Draft Genome Sequences of Two Extensively Drug-Resistant Strains of Acinetobacter baumannii Isolated from Clinical Samples in Pakistan

Infections in immunocompromised patients that are caused by extensively drug-resistant (XDR) Acinetobacter baumannii strains have been increasingly reported worldwide. In particular, carbapenem-resistant A. baumannii strains are a prominent cause of health care-associated infections. Here, we report draft genome assemblies for two clinical XDR A. baumannii isolates obtained from hospitalized patients in Pakistan.

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Whole-Genome-Sequence-Based Characterization of Extensively Drug-Resistant Acinetobacter baumannii Hospital Outbreak

mSphere ◽

10.1128/msphere.00934-19 ◽

2020 ◽

Vol 5 (1) ◽

Cited By ~ 3

Author(s):

Ghiwa Makke ◽

Ibrahim Bitar ◽

Tamara Salloum ◽

Balig Panossian ◽

Sahar Alousi ◽

...

Keyword(s):

Acinetobacter Baumannii ◽

Tertiary Hospital ◽

Outbreak Detection ◽

Whole Genome ◽

Transmission Network ◽

Drug Resistant ◽

Content Type ◽

Carbapenem Resistant ◽

Extensively Drug Resistant ◽

Long Read

ABSTRACT Carbapenem-resistant Acinetobacter baumannii (CRAB) is an important opportunistic pathogen linked to a variety of nosocomial infections and hospital outbreaks worldwide. This study aimed at investigating and characterizing a CRAB outbreak at a large tertiary hospital in Lebanon. A total of 41 isolates were collected and analyzed using pulsed-field gel electrophoresis (PFGE). Whole-genome sequencing (WGS) was performed on all the isolates, and long-read PacBio sequencing was used to generate reference genomes. The multilocus sequence types (MLST), repertoire of resistance genes, and virulence factors were determined from the sequencing data. The plasmid content was analyzed both in silico and using the A. baumannii PCR-based replicon typing (AB-PBRT) method. Genome analysis initially revealed two clones, one carrying blaOXA-23 on Tn2006 (ST-1305, ST-195, and ST-218) and another carrying blaOXA-72 on pMAL-1 (ST-502 and ST-2059, a new ST), with the latter having two subclones, as revealed using the Bayesian transmission network. All isolates were extensively drug resistant (XDR). WGS analysis revealed the transmission pathways and demonstrated the diversity of CRAB isolates and mobile genetic elements in this health care setting. Outbreak detection using WGS and immediate implementation of infection control measures contribute to restraining the spread and decreasing mortality. IMPORTANCE Carbapenem-resistant Acinetobacter baumannii (CRAB) has been implicated in hospital outbreaks worldwide. Here, we present a whole-genome-based investigation of an extensively drug-resistant CRAB outbreak rapidly spreading and causing high incidences of mortality at numerous wards of a large tertiary hospital in Lebanon. This is the first study of its kind in the region. Two circulating clones were identified using a combination of molecular typing approaches, short- and long-read sequencing and Bayesian transmission network analysis. One clone carried blaOXA-23 on Tn2006 (ST-1305, ST-195, and ST-218), and another carried blaOXA-72 on a pMAL-1 plasmid (ST-502 and ST-2059, a new ST). A pMAL-2 plasmid was circulating between the two clones. The approaches implemented in this study and the obtained findings facilitate the tracking of outbreak scenarios in Lebanon and the region at large.

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Molecular epidemiology of carbapenem-resistant Acinetobacter baumannii strains in Belgian acute-care hospitals

10.1101/2021.07.06.21259728 ◽

2021 ◽

Author(s):

Adam Valcek ◽

Pierre Bogaerts ◽

Olivier Denis ◽

Te-Din Huang ◽

Charles Van der Henst

Keyword(s):

