Genomic context of resistance genes within a French clinical MDR Proteus mirabilis: identification of the novel genomic resistance island GIPmi1

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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Identification of Proteus genomic island 2 variants in two clonal Proteus mirabilis isolates with coexistence of a novel genomic resistance island PmGRI1

Journal of Antimicrobial Chemotherapy ◽

10.1093/jac/dkaa215 ◽

2020 ◽

Vol 75 (9) ◽

pp. 2503-2507

Author(s):

Chang-Wei Lei ◽

Tian-Ge Yao ◽

Jia Yan ◽

Bo-Yang Li ◽

Xue-Chun Wang ◽

...

Keyword(s):

Resistance Genes ◽

Proteus Mirabilis ◽

Genomic Island ◽

Genomic Islands ◽

Class 1 Integron ◽

E Coli ◽

Class 1 Integrons ◽

Class 1 ◽

Resistance Island ◽

Integrative And Conjugative Element

Abstract Objectives To characterize the MDR genomic islands (GIs) in Proteus mirabilis isolates. Methods Two P. mirabilis strains (C55 and C74) of chicken origin were subjected to WGS (HiSeq and PacBio) and the MDR GIs were determined. Results P. mirabilis strains C55 and C74 are clonal strains and harbour different Proteus genomic island 2 (PGI2) variants (PGI2-C55 and PGI2-C74). The MDR region of PGI2-C55 is composed of two class 1 integrons, separated by a region containing seven copies of IS26 and eight resistance genes, including blaCTX-M-3 and fosA3. The region in PGI2-C74 is a complete In4-type class 1 integron, harbouring five gene cassettes (dfrA16, blaCARB-2, aadA2, cmlA1 and aadA1). In addition, C55 and C74 carry an SXT/R391 integrative and conjugative element (ICEPmiJpn1), harbouring blaCMY-2, and a novel 50.46 kb genomic resistance island named PmGRI1-C55. PmGRI1-C55 harbours a tyrosine-type recombinase/integrase that might be responsible for the integration of PmGRI1-C55 at the 3′ end of tRNA-Sec. It carries an MDR region derived from Tn2670 that harbours a Tn21 region and carries six resistance genes (catA1, blaTEM-1b, aphA1a, sul2, strA and strB). Blast analysis showed diverse PmGRI1 variants in P. mirabilis and Escherichia coli strains. Conclusions The finding of the two new PGI2 variants highlights that the homologous recombination between shared components of class 1 integrons and transposition by IS26 promote the diversity of MDR regions in PGI2. PmGRI1 is a new GI that carries various resistance genes identified in P. mirabilis and E. coli.

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atpD gene sequencing, multidrug resistance traits, virulence-determinants, and antimicrobial resistance genes of emerging XDR and MDR-Proteus mirabilis

Scientific Reports ◽

10.1038/s41598-021-88861-w ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Abdelazeem M. Algammal ◽

Hany R. Hashem ◽

Khyreyah J. Alfifi ◽

Helal F. Hetta ◽

Norhan S. Sheraba ◽

...

Keyword(s):

