1
|
Shih YL, Bregente CJB, Chen PK, Thuy TTD, Chen YC, Kuo HY, Lu HF, Kao CY. First report of the chromosomal integration of carbapenemase gene blaIMP-19 in Acinetobacter baumannii AB322: the legacy of integron in phage-plasmid? Microbiol Spectr 2024; 12:e0038224. [PMID: 38651885 PMCID: PMC11237583 DOI: 10.1128/spectrum.00382-24] [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: 02/13/2024] [Accepted: 04/02/2024] [Indexed: 04/25/2024] Open
Abstract
Integration of carbapenemase gene blaIMP into the chromosome of carbapenem-resistant Acinetobacter baumannii (CRAB) has not been reported. The aim of this study was to explore the genomic characteristics of CRAB AB322 isolated from a Taiwanese patient diagnosed with bacteremia in 2011, whose chromosome harbors blaIMP-19. Disk diffusion and broth microdilution were employed to analyze the antimicrobial susceptibility of AB322 to 14 antimicrobials. Nanopore whole-genome sequencing platform was utilized for AB322 genome sequencing, and conjugation was further performed to investigate the transferability of blaIMP-19 to amikacin-resistant A. baumannii 218 (AB218) and Acinetobacter nosocomialis 254 (AN254). The results showed that AB322 was classified as multidrug-resistant A. baumannii but remained susceptible to ampicillin/sulbactam, colistin, and tigecycline. Whole-genome sequencing revealed the AB322 genome, consisting of a 4,098,985-bp chromosome, a 71,590-bp conjugative plasmid named pAB322-1, and an 8,726-bp plasmid named pAB322-2. Multilocus sequence typing analysis indicated that AB322 belonged to sequence type 1. AB322 chromosome harbored numerous acquired antimicrobial resistance genes, including aph(3')-Ia, aadA1b, aadA1, aac(6')-Ib3, aac (3)-Ia, blaADC-25, blaOXA-69, blaIMP-19, catA1, sul1, and tet(A), conferring resistance to β-lactams, aminoglycosides, chloramphenicol, sulfamethoxazole, and tetracyclines. Moreover, blaIMP-19 was identified to be situated within class 1 integron In240 and an incomplete PHAGE_Salmon_SJ46_NC_031129 on AB322 chromosome. However, conjugation experiments revealed that blaIMP-19 could not be transferred to AB218 and AN254 in our testing conditions. In conclusion, we first report the presence of chromosomal-integrated blaIMP-19 in CRAB, possibly mediated by integron. The future dissemination of blaIMP-19 among different species, leading to carbapenem resistance dissemination, requires close monitoring. IMPORTANCE The horizontal transfer of antimicrobial-resistant genes is crucial for the dissemination of resistance, especially as Acinetobacter baumannii has emerged as a clinically significant pathogen. However, in this study, we first report the integration of the blaIMP-19 gene into the chromosome of A. baumannii, and such horizontal transfer may be associated with integron-phage elements. Additionally, it is possible that these DNA fragments carrying antimicrobial-resistant genes could further spread to other pathogens by moving horizontally onto conjugative plasmids.
Collapse
Affiliation(s)
- Yung-Luen Shih
- School of Medicine, College of Medicine, Fu-Jen Catholic University, New Taipei, Taiwan
- Department of Pathology and Laboratory Medicine, Shin Kong Wu Ho-Su Memorial Hospital, Taipei, Taiwan
| | - Carl Jay Ballena Bregente
- Institute of Microbiology and Immunology, College of Life Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan
- College of Medical Technology, Southwestern University PHINMA, Cebu, Philippines
| | - Pek Kee Chen
- Institute of Microbiology and Immunology, College of Life Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Tran Thi Dieu Thuy
- Institute of Microbiology and Immunology, College of Life Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Yu-Chen Chen
- Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung, Taiwan
| | - Han-Yueh Kuo
- National Taiwan University Hospital Hsin-Chu Branch, Hsin-Chu, Taiwan
- National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Hsu-Feng Lu
- Department of Laboratory Medicine, China Medical University Hospital, Taichung, Taiwan
- Department of Medical Laboratory Science and Biotechnology, Asia University, Taichung City, Taiwan
| | - Cheng-Yen Kao
- Institute of Microbiology and Immunology, College of Life Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Health Innovation Center, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Microbiota Research Center, National Yang Ming Chiao Tung University, Taipei, Taiwan
| |
Collapse
|
2
|
Migliaccio A, Bray J, Intoccia M, Stabile M, Scala G, Jolley KA, Brisse S, Zarrilli R. Phylogenomics of Acinetobacter species and analysis of antimicrobial resistance genes. Front Microbiol 2023; 14:1264030. [PMID: 37928684 PMCID: PMC10620307 DOI: 10.3389/fmicb.2023.1264030] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 09/26/2023] [Indexed: 11/07/2023] Open
Abstract
Introduction Non-baumannii Acinetobacter species are increasingly isolated in the clinical setting and the environment. The aim of the present study was to analyze a genome database of 837 Acinetobacter spp. isolates, which included 798 non-baumannii Acinetobacter genomes, in order to define the concordance of classification and discriminatory power of 7-gene MLST, 53-gene MLST, and single-nucleotide polymorphism (SNPs) phylogenies. Methods Phylogenies were performed on Pasteur Multilocus Sequence Typing (MLST) or ribosomal Multilocus Sequence Typing (rMLST) concatenated alleles, or SNPs extracted from core genome alignment. Results The Pasteur MLST scheme was able to identify and genotype 72 species in the Acinetobacter genus, with classification results concordant with the ribosomal MLST scheme. The discriminatory power and genotyping reliability of the Pasteur MLST scheme were assessed in comparison to genome-wide SNP phylogeny on 535 non-baumannii Acinetobacter genomes assigned to Acinetobacter pittii, Acinetobacter nosocomialis, Acinetobacter seifertii, and Acinetobacter lactucae (heterotypic synonym of Acinetobacter dijkshoorniae), which were the most clinically relevant non-baumannii species of the A. baumannii group. The Pasteur MLST and SNP phylogenies were congruent at Robinson-Fould and Matching cluster tests and grouped genomes into four and three clusters in A. pittii, respectively, and one each in A. seifertii. Furthermore, A. lactucae genomes were grouped into one cluster within A. pittii genomes. The SNP phylogeny of A. nosocomialis genomes showed a heterogeneous population and did not correspond to the Pasteur MLST phylogeny, which identified two recombinant clusters. The antimicrobial resistance genes belonging to at least three different antimicrobial classes were identified in 91 isolates assigned to 17 distinct species in the Acinetobacter genus. Moreover, the presence of a class D oxacillinase, which is a naturally occurring enzyme in several Acinetobacter species, was found in 503 isolates assigned to 35 Acinetobacter species. Conclusion In conclusion, Pasteur MLST phylogeny of non-baumannii Acinetobacter isolates coupled with in silico detection of antimicrobial resistance makes it important to study the population structure and epidemiology of Acinetobacter spp. isolates.
