids were found to be responsible for disseminating different antibiotic resistance genes worldwide, accounting for almost 40% (n = 254) of plasmid-borne carbapenemases. blaCTX-M , blaTEM , blaSHV , blaOXA-1/9 , qnr, and aac-(6')-lb were mostly detected concurrently with carbapenemases. Most reported plasmids were conjugative but not present in multiple countries or species, suggesting limited interspecies and interboundary transmission of a common plasmid. A major limitation to effective characterization of plasmid evolution was the use of PCR-based instead of whole-plasmid sequencing-based plasmid typing.
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Affiliation(s)
- Katlego Kopotsa
- Department of Medical Microbiology, Faculty of Health Sciences, School of Medicine, University of Pretoria, Pretoria, Gauteng, South Africa
| | - John Osei Sekyere
- Department of Medical Microbiology, Faculty of Health Sciences, School of Medicine, University of Pretoria, Pretoria, Gauteng, South Africa
| | - Nontombi Marylucy Mbelle
- Department of Medical Microbiology, Faculty of Health Sciences, School of Medicine, University of Pretoria, Pretoria, Gauteng, South Africa.,National Health Laboratory Service, Tshwane Division, Department of Medical Microbiology, University of Pretoria, Pretoria, Gauteng, South Africa
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Kinetic Profile and Molecular Dynamic Studies Show that Y229W Substitution in an NDM-1/L209F Variant Restores the Hydrolytic Activity of the Enzyme toward Penicillins, Cephalosporins, and Carbapenems. Antimicrob Agents Chemother 2019; 63:AAC.02270-18. [PMID: 30917978 DOI: 10.1128/aac.02270-18] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Accepted: 01/23/2019] [Indexed: 01/01/2023] Open
Abstract
The New Delhi metallo-β-lactamase-1 (NDM-1) enzyme is the most common metallo-β-lactamase identified in many Gram-negative bacteria causing severe nosocomial infections. The aim of this study was to focus the attention on non-active-site residues L209 and Y229 of NDM-1 and to investigate their role in the catalytic mechanism. Specifically, the effect of the Y229W substitution in the L209F variant was evaluated by antimicrobial susceptibility testing, kinetic, and molecular dynamic (MD) studies. The Y229W single mutant and L209F-Y229W double mutant were generated by site-directed mutagenesis. The Km , k cat, and k cat/Km kinetic constants, calculated for the two mutants, were compared with those of (wild-type) NDM-1 and the L209F variant. Compared to the L209F single mutant, the L209F-Y229W double mutant showed a remarkable increase in k cat values of 100-, 240-, 250-, and 420-fold for imipenem, meropenem, benzylpenicillin, and cefepime, respectively. In the L209F-Y229W enzyme, we observed a remarkable increase in k cat/Km of 370-, 140-, and 80-fold for cefepime, meropenem, and cefazolin, respectively. The same behavior was noted using the antimicrobial susceptibility test. MD simulations were carried out on both L209F and L209F-Y229W enzymes complexed with benzylpenicillin, focusing attention on the overall mechanical features and on the differences between the two systems. With respect to the L209F variant, the L209F-Y229W double mutant showed mechanical stabilization of loop 10 and the N-terminal region. In addition, Y229W substitution destabilized both the C-terminal region and the region from residues 149 to 154. The epistatic effect of the Y229W mutation jointly with the stabilization of loop 10 led to a better catalytic efficiency of β-lactams. NDM numbering is used in order to facilitate the comparison with other NDM-1 studies.
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