Complete Genome Sequence of a Multidrug-Resistant Acinetobacter baumannii Isolate Obtained from a Mexican Hospital (Sequence Type 422)

Castro-Jaimes, Semiramis; Salgado-Camargo, Abraham David; Graña-Miraglia, Lucía; Lozano, Luis; Bocanegra‐Ibarias, Paola; Volkow-Fernández, Patricia; Silva-Sánchez, Jesús; Castillo-Ramírez, Santiago; Cevallos, Miguel A.

doi:10.1128/genomea.00583-16

Cited by 11 publications

(7 citation statements)

References 6 publications

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“…The genome sequences of three isolates, namely, 7804, 810CP and 3207, have previously been reported by some of the authors of this manuscript (Castro-Jaimes et al, 2016;Pérez-Oseguera et al, 2017).…”

Section: Plasmid Collectionmentioning

confidence: 74%

Structure and Evolution of Acinetobacter baumannii Plasmids

et al. 2020

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Acinetobacter baumannii is an emergent bacterial pathogen that provokes many types of infections in hospitals around the world. The genome of this organism consists of a chromosome and plasmids. These plasmids vary over a wide size range and many of them have been linked to the acquisition of antibiotic-resistance genes. Our bioinformatic analyses indicate that A. baumannii plasmids belong to a small number of plasmid lineages. The general structure of these lineages seems to be very stable and consists not only of genes involved in plasmid maintenance functions but of gene sets encoding poorly characterized proteins, not obviously linked to survival in the hospital setting, and opening the possibility that they improve the parasitic properties of plasmids. An analysis of genes involved in replication, suggests that members of the same plasmid lineage are part of the same plasmid incompatibility group. The same analysis showed the necessity of classifying the Rep proteins in ten new groups, under the scheme proposed by Bertini et al. (2010). Also, we show that some plasmid lineages have the potential capacity to replicate in many bacterial genera including those embracing human pathogen species, while others seem to replicate only within the limits of the Acinetobacter genus. Moreover, some plasmid lineages are widely distributed along the A. baumannii phylogenetic tree. Despite this, a number of them lack genes involved in conjugation or mobilization functions. Interestingly, only 34.6% of the plasmids analyzed here possess antibiotic resistance genes and most of them belong to fourteen plasmid lineages of the twenty one described here. Gene flux between plasmid lineages appears primarily limited to transposable elements, which sometimes carry antibiotic resistance genes. In most plasmid lineages transposable elements and antibiotic resistance genes are secondary acquisitions. Finally, broad host-range plasmids appear to have played a crucial role.

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Section: Plasmid Collectionmentioning

confidence: 74%

Structure and Evolution of Acinetobacter baumannii Plasmids

et al. 2020

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“…Further examination of publicly available genome sequences (NCBI release February 2019) by blastn searching revealed the fragment to be 100 % identical to a part of the pU12A_D plasmid present in the Escherichia coli ST131 urinary tract isolate (accession number: PRJNA516746). The complete sequence was also detected in a few other bacterial strains, including a multi-drug-resistant Acinetobacter baumannii isolate recovered from bronchoalveolar lavage fluid [48]. The element is an isoform of ISPst2 and belongs to the ISL3 family, and we therefore named it CLJ-ISL3.…”

Section: Resultsmentioning

confidence: 99%

Insertion sequences drive the emergence of a highly adapted human pathogen

et al. 2020

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Pseudomonas aeruginosa is a highly adaptive opportunistic pathogen that can have serious health consequences in patients with lung disorders. Taxonomic outliers of P. aeruginosa of environmental origin have recently emerged as infectious for humans. Here, we present the first genome-wide analysis of an isolate that caused fatal haemorrhagic pneumonia. In two clones, CLJ1 and CLJ3, sequentially recovered from a patient with chronic pulmonary disease, insertion of a mobile genetic element into the P. aeruginosa chromosome affected major virulence-associated phenotypes and led to increased resistance to the antibiotics used to combat the infection. Comparative genome, proteome and transcriptome analyses revealed that this ISL3-family insertion sequence disrupted the genes for flagellar components, type IV pili, O-specific antigens, translesion polymerase and enzymes producing hydrogen cyanide. Seven-fold more insertions were detected in the later isolate, CLJ3, than in CLJ1, some of which modified strain susceptibility to antibiotics by disrupting the genes for the outer-membrane porin OprD and the regulator of β-lactamase expression AmpD. In the Galleria mellonella larvae model, the two strains displayed different levels of virulence, with CLJ1 being highly pathogenic. This study revealed insertion sequences to be major players in enhancing the pathogenic potential of a P. aeruginosa taxonomic outlier by modulating both its virulence and its resistance to antimicrobials, and explains how this bacterium adapts from the environment to a human host.

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“…We now know much about the microevolution of a few pathogens, such as Neisseria gonorrhea or the species from the genus Chlamydia (Ezewudo et al, 2015 ; Joseph et al, 2015 ), however for most bacterial species we do not know very much. While Staphylococcus aureus has been extensively studied (Holden et al, 2010 ; Nubel et al, 2010 ; Castillo-Ramirez et al, 2011 , 2012 ), much less is known about the evolutionary dynamics of A. baumannii , especially in developing countries (Castro-Jaimes et al, 2016 ; Grana-Miraglia et al, 2016 ; Silva et al, 2016 ; Zenati et al, 2016 ). Importantly, this bacterial species has emerged as one of the main causes of nosocomial infections over the last decades (Zarrilli et al, 2013 ; Antunes et al, 2014 ).…”

Section: Introductionmentioning

confidence: 99%

Rapid Gene Turnover as a Significant Source of Genetic Variation in a Recently Seeded Population of a Healthcare-Associated Pathogen

et al. 2017

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Genome sequencing has been useful to gain an understanding of bacterial evolution. It has been used for studying the phylogeography and/or the impact of mutation and recombination on bacterial populations. However, it has rarely been used to study gene turnover at microevolutionary scales. Here, we sequenced Mexican strains of the human pathogen Acinetobacter baumannii sampled from the same locale over a 3 year period to obtain insights into the microevolutionary dynamics of gene content variability. We found that the Mexican A. baumannii population was recently founded and has been emerging due to a rapid clonal expansion. Furthermore, we noticed that on average the Mexican strains differed from each other by over 300 genes and, notably, this gene content variation has accrued more frequently and faster than the accumulation of mutations. Moreover, due to its rapid pace, gene content variation reflects the phylogeny only at very short periods of time. Additionally, we found that the external branches of the phylogeny had almost 100 more genes than the internal branches. All in all, these results show that rapid gene turnover has been of paramount importance in producing genetic variation within this population and demonstrate the utility of genome sequencing to study alternative forms of genetic variation.

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Complete Genome Sequence of a Multidrug-Resistant Acinetobacter baumannii Isolate Obtained from a Mexican Hospital (Sequence Type 422)

Cited by 11 publications

References 6 publications

Structure and Evolution of Acinetobacter baumannii Plasmids

Structure and Evolution of Acinetobacter baumannii Plasmids

Insertion sequences drive the emergence of a highly adapted human pathogen

Rapid Gene Turnover as a Significant Source of Genetic Variation in a Recently Seeded Population of a Healthcare-Associated Pathogen

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