Antimicrobial Resistance ◽

Resistance Genes ◽

Proteus Mirabilis ◽

Biofilm Formation ◽

Gene Sequencing ◽

Opportunistic Pathogen ◽

Severe Illness ◽

Virulence Determinants ◽

Antimicrobial Resistance Genes ◽

Port Said

AbstractProteus mirabilis is a common opportunistic pathogen causing severe illness in humans and animals. To determine the prevalence, antibiogram, biofilm-formation, screening of virulence, and antimicrobial resistance genes in P. mirabilis isolates from ducks; 240 samples were obtained from apparently healthy and diseased ducks from private farms in Port-Said Province, Egypt. The collected samples were examined bacteriologically, and then the recovered isolates were tested for atpD gene sequencing, antimicrobial susceptibility, biofilm-formation, PCR detection of virulence, and antimicrobial resistance genes. The prevalence of P. mirabilis in the examined samples was 14.6% (35/240). The identification of the recovered isolates was confirmed by the atpD gene sequencing, where the tested isolates shared a common ancestor. Besides, 94.3% of P. mirabilis isolates were biofilm producers. The recovered isolates were resistant to penicillins, sulfonamides, β-Lactam-β-lactamase-inhibitor-combinations, tetracyclines, cephalosporins, macrolides, and quinolones. Using PCR, the retrieved strains harbored atpD, ureC, rsbA, and zapA virulence genes with a prevalence of 100%, 100%, 94.3%, and 91.4%, respectively. Moreover, 31.4% (11/35) of the recovered strains were XDR to 8 antimicrobial classes that harbored blaTEM, blaOXA-1, blaCTX-M, tetA, and sul1 genes. Besides, 22.8% (8/35) of the tested strains were MDR to 3 antimicrobial classes and possessed blaTEM, tetA, and sul1genes. Furthermore, 17.1% (6/35) of the tested strains were MDR to 7 antimicrobial classes and harbored blaTEM, blaOXA-1, blaCTX-M, tetA, and sul1 genes. Alarmingly, three strains were carbapenem-resistant that exhibited PDR to all the tested 10 antimicrobial classes and shared blaTEM, blaOXA-1, blaCTX-M, tetA, and sul1 genes. Of them, two strains harbored the blaNDM-1 gene, and one strain carried the blaKPC gene. In brief, to the best of our knowledge, this is the first study demonstrating the emergence of XDR and MDR-P.mirabilis in ducks. Norfloxacin exhibited promising antibacterial activity against the recovered XDR and MDR-P. mirabilis. The emergence of PDR, XDR, and MDR-strains constitutes a threat alarm that indicates the complicated treatment of the infections caused by these superbugs.

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Salmonella enterica Serovar Typhi Strains Isolated in Korea Containing a Multidrug Resistance Class 1 Integron

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.47.6.2006-2008.2003 ◽

2003 ◽

Vol 47 (6) ◽

pp. 2006-2008 ◽

Cited By ~ 21

Author(s):

Hyunjoo Pai ◽

Jeong-hum Byeon ◽

Sunmi Yu ◽

Bok Kwon Lee ◽

Shukho Kim

Keyword(s):

Multidrug Resistance ◽

Resistance Genes ◽

Salmonella Enterica ◽

Multidrug Resistant ◽

Conjugative Plasmid ◽

The Novel ◽

Class 1 Integron ◽

Salmonella Enterica Serovar Typhi ◽

Class 1 ◽

Clonal Spread

ABSTRACT Six strains of Salmonella enterica serovar Typhi which were resistant to ampicillin, chloramphenicol, trimethoprim-sulfamethoxazole, streptomycin, tetracycline, and gentamicin were isolated in Korea. This multidrug resistance was transferred by a conjugative plasmid of about 50 kb. The plasmid harbored a class 1 integron, which included six resistance genes, aacA4b, catB8, aadA1, dfrA1, aac(6′)-IIa, and the novel blaP2, in that order. All of the isolates showed the same-size plasmids and the same ribotyping patterns, which suggests a clonal spread of these multidrug-resistant isolates.

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Molecular Basis of Sulfonamide and Trimethoprim Resistance in Fish-Pathogenic Aeromonas Isolates

Applied and Environmental Microbiology ◽

10.1128/aem.00560-11 ◽

2011 ◽

Vol 77 (20) ◽

pp. 7147-7150 ◽

Cited By ~ 26

Author(s):

Kristina Kadlec ◽

Ellen von Czapiewski ◽

Heike Kaspar ◽

Jürgen Wallmann ◽

Geovana Brenner Michael ◽

...