Collapse
Affiliation(s)
| | - James Bray
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Michele Intoccia
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Maria Stabile
- Department of Public Health, University of Naples “Federico II”, Naples, Italy
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
| | - Giovanni Scala
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Keith A. Jolley
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Sylvain Brisse
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Raffaele Zarrilli
- Department of Public Health, University of Naples “Federico II”, Naples, Italy
| |
Collapse
|
3
|
Merlino J, Rizzo S, Beresford R, Gray T. Isolation of Acinetobacter bereziniae harbouring plasmid bla NDM-1 in central Sydney, Australia. Pathology 2023; 55:867-868. [PMID: 37169647 DOI: 10.1016/j.pathol.2023.02.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 02/07/2023] [Accepted: 02/23/2023] [Indexed: 05/13/2023]
Affiliation(s)
- John Merlino
- Department of Microbiology and Infectious Diseases, Concord Hospital, NSW Health Pathology, Sydney, NSW, Australia; School of Medical Sciences, Department of Infection and Immunity, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia.
| | - Sophia Rizzo
- Department of Microbiology and Infectious Diseases, Concord Hospital, NSW Health Pathology, Sydney, NSW, Australia
| | - Rohan Beresford
- Department of Microbiology and Infectious Diseases, Concord Hospital, NSW Health Pathology, Sydney, NSW, Australia
| | - Timothy Gray
- Department of Microbiology and Infectious Diseases, Concord Hospital, NSW Health Pathology, Sydney, NSW, Australia; Concord Hospital Clinical School, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| |
Collapse
|
4
|
Sheck E, Romanov A, Shapovalova V, Shaidullina E, Martinovich A, Ivanchik N, Mikotina A, Skleenova E, Oloviannikov V, Azizov I, Vityazeva V, Lavrinenko A, Kozlov R, Edelstein M. Acinetobacter Non- baumannii Species: Occurrence in Infections in Hospitalized Patients, Identification, and Antibiotic Resistance. Antibiotics (Basel) 2023; 12:1301. [PMID: 37627721 PMCID: PMC10451542 DOI: 10.3390/antibiotics12081301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 08/05/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023] Open
Abstract
BACKGROUND Acinetobacter species other than A. baumannii are becoming increasingly more important as opportunistic pathogens for humans. The primary aim of this study was to assess the prevalence, species distribution, antimicrobial resistance patterns, and carbapenemase gene content of clinical Acinetobacter non-baumannii (Anb) isolates that were collected as part of a sentinel surveillance program of bacterial infections in hospitalized patients. The secondary aim was to evaluate the performance of MALDI-TOF MS systems for the species-level identification of Anb isolates. METHODS Clinical bacterial isolates were collected from multiple sites across Russia and Kazakhstan in 2016-2022. Species identification was performed by means of MALDI-TOF MS, with the Autobio and Bruker systems used in parallel. The PCR detection of the species-specific blaOXA-51-like gene was used as a means of differentiating A. baumannii from Anb species, and the partial sequencing of the rpoB gene was used as a reference method for Anb species identification. The susceptibility of isolates to antibiotics (amikacin, cefepime, ciprofloxacin, colistin, gentamicin, imipenem, meropenem, sulbactam, tigecycline, tobramycin, and trimethoprim-sulfamethoxazole) was determined using the broth microdilution method. The presence of the most common in Acinetobacter-acquired carbapenemase genes (blaOXA-23-like, blaOXA-24/40-like, blaOXA-58-like, blaNDM, blaIMP, and blaVIM) was assessed using real-time PCR. RESULTS In total, 234 isolates were identified as belonging to 14 Anb species. These comprised 6.2% of Acinetobacter spp. and 0.7% of all bacterial isolates from the observations. Among the Anb species, the most abundant were A. pittii (42.7%), A. nosocomialis (13.7%), the A. calcoaceticus/oleivorans group (9.0%), A. bereziniae (7.7%), and A. geminorum (6.0%). Notably, two environmental species, A. oleivorans and A. courvalinii, were found for the first time in the clinical samples of patients with urinary tract infections. The prevalence of resistance to different antibiotics in Anb species varied from <4% (meropenem and colistin) to 11.2% (gentamicin). Most isolates were susceptible to all antibiotics; however, sporadic isolates of A. bereziniae, A. johnsonii, A. nosocomialis, A. oleivorans, A. pittii, and A. ursingii were resistant to carbapenems. A. bereziniae was more frequently resistant to sulbactam, aminoglycosides, trimethoprim-sulfamethoxazole, and tigecycline than the other species. Four (1.7%) isolates of A. bereziniae, A. johnsonii, A. pittii were found to carry carbapenemase genes (blaOXA-58-like and blaNDM, either alone or in combination). The overall accuracy rates of the species-level identification of Anb isolates with the Autobio and Bruker systems were 80.8% and 88.5%, with misidentifications occurring in 5 and 3 species, respectively. CONCLUSIONS This study provides important new insights into the methods of identification, occurrence, species distribution, and antibiotic resistance traits of clinical Anb isolates.
Collapse
Affiliation(s)
- Eugene Sheck
- Institute of Antimicrobial Chemotherapy, Smolensk State Medical University, 214019 Smolensk, Russia; (E.S.); (I.A.)
| | - Andrey Romanov
- Institute of Antimicrobial Chemotherapy, Smolensk State Medical University, 214019 Smolensk, Russia; (E.S.); (I.A.)
| | - Valeria Shapovalova
- Institute of Antimicrobial Chemotherapy, Smolensk State Medical University, 214019 Smolensk, Russia; (E.S.); (I.A.)
| | - Elvira Shaidullina
- Institute of Antimicrobial Chemotherapy, Smolensk State Medical University, 214019 Smolensk, Russia; (E.S.); (I.A.)
| | - Alexey Martinovich
- Institute of Antimicrobial Chemotherapy, Smolensk State Medical University, 214019 Smolensk, Russia; (E.S.); (I.A.)
| | - Natali Ivanchik
- Institute of Antimicrobial Chemotherapy, Smolensk State Medical University, 214019 Smolensk, Russia; (E.S.); (I.A.)
| | - Anna Mikotina
- Institute of Antimicrobial Chemotherapy, Smolensk State Medical University, 214019 Smolensk, Russia; (E.S.); (I.A.)
| | - Elena Skleenova
- Institute of Antimicrobial Chemotherapy, Smolensk State Medical University, 214019 Smolensk, Russia; (E.S.); (I.A.)
| | - Vladimir Oloviannikov
- Institute of Antimicrobial Chemotherapy, Smolensk State Medical University, 214019 Smolensk, Russia; (E.S.); (I.A.)
| | - Ilya Azizov
- Institute of Antimicrobial Chemotherapy, Smolensk State Medical University, 214019 Smolensk, Russia; (E.S.); (I.A.)