Acinetobacter Baumannii ◽

Acute Care ◽

De Novo ◽

Acquired Resistance ◽

Acute Care Hospitals ◽

Clinical Samples ◽

Drug Resistant ◽

Carbapenem Resistant ◽

Extensively Drug Resistant ◽

Pcr Targeting

Objectives: To describe the genotypic epidemiological distribution and the antibiotic resistance mechanisms of recent carbapenem-resistant Acinetobacter baumannii (CRAb) strains recovered from clinical samples in Belgium. Methods: A total of 40 clinical isolates of CRAb collected by the national reference center from 19 acute-care hospitals through national microbiological surveillance in 2014 and 2017 were analysed in this study. The isolates were tested for antimicrobial susceptibility by broth microdilution and determined for carbapenemase-encoding genes by multiplex PCR targeting major carbapenemases families. Isolates were subjected to whole-genome sequencing (WGS) with Illumina technology and the complete chromosomal sequences were de novo assembled. Genome analysis was performed to identify intrinsic and acquired resistance determinants and to characterize clonal lineage according to the sequence type (ST). Results: All 40 isolates were resistant to carbapenems and exhibited extensively drug-resistant phenotype with blaOXA-23 (n=29) being the most abundant detected acquired AMR gene with 38 isolates encoding at least two different types of OXA enzymes. The majority of the isolates were globally disseminated clones of ST2 (n=25) while less frequent sequence types such as ST636 (n=6), ST1 (n=3), ST85 (n=2) and per one isolate from ST604, ST215, ST158 and ST78 were also detected. Conclusions: We have detected extensively drug-resistant globally occurring clones of A. baumannii ST1 and ST2 throughout Belgium as well as other sporadic ST including ST636 causing local outbreaks. Our results show the presence of high-risk clones of A. baumannii with common travel importation and the crucial need of constant surveillance.

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Nosocomial Outbreak of Extensively Drug-Resistant Acinetobacter baumannii Isolates Containing blaOXA-237 Carried on a Plasmid

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00797-17 ◽

2017 ◽

Vol 61 (11) ◽

Cited By ~ 13

Author(s):

Andrea M. Hujer ◽

Paul G. Higgins ◽

Susan D. Rudin ◽

Genevieve L. Buser ◽

Steven H. Marshall ◽

...

Keyword(s):

United States ◽

Acinetobacter Baumannii ◽

Health Care Facilities ◽

Pcr Analysis ◽

Drug Resistant ◽

Content Type ◽

Carbapenem Resistant ◽

Extensively Drug Resistant ◽

Separate Branch ◽

Carbapenemase Gene

ABSTRACT Carbapenem antibiotics are among the mainstays for treating infections caused by Acinetobacter baumannii, especially in the Northwest United States, where carbapenem-resistant A. baumannii remains relatively rare. However, between June 2012 and October 2014, an outbreak of carbapenem-resistant A. baumannii occurred in 16 patients from five health care facilities in the state of Oregon. All isolates were defined as extensively drug resistant. Multilocus sequence typing revealed that the isolates belonged to sequence type 2 (international clone 2 [IC2]) and were >95% similar as determined by repetitive-sequence-based PCR analysis. Multiplex PCR revealed the presence of a bla OXA carbapenemase gene, later identified as bla OXA-237. Whole-genome sequencing of all isolates revealed a well-supported separate branch within a global A. baumannii phylogeny. Pacific Biosciences (PacBio) SMRT sequencing was also performed on one isolate to gain insight into the genetic location of the carbapenem resistance gene. We discovered that bla OXA-237, flanked on either side by ISAba1 elements in opposite orientations, was carried on a 15,198-bp plasmid designated pORAB01-3 and was present in all 16 isolates. The plasmid also contained genes encoding a TonB-dependent receptor, septicolysin, a type IV secretory pathway (VirD4 component, TraG/TraD family) ATPase, an integrase, a RepB family plasmid DNA replication initiator protein, an alpha/beta hydrolase, and a BrnT/BrnA type II toxin-antitoxin system. This is the first reported outbreak in the northwestern United States associated with this carbapenemase. Particularly worrisome is that bla OXA-237 was carried on a plasmid and found in the most prominent worldwide clonal group IC2, potentially giving pORAB01-3 great capacity for future widespread dissemination.

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Spread of Plasmid-Encoded NDM-1 and GES-5 Carbapenemases among Extensively Drug-Resistant and Pandrug-Resistant Clinical Enterobacteriaceae in Durban, South Africa

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.02178-17 ◽

2018 ◽

Vol 62 (5) ◽

Cited By ~ 30

Author(s):

Torunn Pedersen ◽

John Osei Sekyere ◽

Usha Govinden ◽

Krishnee Moodley ◽

Audun Sivertsen ◽

...

Keyword(s):