Keyword(s):

Resistance Genes ◽

Molecular Basis ◽

Aeromonas Salmonicida ◽

The Novel ◽

Content Type ◽

Gene Cassettes ◽

Class 1 Integrons ◽

Novel Gene ◽

Class 1 ◽

Diseased Fish

ABSTRACTSulfonamide-trimethoprim-resistantAeromonas salmonicidaand motileAeromonasspp. from diseased fish of the GERM-Vet study carried thesul1gene together with mostly cassette-borne trimethoprim resistance genes, including the novel genedfrA28. The sevendfrAanddfrBgenes identified were located mostly in class 1 integrons which commonly harbored other gene cassettes.

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Acquisition of a genomic resistance island (AbGRI5) from global clone 2 through homologous recombination in a clinical Acinetobacter baumannii isolate

Journal of Antimicrobial Chemotherapy ◽

10.1093/jac/dkaa389 ◽

2020 ◽

Vol 76 (1) ◽

pp. 65-69

Author(s):

Xiaoting Hua ◽

Robert A Moran ◽

Qingye Xu ◽

Jintao He ◽

Youhong Fang ◽

...

Keyword(s):

Antibiotic Resistance ◽

Acinetobacter Baumannii ◽

Resistance Genes ◽

Antibiotic Resistance Genes ◽

Whole Genome Sequence ◽

Oxford Nanopore ◽

History Of ◽

Agar Dilution ◽

Resistance Island ◽

New Location

Abstract Objectives To reconstruct the evolutionary history of the clinical Acinetobacter baumannii XH1056, which lacks the Oxford scheme allele gdhB. Methods Susceptibility testing was performed using broth microdilution and agar dilution. The whole-genome sequence of XH1056 was determined using the Illumina and Oxford Nanopore platforms. MLST was performed using the Pasteur scheme and the Oxford scheme. Antibiotic resistance genes were identified using ABRicate. Results XH1056 was resistant to all antibiotics tested, apart from colistin, tigecycline and eravacycline. MLST using the Pasteur scheme assigned XH1056 to ST256. However, XH1056 could not be typed with the Oxford MLST scheme as gdhB is not present. Comparative analyses revealed that XH1056 contains a 52 933 bp region acquired from a global clone 2 (GC2) isolate, but is otherwise closely related to the ST23 A. baumannii XH858. The acquired region in XH1056 also contains a 34 932 bp resistance island that resembles AbGRI3 and contains the armA, msrE-mphE, sul1, blaPER-1, aadA1, cmlA1, aadA2, blaCARB-2 and ere(B) resistance genes. Comparison of the XH1056 chromosome to that of GC2 isolate XH859 revealed that the island in XH1056 is in the same chromosomal region as that in XH859. As this island is not in the standard AbGRI3 position, it was named AbGRI5. Conclusions XH1056 is a hybrid isolate generated by the acquisition of a chromosomal segment from a GC2 isolate that contains a resistance island in a new location—AbGRI5. As well as generating ST256, it appears likely that a single recombination event is also responsible for the acquisition of AbGRI5 and its associated antibiotic resistance genes.

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Multihospital Occurrence of Pan-Resistant Klebsiella pneumoniae Sequence Type 147 with an ISEcp1-Directed blaOXA-181 Insertion in the mgrB Gene in the United Arab Emirates

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00418-17 ◽

2017 ◽

Vol 61 (7) ◽

Cited By ~ 28

Author(s):

Ágnes Sonnevend ◽

Akela Ghazawi ◽

Rayhan Hashmey ◽

Aliasgher Haidermota ◽

Safinaz Girgis ◽

...

Keyword(s):