| | - Vera Vityazeva
- Republican Children’s Hospital, 185000 Petrozavodsk, Republic of Karelia, Russia
| | - Alyona Lavrinenko
- Shared Resource Laboratory, Karaganda Medical University, 100008 Karaganda, Kazakhstan
| | - Roman Kozlov
- Institute of Antimicrobial Chemotherapy, Smolensk State Medical University, 214019 Smolensk, Russia; (E.S.); (I.A.)
| | - Mikhail Edelstein
- Institute of Antimicrobial Chemotherapy, Smolensk State Medical University, 214019 Smolensk, Russia; (E.S.); (I.A.)
| |
Collapse
|
5
|
Castanheira M, Mendes RE, Gales AC. Global Epidemiology and Mechanisms of Resistance of Acinetobacter baumannii-calcoaceticus Complex. Clin Infect Dis 2023; 76:S166-S178. [PMID: 37125466 PMCID: PMC10150277 DOI: 10.1093/cid/ciad109] [Citation(s) in RCA: 45] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023] Open
Abstract
Acinetobacter baumannii-calcoaceticus complex is the most commonly identified species in the genus Acinetobacter and it accounts for a large percentage of nosocomial infections, including bacteremia, pneumonia, and infections of the skin and urinary tract. A few key clones of A. baumannii-calcoaceticus are currently responsible for the dissemination of these organisms worldwide. Unfortunately, multidrug resistance is a common trait among these clones due to their unrivalled adaptive nature. A. baumannii-calcoaceticus isolates can accumulate resistance traits by a plethora of mechanisms, including horizontal gene transfer, natural transformation, acquisition of mutations, and mobilization of genetic elements that modulate expression of intrinsic and acquired genes.
Collapse
Affiliation(s)
| | | | - Ana C Gales
- Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina (EPM), Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
| |
Collapse
|
6
|
Mohamed HMA, Abd-Elhafeez HH, Al-Jabr OA, El-Zamkan MA. Characterization of Acinetobacter baumannii Isolated from Raw Milk. BIOLOGY 2022; 11:biology11121845. [PMID: 36552354 PMCID: PMC9775129 DOI: 10.3390/biology11121845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/10/2022] [Accepted: 12/14/2022] [Indexed: 12/24/2022]
Abstract
Acinetobacter baumannii (A. baumannii) is an opportunistic pathogen associated with nosocomial infections. In this study, 100 raw milk samples were collected from Qena, Egypt, and subjected to conventional and molecular assays to determine the presence of A. baumannii and investigate their antimicrobial resistance and biofilm formation. Our findings revealed that, among the 100 samples, Acinetobacter spp. were found in 13 samples based on CHROM agar results. We further characterized them using rpoB and 16S-23SrRNA sequencing and gyrB multiplex PCR analysis and confirmed that 9 out of the 13 Acinetobacter spp. isolates were A. baumannii and 4 were other species. The A. baumannii isolates were resistant to β-lactam drugs, including cefotaxime (44%), ampicillin-sulbactam and levofloxacin (33.3% for each), imipenem, meropenem and aztreonam (22.2% for each). We observed different antimicrobial resistance patterns, with a multi-antibiotic resistant (MAR) index ranging from 0.2 to 0.3. According to the PCR results, blaOXA-51 and blaOXA-23 genes were amplified in 100% and 55.5% of the A. baumannii isolates, respectively, while the blaOXA-58 gene was not amplified. Furthermore, the metallo-β-lactamases (MBL) genes blaIMP and blaNDM were found in 11.1% and 22.2% of isolates, respectively, while blaVIM was not amplified. Additionally, eight A. baumannii isolates (88.8%) produced black-colored colonies on Congo red agar, demonstrating their biofilm production capacity. These results showed that, besides other foodborne pathogens, raw milk should also be examined for A. baumannii, which could be a public health concern.
Collapse
Affiliation(s)
- Hams M. A. Mohamed
- Department of Microbiology, Faculty of Veterinary Medicine, South Valley University, Qena 83523, Egypt
| | - Hanan H. Abd-Elhafeez
- Department of Cells and Tissues, Faculty of Veterinary Medicine, Assiut University, Assiut 71526, Egypt
- Correspondence:
| | - Omar A. Al-Jabr
- Department of Microbiology, College of Veterinary Medicine, King Faisal University, P.O. Box 400, Al-Ahsa 31982, Saudi Arabia
| | - Mona A. El-Zamkan
- Department of Food Hygiene and Control, Faculty of Veterinary Medicine, South Valley University, Qena 83523, Egypt
| |
Collapse
|
7
|
The prevalence of antibiotic-resistant Acinetobacter baumannii infections among the Iranian ICU patients: A systematic review and meta-analysis. GENE REPORTS 2022. [DOI: 10.1016/j.genrep.2022.101731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
|
8
|
Kanahashi T, Matsumura Y, Yamamoto M, Tanaka M, Nagao M. Comparison of the Xpert Carba-R and NG-Test CARBA5 for the detection of carbapenemases in an IMP-type carbapenemase endemic region in Japan. J Infect Chemother 2021; 27:503-506. [PMID: 33214070 DOI: 10.1016/j.jiac.2020.11.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 09/28/2020] [Accepted: 11/03/2020] [Indexed: 12/31/2022]
Abstract
INTRODUCTION The real-time PCR assay Xpert Carba-R and the lateral flow immunoassay NG-Test CARBA5 were developed to detect 5 types of carbapenemase genes (blaIMP, blaKPC, blaVIM, blaOXA-48, and blaNDM). METHODS We compared the diagnostic performance, turn-around time, and cost of these assays. Carbapenemase genes were defined using the Carba NP test, modified Carbapenem Inactivation Methods (mCIM), multiplex PCR, and whole-genome sequencing. We included clinical Enterobacterales isolates (n = 36) and nonfermenting gram-negative bacilli isolates (n = 17) collected from 16 acute-care hospitals in the Kinki region of Japan. RESULTS Twenty-six of these 53 isolates were positive according to both of the Carba NP test and mCIM and, contained the following carbapenemase genes: blaIMP-1 (n = 3), blaIMP-6 (n = 1), blaIMP-19 (n = 12), blaIMP-26 (n = 1), blaIMP-41 (n = 2), blaIMP-66 (n = 2), blaNDM-1 (n = 3), and blaVIM-2 (n = 2). All of the remaining 27 isolates were negative according to the Carba NP test, mCIM, and multiplex PCR. The specificities of both assays were 100%. The sensitivity of the Xpert Carba-R assay was as low as 53.8% and that of the NG-Test CARBA5 was 92.3% because the former failed to detect all isolates with blaIMP-19 (n = 12) and the latter failed to detect isolates with blaIMP-66 (n = 2). Both assays can easily be performed in less than 5 min. CONCLUSIONS The NG-Test CARBA5 assay was superior with regard to assay time and cost per sample. We propose the use of the NG-Test CARBA5 assay in clinical laboratories where IMP-type carbapenemases are endemic.