South Africa ◽

South African ◽

Molecular Mechanisms ◽

Whole Genome Sequence ◽

Drug Resistant ◽

Content Type ◽

Carbapenem Resistant ◽

Extensively Drug Resistant ◽

Horizontal Spread ◽

Genome Assemblies

ABSTRACT Whole-genome sequence analyses revealed the presence of bla NDM-1 ( n = 31), bla GES-5 ( n = 8), bla OXA-232 ( n = 1), or bla NDM-5 ( n = 1) in extensively drug-resistant and pandrug-resistant Enterobacteriaceae organisms isolated from in-patients in 10 private hospitals (2012 to 2013) in Durban, South Africa. Two novel NDM-1-encoding plasmids from Klebsiella pneumoniae were circularized by PacBio sequencing. In p19-10_01 [IncFIB(K); 223.434 bp], bla NDM-1 was part of a Tn 1548 -like structure (16.276 bp) delineated by IS 26 . The multireplicon plasmid p18-43_01 [IncR_1/IncFIB(pB171)/IncFII(Yp); 212.326 bp] shared an 80-kb region with p19-10_01, not including the bla NDM-1 -containing region. The two plasmids were used as references for tracing NDM-1-encoding plasmids in the other genome assemblies. The p19-10_01 sequence was detected in K. pneumoniae ( n = 7) only, whereas p18-43_01 was tracked to K. pneumoniae ( n = 4), Klebsiella michiganensis ( n = 1), Serratia marcescens ( n = 11), Enterobacter spp. ( n = 7), and Citrobacter freundii ( n = 1), revealing horizontal spread of this bla NDM-1 -bearing plasmid structure. Global phylogeny showed clustering of the K. pneumoniae (18/20) isolates together with closely related carbapenemase-negative ST101 isolates from other geographical origins. The South African isolates were divided into three phylogenetic subbranches, where each group had distinct resistance and replicon profiles, carrying either p19-10_01, p18-10_01, or pCHE-A1 (8,201 bp). The latter plasmid carried bla GES-5 and aacA4 within an integron mobilization unit. Our findings imply independent plasmid acquisition followed by local dissemination. Additionally, we detected bla OXA-232 carried by pPKPN4 in K. pneumoniae (ST14) and bla NDM-5 contained by a pNDM-MGR194-like genetic structure in Escherichia coli (ST167), adding even more complexity to the multilayer molecular mechanisms behind nosocomial spread of carbapenem-resistant Enterobacteriaceae in Durban, South Africa.

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Decreased carO gene expression and OXA-type carbapenemases among extensively drug-resistant Acinetobacter baumannii strains isolated from burn patients in Tehran, Iran

Acta Microbiologica et Immunologica Hungarica ◽

10.1556/030.2020.01138 ◽

2020 ◽

Cited By ~ 1

Author(s):

Elham Abbasi ◽

Hossein Goudarzi ◽

Ali Hashemi ◽

Alireza Salimi Chirani ◽

Abdollah Ardebili ◽

...

Keyword(s):

Gene Expression ◽

Acinetobacter Baumannii ◽

High Rate ◽

Burn Patients ◽

Drug Resistant ◽

Disc Diffusion ◽

Carbapenem Resistant ◽

Extensively Drug Resistant ◽

Sds Page ◽

Extensively Drug Resistance

AbstractA major challenge in the treatment of infections has been the rise of extensively drug resistance (XDR) and multidrug resistance (MDR) in Acinetobacter baumannii. The goals of this study were to determine the pattern of antimicrobial susceptibility, blaOXA and carO genes among burn-isolated A. baumannii strains. In this study, 100 A. baumannii strains were isolated from burn patients and their susceptibilities to different antibiotics were determined using disc diffusion testing and broth microdilution. Presence of carO gene and OXA-type carbapenemase genes was tested by PCR and sequencing. SDS-PAGE was done to survey CarO porin and the expression level of carO gene was evaluated by Real-Time PCR. A high rate of resistance to meropenem (98%), imipenem (98%) and doripenem (98%) was detected. All tested A. baumannii strains were susceptible to colistin. The results indicated that 84.9% were XDR and 97.9% of strains were MDR. In addition, all strains bore blaOXA-51 like and blaOXA-23 like and carO genes. Nonetheless, blaOXA-58 like and blaOXA-24 like genes were harbored by 0 percent and 76 percent of strains, respectively. The relative expression levels of the carO gene ranged from 0.06 to 35.01 fold lower than that of carbapenem-susceptible A. baumannii ATCC19606 and SDS – PAGE analysis of the outer membrane protein showed that all 100 isolates produced CarO. The results of current study revealed prevalence of blaOXA genes and changes in carO gene expression in carbapenem resistant A.baumannii.

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Complete Genome Sequences of Four Extensively Drug-Resistant Acinetobacter baumannii Isolates from Thailand

Microbiology Resource Announcements ◽

10.1128/mra.00949-20 ◽

2020 ◽

Vol 9 (40) ◽

Author(s):

Peechanika Chopjitt ◽

Thidathip Wongsurawat ◽

Piroon Jenjaroenpun ◽

Parichart Boueroy ◽

Rujirat Hatrongjit ◽

...

Keyword(s):

Acinetobacter Baumannii ◽

Complete Genome ◽

Sequence Type ◽

Clinical Isolates ◽

Drug Resistant ◽

Genome Sequences ◽

Content Type ◽

Type Isolate ◽

Resistant Genes ◽

Extensively Drug Resistant

ABSTRACT Here, we report the complete genome sequences of four clinical isolates of extensively drug-resistant Acinetobacter baumannii (XDRAB), isolated in Thailand. These results revealed multiple antimicrobial-resistant genes, each involving two sequence type 16 (ST16) isolates, ST2, and a novel sequence type isolate, ST1479.