Klebsiella Pneumoniae ◽

South Korea ◽

United Arab Emirates ◽

Resistance Genes ◽

Extended Period ◽

Sequence Type ◽

Resistant Clone ◽

Colistin Resistance ◽

Content Type ◽

Resistance Island

ABSTRACT The emergence of pan-resistant Klebsiella pneumoniae strains is an increasing concern. In the present study, we describe a cluster of 9 pan-resistant K. pneumoniae sequence type 147 (ST147) isolates encountered in 4 patients over nearly 1 year in 3 hospitals of the United Arab Emirates (UAE). The isolates exhibited highly similar genotypes. All produced chromosomally encoded OXA-181, and the majority also produced the NDM-5 carbapenemase. As with the previously described single isolate from the UAE, MS6671, the mgrB was disrupted by a functional, ISEcp1-driven bla OXA-181 insertion causing resistance to carbapenems. The mutation was successfully complemented with an intact mgrB gene, indicating that it was responsible for colistin resistance. bla NDM-5 was located within a resistance island of an approximately 100-kb IncFII plasmid carrying ermB, mph(A), bla TEM-1B, rmtB, bla NDM-5, sul1, aadA2, and dfrA12 resistance genes. Sequencing this plasmid (pABC143-NDM) revealed that its backbone was nearly identical to that of plasmid pMS6671E from which several resistance genes, including bla NDM-5, had been deleted. More extensive similarities of the backbone and the resistance island were found between pABC143C-NDM and the bla NDM-5-carrying IncFII plasmids of two K. pneumoniae ST147 isolates from South Korea, one of which was colistin resistant, and both also produced OXA-181. Notably, one of these strains was isolated from a patient transferred from the UAE. Our data show that this pan-resistant clone has an alarming capacity to maintain itself over an extended period of time and is even likely to be transmitted internationally.

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Characterization of SXT/R391 Integrative and Conjugative Elements in Proteus mirabilis Isolates from Food-Producing Animals in China

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.02852-15 ◽

2016 ◽

Vol 60 (3) ◽

pp. 1935-1938 ◽

Cited By ~ 25

Author(s):

Chang-Wei Lei ◽

An-Yun Zhang ◽

Hong-Ning Wang ◽

Bi-Hui Liu ◽

Li-Qin Yang ◽

...

Keyword(s):

Escherichia Coli ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Resistance Genes ◽

Proteus Mirabilis ◽

Whole Genome ◽

Content Type ◽

Integrative And Conjugative Elements ◽

Animal Farms

SXT/R391 integrative and conjugative elements (ICEs) were detected in 8 out of 125Proteus mirabilisisolates from food-producing animals in China. Whole-genome sequencing revealed that seven ICEs were identical to ICEPmiJpn1, carrying the cephalosporinase geneblaCMY-2. Another one, designated ICEPmiChn1, carried five resistance genes. All eight ICEs could be transferred toEscherichia colivia conjugation. The results highlight the idea that animal farms are important reservoir of the SXT/R391 ICE-containingP. mirabilis.

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Characterization of a Novel SXT/R391 Integrative and Conjugative Element Carrying cfr, blaCTX-M-65, fosA3, and aac(6′)-Ib-cr in Proteus mirabilis

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00849-18 ◽

2018 ◽

Vol 62 (9) ◽

Cited By ~ 10

Author(s):

Chang-Wei Lei ◽

Yan-Peng Chen ◽

Zhuang-Zhuang Kang ◽

Ling-Han Kong ◽

Hong-Ning Wang

Keyword(s):

Resistance Gene ◽

Resistance Genes ◽

Proteus Mirabilis ◽

Hot Spot ◽

Fluoroquinolone Resistance ◽

Content Type ◽

Antimicrobial Resistance Genes ◽

Methyltransferase Gene ◽

Lactamase Gene ◽

Integrative And Conjugative Element

ABSTRACT A novel 139,487-bp SXT/R391 integrative and conjugative element, ICEPmiChnBCP11, was characterized in Proteus mirabilis of swine origin in China. ICEPmiChnBCP11 harbors 20 different antimicrobial resistance genes, including the clinically important rRNA methyltransferase gene cfr, the extended-spectrum β-lactamase gene blaCTX-M-65, fosfomycin resistance gene fosA3, and fluoroquinolone resistance gene aac(6′)-Ib-cr. An ISPpu12-mediated composite transposon containing various resistance genes and 10 copies of IS26 is inserted in hot spot 4. ICEPmiChnBCP11 was successfully transferred to Escherichia coli.

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