Collapse
Affiliation(s)
- Toru Kanahashi
- Department of Clinical Laboratory and Department of Infection Control and Prevention, Kyoto University Hospital, 54 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan.
| | - Yasufumi Matsumura
- Department of Clinical Laboratory and Department of Infection Control and Prevention, Kyoto University Hospital, 54 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan; Department of Clinical Laboratory Medicine, Kyoto University Graduate School of Medicine, 54 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan.
| | - Masaki Yamamoto
- Department of Clinical Laboratory and Department of Infection Control and Prevention, Kyoto University Hospital, 54 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan; Department of Clinical Laboratory Medicine, Kyoto University Graduate School of Medicine, 54 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan.
| | - Michio Tanaka
- Department of Clinical Laboratory Medicine, Kyoto University Graduate School of Medicine, 54 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan.
| | - Miki Nagao
- Department of Clinical Laboratory and Department of Infection Control and Prevention, Kyoto University Hospital, 54 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan; Department of Clinical Laboratory Medicine, Kyoto University Graduate School of Medicine, 54 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan.
| |
Collapse
|
9
|
Genomic Characterization of Clinical Extensively Drug-Resistant Acinetobacter pittii Isolates. Microorganisms 2021; 9:microorganisms9020242. [PMID: 33503968 PMCID: PMC7912037 DOI: 10.3390/microorganisms9020242] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 01/20/2021] [Accepted: 01/20/2021] [Indexed: 01/26/2023] Open
Abstract
Carbapenem-resistant Acinetobacter pittii (CRAP) is a causative agent of nosocomial infections. This study aimed to characterize clinical isolates of CRAP from a tertiary hospital in Northeast Thailand. Six isolates were confirmed as extensively drug-resistant Acinetobacter pittii (XDRAP). The blaNDM-1 gene was detected in three isolates, whereas blaIMP-14 and blaIMP-1 were detected in the others. Multilocus sequence typing with the Pasteur scheme revealed ST220 in two isolates, ST744 in two isolates, and ST63 and ST396 for the remaining two isolates, respectively. Genomic characterization revealed that six XDRAP genes contained antimicrobial resistance genes: ST63 (A436) and ST396 (A1) contained 10 antimicrobial resistance genes, ST220 (A984 and A864) and ST744 (A56 and A273) contained 9 and 8 antimicrobial resistance genes, respectively. The single nucleotide polymorphism (SNP) phylogenetic tree revealed that the isolates A984 and A864 were closely related to A. pittii YB-45 (ST220) from China, while A436 was related to A. pittii WCHAP100020, also from China. A273 and A56 isolates (ST744) were clustered together; these isolates were closely related to strains 2014S07-126, AP43, and WCHAP005069, which were isolated from Taiwan and China. Strict implementation of infection control based upon the framework of epidemiological analyses is essential to prevent outbreaks and contain the spread of the pathogen. Continued surveillance and close monitoring with molecular epidemiological tools are needed.
Collapse
|
10
|
Alzuhairi MA, Abdulmohsen AM, Falih MN, Hanafiah MM. Genomic sequencing analysis of Acinetobacter baumannii strain ABIQM1, isolated from a meningitis patient. GENE REPORTS 2020. [DOI: 10.1016/j.genrep.2020.100631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
11
|
Gan HM, Wengert P, Barton HA, Hudson AO, Savka MA. Insight into the resistome and quorum sensing system of a divergent Acinetobacter pittii isolate from an untouched site of the Lechuguilla Cave. Access Microbiol 2020; 2:acmi000089. [PMID: 34568753 PMCID: PMC8459101 DOI: 10.1099/acmi.0.000089] [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: 08/27/2019] [Accepted: 12/11/2019] [Indexed: 11/18/2022] Open
Abstract
Acinetobacter are Gram-negative bacteria belonging to the sub-phyla Gammaproteobacteria, commonly associated with soils, animal feeds and water. Some members of the Acinetobacter have been implicated in hospital-acquired infections, with broad-spectrum antibiotic resistance. Here we report the whole-genome sequence of LC510, an Acinetobacter species isolated from deep within a pristine location of the Lechuguilla Cave. Pairwise nucleotide comparison to three type strains within the genus Acinetobacter assigned LC510 as an Acinetobacter pittii isolate. Scanning of the LC510 genome identified two genes coding for b-lactamase resistance, despite the fact that LC510 was isolated from a portion of the cave not previously visited by humans and protected from anthropogenic input. The ability to produce acyl-homoserine lactone (AHL) signal in culture medium, an observation that is consistent with the identification of the luxI and luxR homologues in its genome, suggests that cell-to-cell communication remains important in an isolated cave ecosystem.
Collapse
Affiliation(s)
- Han Ming Gan
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong 3220, Victoria, Australia.,Deakin Genomics Centre, Deakin University, Geelong 3220, Victoria, Australia.,School of Science, Monash University Malaysia, Bandar Sunway, 47500 Petaling Jaya, Selangor, Malaysia
| | - Peter Wengert
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, USA
| | - Hazel A Barton
- Department of Biology, University of Akron, Akron, OH, USA
| | - André O Hudson
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, USA
| | - Michael A Savka
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, USA
| |
Collapse
|
12
|
Kiyasu Y, Hitomi S, Funayama Y, Saito K, Ishikawa H. Characteristics of invasive Acinetobacter infection: A multicenter investigation with molecular identification of causative organisms. J Infect Chemother 2020; 26:475-482. [PMID: 31924521 DOI: 10.1016/j.jiac.2019.12.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 12/02/2019] [Accepted: 12/06/2019] [Indexed: 11/24/2022]
Abstract
We examined microbiological and clinical characteristics of invasive Acinetobacter infection occurring in four hospitals located in the Minami-Ibaraki Area. Glucose-non-fermentative Gram-negative bacilli isolated from the blood and the cerebrospinal fluid in independent cases between 2001 and 2014 were consecutively collected and those possibly to be Acinetobacter species were re-identified using molecular methods. Of 158 strains identified as Acinetobacter species, 155 were classified into 16 officially designated species, including 42 Acinetobacter pittii and 40 Acinetobacter baumannii. Imipenem non-susceptibility was detected only in 4 strains, none of which demonstrated multidrug resistance. Retrospective analyses of 154 cases for which medical records were fully available showed that the most common cause of infection was primary bloodstream infection (134 cases), of which 128 were related to intravascular catheter use. The mortality on day 28 after the onset was independently associated with cerebrovascular disease, moderate to severe renal disease, the Pitt bacteremia score, and infection other than primary bloodstream infection but not with appropriate empiric antimicrobial therapy. Isolation of A. baumannii was significantly associated with septic shock but not with the 28-day mortality. These findings, obtained in a region where drug-resistant Acinetobacter strains were much less prevailing, indicated that non-baumannii Acinetobacter species were common pathogens, that the most predominant cause of invasive Acinetobacter infection was intravascular catheter-related infection, that virulence of A. baumannii might be higher than those of other species but its association with mortality was unclear, and that administration of broad-spectrum antibiotics targeting Acinetobacter species might be deferrable in a certain situation.