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Correlation of Checkerboard Synergy Testing with Time-Kill Analysis and Clinical Outcomes of Extensively Drug-Resistant Acinetobacter baumannii Respiratory Infections

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00981-16 ◽

2016 ◽

Vol 60 (11) ◽

pp. 6892-6895 ◽

Cited By ~ 12

Author(s):

Derek N. Bremmer ◽

Karri A. Bauer ◽

Stephanie M. Pouch ◽

Keelie Thomas ◽

Debra Smith ◽

...

Keyword(s):

Acinetobacter Baumannii ◽

Clinical Outcomes ◽

Clinical Utility ◽

Respiratory Infections ◽

Drug Resistant ◽

Content Type ◽

Extensively Drug Resistant ◽

Time Kill ◽

Synergy Testing

ABSTRACTWe tested 76 extensively drug-resistant (XDR)Acinetobacter baumanniiisolates by the checkerboard method using only wells containing serum-achievable concentrations (SACs) of drugs. Checkerboard results were correlated by time-kill assay and clinical outcomes. Minocycline-colistin was the best combinationin vitro, as it inhibited growth in one or more SAC wells in all isolates. Patients who received a combination that inhibited growth in one or more SAC wells demonstrated better microbiological clearance than those who did not (88% versus 30%;P= 0.025). The checkerboard platform may have clinical utility for XDRA. baumanniiinfections.

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Draft Genome Sequences of Two Acinetobacter baumannii Isolates from a Fatal Case of Necrotizing Fasciitis

Microbiology Resource Announcements ◽

10.1128/mra.00047-20 ◽

2020 ◽

Vol 9 (13) ◽

Author(s):

Brock A. Arivett ◽

Angella Charnot-Katsikas ◽

Cindy Bethel ◽

Steven E. Fiester ◽

Luis A. Actis

Keyword(s):

Necrotizing Fasciitis ◽

Acinetobacter Baumannii ◽

Fatal Case ◽

Draft Genome ◽

Bacterial Pathogen ◽

Genome Sequences ◽

Content Type ◽

Carbapenem Resistant ◽

Control And Prevention ◽

Total Dna

Carbapenem-resistant Acinetobacter baumannii is a bacterial pathogen with serious implications for human health and is recognized as an urgent threat by the Centers for Disease Control and Prevention (CDC). Total DNA from two A. baumannii clinical isolates collected over 3 days from a fatal case of necrotizing fasciitis has been sequenced to >30× coverage.

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Draft Genome Sequence of an Extensively Drug-Resistant Salmonella enterica Serovar Typhi Strain from a Returned Traveler from Pakistan

Microbiology Resource Announcements ◽

10.1128/mra.00427-20 ◽

2020 ◽

Vol 9 (31) ◽

Author(s):

Samantha Hao ◽

Tess Veuthey ◽

Saharai Caldera ◽

Paula Hayakawa Serpa ◽

Barbara Haller ◽

...

Keyword(s):

Genome Sequencing ◽

Genome Sequence ◽

Salmonella Enterica ◽

Draft Genome ◽

Draft Genome Sequence ◽

Whole Genome ◽

Drug Resistant ◽

Content Type ◽

Salmonella Enterica Serovar Typhi ◽

Extensively Drug Resistant

ABSTRACT We report a draft genome sequence of extensively drug-resistant (XDR) Salmonella enterica serotype Typhi isolated from a returned traveler from Pakistan who developed sepsis. Whole-genome sequencing revealed relatedness to a previously reported outbreak in Pakistan and identified the blaCTX-M-15 and qnrS resistance genes.

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New Variant of mcr-3 in an Extensively Drug-Resistant Escherichia coli Clinical Isolate Carrying mcr-1 and blaNDM-5

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.01757-17 ◽

2017 ◽

Vol 61 (12) ◽

Cited By ~ 37

Author(s):

Lu Liu ◽

Yu Feng ◽

Xiaoxia Zhang ◽

Alan McNally ◽

Zhiyong Zong

Keyword(s):

Escherichia Coli ◽

Clinical Isolate ◽

Amino Acid Substitutions ◽

Drug Resistant ◽

Content Type ◽

Carbapenem Resistant ◽

Resistant Genes ◽

Extensively Drug Resistant ◽

New Variant ◽

Carbapenemase Gene

ABSTRACT A colistin- and carbapenem-resistant Escherichia coli clinical isolate was found to carry two plasmid-borne colistin-resistant genes, mcr-1 and the newly identified mcr-3, and a carbapenemase gene, bla NDM-5. mcr-3 is a new variant (mcr-3.5) in the isolate and encodes three amino acid substitutions compared with the original MCR-3. mcr-3 was carried by a TnAs3-like transposon on a self-transmissible IncP plasmid in the isolate, highlighting that mcr-3 may have widely spread.

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