RiteeshGrandhi/sciclaimeval-shared-task huggingface dataset:
Introduction
Acinetobacter species are aerobic, Gram-negative pleomorphic, and non-lactose fermenting bacilli ( Murray, Rosenthal & Pfaller, 2021 ) and they are ubiquitous in nature, including human skin ( Almasaudi, 2016 ). In the past two decades, multidrug-resistant Acinetobacter spp. have become an important cause of health care-associated infections (HAIs), contributing to increase mortality rates in intensive care units (ICUs) ( Castanheira, Mendes & Gales, 2023 ). Of the all Acinetobacter species, A. baumannii is predominant in clinical settings ( Evans, Hamouda & Amyes, 2013 ; Silva et al., 2022 ) although non- baumannii species are also considered clinically important ( Al Atrouni et al., 2016a ). The World Health Organization (2017) elevated A. baumannii to the top of the list of critical pathogens. In Ecuador, A . baumannii was the main bacterium associated with HAIs in the ICU in 2010 and 2011 ( Jiménez, 2013 ).

Acinetobacter species have high carbapenem resistance by the acquisition of genetic determinants of resistance through horizontal gene transfer ( Castanheira, Mendes & Gales, 2023 ). The environment plays a key role in the spread of resistance to clinically relevant antibiotics ( Singer et al., 2016 ); the spread of antibiotic resistance genes in river systems is a potential threat to public health ( Wang et al., 2018 ). Environmental strains harbor antibiotic resistance mechanisms, serving as reservoirs for resistant elements and some of them could cause HAIs ( Finley et al., 2013 ; Al Atrouni et al., 2016a ). Horizontal gene transfer plays an important role in the transmission antibiotic resistance between non-pathogens and human pathogens ( Wang et al., 2018 ). Worldwide, A. baumannii has increased the carbapenem resistance in around 90% in the last decade ( Rosenthal et al., 2021 ). In Latin America, Acinetobacter spp. resistance to imipenem and meropenem varied from 8% to 89% ( Pan American Health Organization, 2021 ). In 2010, Ecuador reported that 54% of A. baumannii strains were resistant to meropenem and 51% to imipenem ( Labarca et al., 2016 ); however, the percentage of carbapenem resistant increased to 70% according to the Antimicrobial Resistance Surveillance Network of Ecuador ( Satán et al., 2023 ).

The main mechanism of carbapenem resistance in Acinetobacter species is the production of serin-β-lactamases and metallo-β-lactamases enzymes ( Castanheira, Mendes & Gales, 2023 ). In South America, the most common enzymes are oxacillinases (OXA) encoded by bla OXA-23 , bla OXA-72 , bla OXA-51 , bla OXA-58 , bla OXA-235 , and bla OXA-143 genes ( Escandón-Vargas et al., 2017 ; García-Betancur et al., 2021 ). There is scarce information about carbapenem-resistant strains from clinical and environmental settings in Ecuador. In the country, studies reported the presence of bla NDM-1 , bla OXA-23 , and bla OXA-72 genes in A. baumannii clinical isolates ( Nuñez et al., 2016 ; Villacís et al., 2019 ). Thus, the main aim of this study was to determine the presence of carbapenem-resistant clinical and river Acinetobacter spp.
Conclusions
Overall, our results showed that the most of the Acinetobacter spp. clinical isolates came from tracheal aspirates from ICU. Our findings showed that carbapenem-resistant A. baumannii were the main species found in the study. We reported the presence of bla OXA-65 , bla OXA-70 , bla OXA-72 , bla OXA-23 , bla OXA-366 , and bla OXA143 -carrying multidrug-resistant genes in baumannii and no baumannii species. We report a new possible variant of OXA-143 circling in different hospitals in Quito and the possible presence of OXA-259 in aquatic environment. The presence of A. baumannii in the rivers increases the concern, since the resistance can be disseminated, polluting water sources, and promoting community acquired outbreaks.

To our knowledge, this is the first study that has characterized the carbapenemases genes in Acinetobacter spp. carbapenem-resistant isolates from four hospitals and five rivers in Quito. No bla OXA-65 , bla OXA-70 , bla OXA-72 , bla OXA-23 , bla OXA-366 , or bla OXA143 -carrying multidrug-resistant baumanii and no baumannii species have been described in Quito so far.
Supplemental Information
All samples correspond to Zone 9, which represents the code for Quito. The table details the hospital code, INSPI isolate code, geographical coordinates age, sex, sample type, and hospital unit of the patients to which each sample corresponds. In addition, the table indicated the river data, id code, geographical coordinates, and river name. Acronyms: NA: not available.

NA: Not applied, Aba: A. baumannii , Aha: A. haemolyticus , ABC: A. baumannii/calcoaceticus complex, ng/µl: nanograme/microlitre, Y: yes, N: not. Biochemical results are expressed as positive (+) and negative (−). The antibiotic susceptibility profile are expresed as Intermediate (I), Sensistive (S), and Resistance (R).

A. baumannii was identified by the amplification of both products, 490 bp and 294 bp, and A. pittii with a product of 194 bp of gyrB gene. The species identification was corroborate by sequencing on partial rpo gene. PCR results are expressed for carbapenen resistance genes as positive (+) and negative (−). The table details the GenBank number acccess of sequences obtained in this study.
Figure 1: Map of the city of Quito showing sampling locations.
Acinetobacter spp. clinical isolates recovered through the surveillance network from four hospitals in Quito. The hospitals’ localizations are represented by diamond (H1), square (H2), star (H3), and triangle (H4). The river sampling sites are represented by the circles, which indicates the GPS points where we collected the water sample. Rosa de los Ángeles Bayas-Rea made this map.

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DOI: 10.7717/peerj.17199/fig-1
Figure 2: Acinetobacter spp. clinical isolates obtained from four hospitals in Quito.
The percentage of Acinetobacter spp. clinical isolates. (A) Isolates obtained from different hospital service units. (B) Isolates recovered from clinical specimens.

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Figure 3: Clinical and environmental isolates susceptibility profile.
The percentages of clinical isolates that were resistant, intermediate, or sensitive to each antibiotic. (A) Clinical isolates susceptibility profile, (B) river isolates susceptibility profile. Acronyms: CIP, ciprofloxacin; GEN, gentamycin; SXT, trimethoprim/sulfamethoxazole; AMK, amikacin; FEP, cefepime; MEN, meropenem; IMP, imipenem; TOB, tobramycin; SAM, ampicillin/sulbactam; CAZ, ceftazidime; TZP, piperacillin/tazobactam; R, resistant; I, intermediate; S, sensitive.

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DOI: 10.7717/peerj.17199/fig-3
Figure 4: Alignment of OXA-143 amino acid sequences.
The polymorphic sites at the amino acid sequence level. The identity of the sequences was compared to the OXA-143 variant (GenBank protein number access WP_063861042.1 or its nucleic number access NG_049441.1). Numbers in the heading row indicate the base pair position of the polymorphic sites. Dots (.) show the identity with the Aba OXA-143. Acronyms: Aba, Acinetobacter baumannii; Api, A. pittii.

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DOI: 10.7717/peerj.17199/fig-4
Primers used in this study for the identification ofAcinetobacterspp. and detection of carbapenem-resistant genes.
Single and multiplex PCR reaction conditions.