Collapse
Affiliation(s)
- Yoshihiko Kiyasu
- Department of Infectious Diseases, University of Tsukuba Hospital, Japan.
| | - Shigemi Hitomi
- Department of Infectious Diseases, University of Tsukuba Hospital, Japan
| | | | - Kazuhito Saito
- Department of Respiratory Diseases, Tsuchiura Kyodo General Hospital, Japan
| | - Hiroichi Ishikawa
- Department of Respiratory Medicine, Tsukuba Medical Center Hospital, Japan
| |
Collapse
|
13
|
Amoureux L, Riedweg K, Chapuis A, Bador J, Siebor E, Péchinot A, Chrétien ML, de Curraize C, Neuwirth C. Nosocomial Infections with IMP-19-Producing Pseudomonas aeruginosa Linked to Contaminated Sinks, France. Emerg Infect Dis 2018; 23:304-307. [PMID: 28098548 PMCID: PMC5324815 DOI: 10.3201/eid2302.160649] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We isolated IMP-19–producing Pseudomonas aeruginosa from 7 patients with nosocomial infections linked to contaminated sinks in France. We showed that blaIMP-19 was located on various class 1 integrons among 8 species of gram-negative bacilli detected in sinks: P. aeruginosa, Achromobacter xylosoxidans, A. aegrifaciens, P. putida, Stenotrophomonas maltophilia, P. mendocina, Comamonas testosteroni, and Sphingomonas sp.
Collapse
|
14
|
Species distribution, sequence types and antimicrobial resistance of Acinetobacter spp. from cystic fibrosis patients. Epidemiol Infect 2017; 146:524-530. [PMID: 29283077 DOI: 10.1017/s0950268817002849] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Acinetobacter spp. are important healthcare pathogens, being closely linked to antibiotic resistance and outbreaks worldwide. Although such species are rarely observed in patients with cystic fibrosis (CF), we describe the characteristics of 53 strains of Acinetobacter spp. isolated from the sputum of 39 Brazilian patients with CF. The species distribution was A. baumannii (n = 29), A. pittii (n = 13), A. nosocomialis (n = 8), A. seifertii (n = 1), A. soli (n = 1) and A. variabilis (n = 1) determined by partial rpoB gene sequencing. Sixteen strains (10 A. baumannii, 3 A. pittii and 3 A. nosocomialis) were multidrug-resistant (MDR) by disk diffusion test (30%) and eight MDR carbapenem-resistant A. baumannii strains harboured the bla OXA-23-like oxacillinase gene. Thirty-three sequence types (STs) were identified by multilocus sequence typing of which eight were novel (A. baumannii: 843, 844, 845, 847, 848; A. pitti: 643; A. nosocomialis: 862 and A. seifertii: 846); six STs (2 A. baumannii, 3 A. pittii and 1 A. nosocomialis) were found in more than one patient. Four strains of A. baumannii were assigned to two common clonal complexes (CCs), namely, CC1 (ST1, ST20 and ST160), and CC79 (ST79). This study underlines the extensive species diversity of Acinetobacter spp. strains in CF lung infections which may present difficulties for therapy due to significant antimicrobial resistance.
Collapse
|
15
|
Lázaro-Díez M, Chapartegui-González I, Redondo-Salvo S, Leigh C, Merino D, Segundo DS, Fernández A, Navas J, Icardo JM, Acosta F, Ocampo-Sosa A, Martínez-Martínez L, Ramos-Vivas J. Human neutrophils phagocytose and kill Acinetobacter baumannii and A. pittii. Sci Rep 2017; 7:4571. [PMID: 28676640 PMCID: PMC5496873 DOI: 10.1038/s41598-017-04870-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 05/22/2017] [Indexed: 12/23/2022] Open
Abstract
Acinetobacter baumannii is a common cause of health care associated infections worldwide. A. pittii is an opportunistic pathogen also frequently isolated from Acinetobacter infections other than those from A. baumannii. Knowledge of Acinetobacter virulence factors and their role in pathogenesis is scarce. Also, there are no detailed published reports on the interactions between A. pittii and human phagocytic cells. Using confocal laser and scanning electron microscopy, immunofluorescence, and live-cell imaging, our study shows that immediately after bacteria-cell contact, neutrophils rapidly and continuously engulf and kill bacteria during at least 4 hours of infection in vitro. After 3 h of infection, neutrophils start to release neutrophil extracellular traps (NETs) against Acinetobacter. DNA in NETs colocalizes well with human histone H3 and with the specific neutrophil elastase. We have observed that human neutrophils use large filopodia as cellular tentacles to sense local environment but also to detect and retain bacteria during phagocytosis. Furthermore, co-cultivation of neutrophils with human differentiated macrophages before infections shows that human neutrophils, but not macrophages, are key immune cells to control Acinetobacter. Although macrophages were largely activated by both bacterial species, they lack the phagocytic activity demonstrated by neutrophils.
Collapse
Affiliation(s)
- María Lázaro-Díez
- Instituto de Investigación Valdecilla IDIVAL, Santander, 39011, Spain
- Servicio de Microbiología, Hospital Universitario Marqués de Valdecilla, Santander, 39008, Spain
- Red Española de Investigación en Patología Infecciosa (REIPI), Instituto de Salud Carlos III, Madrid, 28029, Spain
| | - Itziar Chapartegui-González
- Instituto de Investigación Valdecilla IDIVAL, Santander, 39011, Spain
- Servicio de Microbiología, Hospital Universitario Marqués de Valdecilla, Santander, 39008, Spain
| | | | - Chike Leigh
- New York University School of Medicine, New York, 10003, USA
| | - David Merino
- Instituto de Investigación Valdecilla IDIVAL, Santander, 39011, Spain
- Servicio de Inmunología, Hospital Universitario Marqués de Valdecilla, Santander, 39008, Spain
| | - David San Segundo
- Instituto de Investigación Valdecilla IDIVAL, Santander, 39011, Spain
- Servicio de Inmunología, Hospital Universitario Marqués de Valdecilla, Santander, 39008, Spain
| | - Adrián Fernández
- Instituto de Investigación Valdecilla IDIVAL, Santander, 39011, Spain
| | - Jesús Navas
- Instituto de Investigación Valdecilla IDIVAL, Santander, 39011, Spain
- Departamento de Biología Molecular, Universidad de Cantabria, Santander, 39011, Spain
| | - José Manuel Icardo
- Departamento de Anatomía y Biología Celular, Universidad de Cantabria, Santander, 39011, Spain
| | - Félix Acosta
- Grupo de Investigación en Acuicultura, Universidad de Las Palmas de Gran Canaria, Gran Canaria, 35214, Spain
| | - Alain Ocampo-Sosa
- Instituto de Investigación Valdecilla IDIVAL, Santander, 39011, Spain
- Servicio de Microbiología, Hospital Universitario Marqués de Valdecilla, Santander, 39008, Spain
- Red Española de Investigación en Patología Infecciosa (REIPI), Instituto de Salud Carlos III, Madrid, 28029, Spain
| | - Luis Martínez-Martínez
- Red Española de Investigación en Patología Infecciosa (REIPI), Instituto de Salud Carlos III, Madrid, 28029, Spain
- Unidad de Gestión Clínica de Microbiología, Hospital Universitario Reina Sofía, Córdoba, 14004, Spain
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Córdoba, 14004, Spain
| | - José Ramos-Vivas
- Instituto de Investigación Valdecilla IDIVAL, Santander, 39011, Spain.
- Servicio de Microbiología, Hospital Universitario Marqués de Valdecilla, Santander, 39008, Spain.
- Red Española de Investigación en Patología Infecciosa (REIPI), Instituto de Salud Carlos III, Madrid, 28029, Spain.
| |
Collapse
|
16
|
Rocha GA, Ferreira AG, Lima DF, Leão RS, Carvalho-Assef APD, Folescu TW, Albano RM, Marques EA. Draft genome sequence of Acinetobacter pittii ST643 shared by cystic fibrosis patients. Mem Inst Oswaldo Cruz 2017; 111:592-3. [PMID: 27653362 PMCID: PMC5027864 DOI: 10.1590/0074-02760160142] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 07/08/2016] [Indexed: 11/22/2022] Open
Abstract
Acinetobacter pittii has emerged as an important hospital pathogen that is associated with outbreaks and drug resistance. In cystic fibrosis (CF) patients, the detection of Acinetobacter spp. is rare; however, we isolated the A. pittii sequence type ST643 in several Brazilian CF patients treated in the same centre. The current study describes the draft genome of A. pittii ST643.
Collapse
Affiliation(s)
- Géssica A Rocha
- Universidade do Estado do Rio de Janeiro, Faculdade de Ciências Médicas, Departamento de Microbiologia, Imunologia e Parasitologia, Rio de Janeiro, RJ, Brasil
| | - Alex G Ferreira
- Universidade do Estado do Rio de Janeiro, Faculdade de Ciências Médicas, Departamento de Microbiologia, Imunologia e Parasitologia, Rio de Janeiro, RJ, Brasil
| | - Danielle F Lima
- Universidade do Estado do Rio de Janeiro, Faculdade de Ciências Médicas, Departamento de Microbiologia, Imunologia e Parasitologia, Rio de Janeiro, RJ, Brasil
| | - Robson S Leão
- Universidade do Estado do Rio de Janeiro, Faculdade de Ciências Médicas, Departamento de Microbiologia, Imunologia e Parasitologia, Rio de Janeiro, RJ, Brasil
| | - Ana Paula D Carvalho-Assef
- Fundação Oswaldo Cruz, Instituto Oswaldo Cruz, Laboratório de Pesquisa em Infecção Hospitalar, Rio de Janeiro, RJ, Brasil
| | - Tânia W Folescu
- Fundação Oswaldo Cruz, Instituto Nacional da Saúde da Mulher, da Criança e do Adolescente Fernandes Figueira, Departamento de Pneumologia Pediátrica, Rio de Janeiro, RJ, Brasil
| | - Rodolpho M Albano
- Universidade do Estado do Rio de Janeiro, Instituto de Biologia Roberto Alcântara Gomes, Departamento de Bioquímica, Rio de Janeiro, RJ, Brasil
| | - Elizabeth A Marques
- Universidade do Estado do Rio de Janeiro, Faculdade de Ciências Médicas, Departamento de Microbiologia, Imunologia e Parasitologia, Rio de Janeiro, RJ, Brasil
| |
Collapse
|
17
|
Amoureux L, Riedweg K, Chapuis A, Bador J, Siebor E, Péchinot A, Chrétien ML, de Curraize C, Neuwirth C. Nosocomial Infections with IMP-19−Producing Pseudomonas aeruginosa Linked to Contaminated Sinks, France. Emerg Infect Dis 2017. [DOI: 10.3201/eid2301.160649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
|
18
|
Insights on the Horizontal Gene Transfer of Carbapenemase Determinants in the Opportunistic Pathogen Acinetobacter baumannii. Microorganisms 2016; 4:microorganisms4030029. [PMID: 27681923 PMCID: PMC5039589 DOI: 10.3390/microorganisms4030029] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 07/21/2016] [Accepted: 08/09/2016] [Indexed: 12/23/2022] Open
Abstract
Horizontal gene transfer (HGT) is a driving force to the evolution of bacteria. The fast emergence of antimicrobial resistance reflects the ability of genetic adaptation of pathogens. Acinetobacter baumannii has emerged in the last few decades as an important opportunistic nosocomial pathogen, in part due to its high capacity of acquiring resistance to diverse antibiotic families, including to the so-called last line drugs such as carbapenems. The rampant selective pressure and genetic exchange of resistance genes hinder the effective treatment of resistant infections. A. baumannii uses all the resistance mechanisms to survive against carbapenems but production of carbapenemases are the major mechanism, which may act in synergy with others. A. baumannii appears to use all the mechanisms of gene dissemination. Beyond conjugation, the mostly reported recent studies point to natural transformation, transduction and outer membrane vesicles-mediated transfer as mechanisms that may play a role in carbapenemase determinants spread. Understanding the genetic mobilization of carbapenemase genes is paramount in preventing their dissemination. Here we review the carbapenemases found in A. baumannii and present an overview of the current knowledge of contributions of the various HGT mechanisms to the molecular epidemiology of carbapenem resistance in this relevant opportunistic pathogen.
Collapse
|
19
|
Pourhajibagher M, Hashemi FB, Pourakbari B, Aziemzadeh M, Bahador A. Antimicrobial Resistance of Acinetobacter baumannii to Imipenem in Iran: A Systematic Review and Meta-Analysis. Open Microbiol J 2016; 10:32-42. [PMID: 27099638 PMCID: PMC4814728 DOI: 10.2174/1874285801610010032] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Revised: 11/10/2015] [Accepted: 11/13/2015] [Indexed: 11/22/2022] Open
Abstract
Imipenem-resistant multi-drug resistant (IR-MDR) Acinetobacter baumannii
has been emerged as a morbidity successful nosocomial pathogen throughout the
world.To address imipenem being yet the most effective antimicrobial
agent against A. baumannii to control outbreaks and treat patients, a
systematic review and meta-analysis was performed to evaluate the prevalence of
IR-MDR A. baumannii. We systematically searched Web of Science, PubMed,
MEDLINE, Science Direct, EMBASE, Scopus, Cochrane Library, Google Scholar, and
Iranian databases to identify studies addressing the antibiotic resistance of
A. baumannii to imipenem and the frequency of MDR strains in Iran. Out of 58
articles and after a secondary screening using inclusion and exclusion criteria
and on the basis of title and abstract evaluation, 51 studies were selected for
analysis. The meta-analysis revealed that 55% [95% confidence interval (CI),
53.0–56.5] of A. baumannii were resistant to imipenem and 74% (95% CI,
61.3–83.9) were MDR. The MDR A. baumannii population in Iran is rapidly
changing toward a growing resistance to imipenem. Our findings highlight the
critical need for a comprehensive monitoring and infection control policy as
well as a national susceptibility review program that evaluates IR-MDR A.
baumannii isolates from various parts of Iran.
Collapse
Affiliation(s)
- Maryam Pourhajibagher
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Farhad B Hashemi
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Babak Pourakbari
- Pediatrics Infectious Disease Research Center, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Masoud Aziemzadeh
- Department of Microbiology, School of Medicine, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Abbas Bahador
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| |
Collapse
|
20
|
Ju F, Li B, Ma L, Wang Y, Huang D, Zhang T. Antibiotic resistance genes and human bacterial pathogens: Co-occurrence, removal, and enrichment in municipal sewage sludge digesters. WATER RESEARCH 2016; 91:1-10. [PMID: 26773390 DOI: 10.1016/j.watres.2015.11.071] [Citation(s) in RCA: 242] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 11/28/2015] [Accepted: 11/30/2015] [Indexed: 05/21/2023]
Abstract
Understanding which/how antibiotic resistance genes (ARGs) contribute to increased acquisition of resistance by pathogens in aquatic environments are challenges of profound significance. We explored the co-occurrence and removal versus enrichment of ARGs and human bacterial pathogens (HBPs) in municipal sewage sludge digesters. We combined metagenomic detection of a wide spectrum of 323 ARGs and 83 HBPs with a correlation-based statistical approach and charted a network of their co-occurrence relationships. The results indicate that most ARGs and a minor proportion of HBPs (mainly Collinsella aerofaciens, Streptococcus salivarius and Gordonia bronchialis) could not be removed by anaerobic digestion, revealing a biological risk of post-digestion sludge in disseminating antibiotic resistance and pathogenicity. Moreover, preferential co-occurrence patterns were evident within one ARG type (e.g., multidrug, beta-lactam, and aminoglycoside) and between two different ARG types (i.e., aminoglycoside and beta-lactam), possibly implicating co-effects of antibiotic selection pressure and co-resistance on shaping antibiotic resistome in sewage sludge. Unlike beta-lactam resistance genes, ARGs of multidrug and macrolide-lincosamide-streptogramin tended to co-occur more with HBPs. Strikingly, we presented evidence that the most straightforward biological origin of an ARG-species co-occurring event is a hosting relationship. Furthermore, a significant and robust HBP-species co-occurrence correlation provides a proper scenario for nominating HBP indicators (e.g., Bifidobacterium spp. are perfect indicators of C. aerofaciens; r = 0.92-0.99 and P-values < 0.01). Combined, this study demonstrates a creative and effective network-based metagenomic approach for exploring ARG hosts and HBP indicators and assessing ARGs acquisition by HBPs in human-impacted environments where ARGs and HBPs may co-thrive.
Collapse
Affiliation(s)
- Feng Ju
- Environmental Biotechnology Lab, The University of Hong Kong, Hong Kong SAR, China
| | - Bing Li
- Key Laboratory of Microorganism Application and Risk Control of Shenzhen, Graduate School at Shenzhen, Tsinghua University, China
| | - Liping Ma
- Environmental Biotechnology Lab, The University of Hong Kong, Hong Kong SAR, China
| | - Yubo Wang
- Environmental Biotechnology Lab, The University of Hong Kong, Hong Kong SAR, China
| | - Danping Huang
- Environmental Biotechnology Lab, The University of Hong Kong, Hong Kong SAR, China
| | - Tong Zhang
- Environmental Biotechnology Lab, The University of Hong Kong, Hong Kong SAR, China.
| |
Collapse
|
21
|
Grosso F, Silva L, Sousa C, Ramos H, Quinteira S, Peixe L. Extending the reservoir of bla IMP-5: the emerging pathogen Acinetobacter bereziniae. Future Microbiol 2015; 10:1609-13. [PMID: 26439605 DOI: 10.2217/fmb.15.88] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AIM Acinetobacter bereziniae clinical relevance is starting to be recognized; however, very few descriptions of its carbapenem resistance currently exist. Here we characterize two carbapenem-resistant A. bereziniae isolates. MATERIALS & METHODS Isolates were obtained from environmental and clinical samples. Carbapenemases were searched by phenotypic, biochemical and PCR assays. Clonality was studied by ApaI-PFGE and genetic location for carbapenemase genes were assessed by I-CeuI and S1 hybridizations. RESULTS Isolates were not clonally related but both produced the 'exclusively Portuguese' IMP-5, with the clinical isolate also producing an OXA-58. The carbapenemase genes were plasmid located. CONCLUSION Our results emphasize the role of non-baumannii Acinetobacter species as important reservoirs of clinically relevant resistance genes that could also contribute to their emergence as nosocomial pathogens.
Collapse
Affiliation(s)
- Filipa Grosso
- UCIBIO-REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Rua Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal
| | - Liliana Silva
- UCIBIO-REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Rua Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal.,Escola Superior de Saúde Dr. Lopes Dias, Instituto Politécnico de Castelo Branco, Castelo Branco, Portugal
| | - Clara Sousa
- CEB- Centro de Engenharia Biológica, Universidade do Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Helena Ramos
- Hospital Geral de Santo António, Porto, Portugal
| | - Sandra Quinteira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos. Universidade do Porto (CIBIO/UP)/InBio Laboratório Associado, Vairão, Portugal.,Faculdade de Ciências da Universidade do Porto, Departamento de Biologia, Porto, Portugal.,CESPU, Instituto de Investigação e Formação Avançada em Ciências e Tecnologias da Saúde, Gandra PRD, Portugal
| | - Luísa Peixe
- UCIBIO-REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Rua Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal
| |
Collapse
|
22
|
Kamolvit W, Sidjabat HE, Paterson DL. Molecular Epidemiology and Mechanisms of Carbapenem Resistance ofAcinetobacterspp. in Asia and Oceania. Microb Drug Resist 2015; 21:424-34. [DOI: 10.1089/mdr.2014.0234] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Witchuda Kamolvit
- UQ Centre of Clinical Research, The University of Queensland, Brisbane, Australia
- Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Hanna E. Sidjabat
- UQ Centre of Clinical Research, The University of Queensland, Brisbane, Australia
| | - David L. Paterson
- UQ Centre of Clinical Research, The University of Queensland, Brisbane, Australia
| |
Collapse
|
23
|
Salimizand H, Noori N, Meshkat Z, Ghazvini K, Amel SJ. Prevalence of Acinetobacter baumannii harboring ISAba1/blaOXA-23-like family in a burn center. Burns 2015; 41:1100-6. [DOI: 10.1016/j.burns.2014.12.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Revised: 10/27/2014] [Accepted: 12/10/2014] [Indexed: 11/29/2022]
|
24
|
Kitanaka H, Sasano MA, Yokoyama S, Suzuki M, Jin W, Inayoshi M, Hori M, Wachino JI, Kimura K, Yamada K, Arakawa Y. Invasive infection caused by carbapenem-resistant Acinetobacter soli, Japan. Emerg Infect Dis 2015; 20:1574-6. [PMID: 25151987 PMCID: PMC4178423 DOI: 10.3201/eid2009.140117] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
|
25
|
Sahuquillo-Arce JM, Hernández-Cabezas A, Yarad-Auad F, Ibáñez-Martínez E, Falomir-Salcedo P, Ruiz-Gaitán A. Carbapenemases: A worldwide threat to antimicrobial therapy. World J Pharmacol 2015; 4:75-95. [DOI: 10.5497/wjp.v4.i1.75] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Revised: 11/07/2014] [Accepted: 12/01/2014] [Indexed: 02/07/2023] Open
Abstract
Carbapenems are potent β-lactams with activity against extended-spectrum cephalosporinases and β-lactamases. These antibiotics, derived from thienamycn, a carbapenem produced by the environmental bacterium Streptomyces cattleya, were initially used as last-resort treatments for severe Gram-negative bacterial infections presenting resistance to most β-lactams but have become an empirical option in countries with high prevalence of Extended Spectrum β-lactamase-producing bacterial infections. Imipenem, the first commercially available carbapenem, was approved for clinical use in 1985. Since then, a wide variety of carbapenem-resistant bacteria has appeared, primarily Enterobacteriaceae such as Escherichia coli or Klebsiella pneumoniae (K. pneumoniae), Pseudomonas aeruginosa and Acinetobacter baumannii, presenting different resistance mechanisms. The most relevant mechanism is the production of carbapenem-hydrolyzing β-lactamases, also known as carbapenemases. These enzymes also inactivate all known β-lactams, and some of these enzymes can be acquired through horizontal gene transfer. Moreover, plasmids, transposons and integrons harboring these genes typically carry other resistance determinants, rendering the recipient bacteria resistant to almost all currently used antimicrobials, as is the case for K. pneumoniae carbapenemase - or New Delhi metallo-β-lactamases-type enzymes. The recent advent of these enzymes in the health landscape presents a serious challenge. First, the emergence of carbapenemases limits the currently available treatment options; second, these enzymes pose a risk to patients, as some studies have demonstrated high mortality associated with carbapenemase-producing bacterial infections; and third, these circumstances require an extra cost to sanitary systems, which are particularly cumbersome in developing countries. Therefore, emphasis should be placed on the early detection of these enzymes, the prevention of the spread of carbapenemase-producing bacteria and the development of new drugs resistant to carbapenemase hydrolysis.
Collapse
|
26
|
A case of IMP-4-, OXA-421-, OXA-96-, and CARB-2-producing Acinetobacter pittii sequence type 119 in Australia. J Clin Microbiol 2014; 53:727-30. [PMID: 25428154 DOI: 10.1128/jcm.02726-14] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
An IMP-4-producing Acinetobacter pittii strain coproducing oxacillinases was isolated from a leg wound of a 67-year-old female patient. Identification to the species level by rpoB and gyrB sequencing and multiplex-PCR-based analysis revealed that the isolate was A. pittii. Whole-genome sequencing of this A. pittii isolate determined the presence of blaOXA-96, blaCARB-2, and a novel blaOXA-421 gene. The position of this novel blaOXA-421 gene was similar to that of blaOXA-51 in A. baumannii, downstream of the phosphinothricin N-acetyltransferase gene and upstream of fxsA in the chromosome. This A. pittii isolate was found to belong to sequence type 119 (ST119). Here, we report the first isolation of IMP-4-producing A. pittii ST119 with a novel blaOXA-421 gene from a patient in Australia and characterize its draft genome.
Collapse
|
27
|
Sun J, Li L, Liu B, Xia J, Liao X, Liu Y. Development of aminoglycoside and β-lactamase resistance among intestinal microbiota of swine treated with lincomycin, chlortetracycline, and amoxicillin. Front Microbiol 2014; 5:580. [PMID: 25408688 PMCID: PMC4219486 DOI: 10.3389/fmicb.2014.00580] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 10/14/2014] [Indexed: 01/28/2023] Open
Abstract
Lincomycin, chlortetracycline, and amoxicillin are commonly used antimicrobials for growth promotion and infectious disease prophylaxis in swine production. In this study, we investigated the shifts and resistance development among intestinal microbiota in pregnant sows before and after lincomycin, chlortetracycline, and amoxicillin treatment by using phylogenetic analysis, bacterial enumeration, and PCR. After the antimicrobial treatment, shifts in microbial community, an increased proportion of resistant bacteria, and genes related to antimicrobial resistance as compared to the day before antimicrobial administration (day 0) were observed. Importantly, a positive correlation between antimicrobial resistance gene expression in different categories, especially those encoding aminoglycoside and β-lactamase and antimicrobial resistance, was observed. These findings demonstrate an important role of antimicrobial usage in animals in the development of antimicrobial resistance, and support the notion that prudent use of antimicrobials in swine is needed to reduce the risk of the emergence of multi-drug resistant zoonotic pathogens.
Collapse
Affiliation(s)
| | | | | | | | | | - Yahong Liu
- Laboratory of Veterinary Pharmacology, College of Veterinary Medicine, South China Agricultural UniversityGuangzhou, China
| |
Collapse
|
28
|
High frequency of Acinetobacter soli among Acinetobacter isolates causing bacteremia at a tertiary hospital in Japan. J Clin Microbiol 2014; 52:911-5. [PMID: 24403303 DOI: 10.1128/jcm.03009-13] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Acinetobacter baumannii is generally the most frequently isolated Acinetobacter species. Sequence analysis techniques allow reliable identification of Acinetobacter isolates at the species level. Forty-eight clinical isolates of Acinetobacter spp. were obtained from blood cultures at Tohoku University Hospital. These isolates were identified at the species level by partial sequencing of the RNA polymerase β-subunit (rpoB), 16S rRNA, and gyrB genes. Then further characterization was done by using the PCR for detection of OXA-type β-lactamase gene clusters, metallo-β-lactamases, and carO genes. Pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing were also performed. The most frequent isolate was Acinetobacter soli (27.1%). Six of the 13 A. soli isolates were carbapenem nonsusceptible, and all of these isolates produced IMP-1. PFGE revealed that the 13 A. soli isolates were divided into 8 clusters. This study demonstrated that A. soli accounted for a high proportion of Acinetobacter isolates causing bacteremia at a Japanese tertiary hospital. Non-A. baumannii species were identified more frequently than A. baumannii and carbapenem-nonsusceptible isolates were found among the non-A. baumannii strains. These results emphasize the importance of performing epidemiological investigations of Acinetobacter species.
Collapse
|