Phenotypic and Molecular Characteristics of Carbapenem-Resistant Acinetobacter baumannii Isolates from Bulgarian Intensive Care Unit Patients

Carbapenem-resistant Acinetobacter baumannii (CRAB) is designated as an urgent public health threat, both due to its remarkable multidrug resistance and propensity for clonal spread. This study aimed to explore the phenotypic and molecular characteristics of antimicrobial resistance in CRAB isolates (n = 73) from intensive care unit (ICU) patients in two university hospitals in Bulgaria (2018–2019). The methodology included antimicrobial susceptibility testing, PCR, whole-genome sequencing (WGS), and phylogenomic analysis. The resistance rates were as follows: imipenem, 100%; meropenem, 100%; amikacin, 98.6%; gentamicin, 89%; tobramycin, 86.3%; levofloxacin, 100%; trimethoprim–sulfamethoxazole, 75.3%; tigecycline, 86.3%; colistin, 0%; and ampicillin–sulbactam, 13.7%. All isolates harbored blaOXA-51-like genes. The frequencies of distribution of other antimicrobial resistance genes (ARGs) were: blaOXA-23-like, 98.6%; blaOXA-24/40-like, 2.7%; armA, 86.3%; and sul1, 75.3%. The WGS of selected extensively drug-resistant A. baumannii (XDR-AB) isolates (n = 3) revealed the presence of OXA-23 and OXA-66 carbapenem-hydrolyzing class D β-lactamases in all isolates, and OXA-72 carbapenemase in one of them. Various insertion sequencies, such as ISAba24, ISAba31, ISAba125, ISVsa3, IS17, and IS6100, were also detected, providing increased ability for horizontal transfer of ARGs. The isolates belonged to the widespread high-risk sequence types ST2 (n = 2) and ST636 (n = 1) (Pasteur scheme). Our results show the presence of XDR-AB isolates, carrying a variety of ARGs, in Bulgarian ICU settings, which highlights the crucial need for nationwide surveillance, especially in the conditions of extensive antibiotic usage during COVID-19.

Prevalence of classes 1 and 2 integrons in multidrug-resistant Acinetobacter baumanni isolates recovered from some aquatic environment in South Africa

The emergence of antibiotic-resistance genes (ARGs) by means of integrons in multidrug-resistant Acinetobacter baumannii (MDR A. baumannii) has become a significant challenge in the management of infections from this pathogen. In this paper, we report on the variable region of class 1 and 2 integrons observed in MDR A. baumanni isolates recovered from rivers in the Eastern Cape Province, South Africa. Class 1 and 2 integrons with their variable regions were evaluated with polymerase chain reaction techniques followed by sequencing. Antibiotic sensitivity testing, checkerboard assay, time-kill independent assay, and Enterobacterial Repetitive Intergenic Consensus Polymerase Chain Reaction (ERIC-PCR) were carried out using standard microbiological techniques. A total of fifty-six (56) isolates were examined, among which 45 (79%) tested positive for class 1 integron, and 7 (12.3%) had class 2 integron. None was found to be class 3 integron positive among the isolates. The variable region contained aadA1, aadA5, and aadA2 genes, which confer resistance against streptomycin and spectinomycin, aac(6')-Ib against amikacin/ tobramycin and dfrA17 genes against trimethoprim. The minimum inhibitory concentrations of the antimicrobials for one of the tested organisms were resistant against meropenem, colistin sodium methanesulfonate, tetracycline, ceftazidime, and ciprofloxacin (16, > 16, > 8, > 256, and 128 ug/mL respectively). The impact of colistin combined with quinolones (ciprofloxacin), with the FICIs (0.31) indicated synergistic effects against MDR A baumanni. However, when colistin was combined with meropenem and ceftazidime, additive effects with fractional inhibitory concentration (FIC) index ranging from 0.52 to 1 were observed. No antagonistic effect was evaluated among the examined isolates. ERIC-PCR analyses of A. baumanni isolates revealed significant genetic diversity, suggesting various sources of environmental contamination. We conclude that A. baumanni harbouring class 1 integrons in aquatic milieus are a significant source of ARGs and can transmit these elements to other organisms and consequently to man with significant public health implications.

Molecular Detection of Integrons, Colistin and β-lactamase Resistant Genes in Salmonella enterica Serovars Enteritidis and Typhimurium Isolated from Chickens and Rats Inhabiting Poultry Farms

The rapid growth of multidrug-resistant Salmonella is a global public health concern. The aim of this study was to detect integrons, colistin and β-lactamase resistance genes in Salmonella enteritidis and typhimurium. A total of 63 isolates of S. enteritidis (n = 18) and S. typhimurium (n = 45) from fecal samples of layers and rats at chicken farms were screened for antibiotic resistant genes. Conventional PCR was performed for the detection of integrons (classes 1, 2, and 3), colistin (mcr-1-5) and β-lactamase (bla_CTX-M, bla_CTX-M-1, bla_CTX-M-2, bla_CTX-M-9, bla_CTX-M-15, bla_TEM, bla_SHV, and bla_OXA) resistant genes. Of these isolates, 77% and 27% of S. typhimurium and S. enteritidis harboured the mcr-4 encoded gene for colistin, respectively. The prevalence of class 1 integrons for S. typhimurium and S. enteritidis was 100% for each serovar, while for class 2 integrons of S. typhimurium and S. enteritidis it was 49% and 33% respectively, while class 3 integron genes was not detected. Our study also detected high levels of β-lactamase encoding genes (bla gene), namely bla_CTX-M, bla_CTX-M-1, bla_CTX-M-9 and bla_TEM from both S. typhimurium and S. enteritidis. This, to our knowledge, is the first report of mcr-4 resistance gene detection in Salmonella serovars in South Africa. This study also highlights the importance of controlling rats at poultry farms in order to reduce the risk of transmission of antibiotic resistance to chickens and eventually to humans.

High Frequency of Class I and II Integrons and the Presence of aadA2 and dfrA12 Gene Cassettes in the Clinical Isolates of Acinetobacter baumannii from Shiraz, Southwest of Iran

Background: Acinetobacter baumannii is a global concern that causes healthcare-associated infections due to multidrug resistance against commercially available antimicrobial agents. Objectives: The present study was conducted to determine the antimicrobial susceptibility of A. baumannii isolates from clinical specimens in Shiraz, Iran. In addition, the possible relationship of susceptibility patterns with the presence of integrons and related gene cassettes is investigated. Methods: A. baumannii isolates were collected, and their susceptibility to various antibiotics was tested using the Kirby-Bauer disk diffusion method. Moreover, molecular analyses were performed to detect the presence of the OXA-51-like gene, as well as class I, II, and III integrons, and associated gene cassettes. Results: The majority of isolates were resistant to imipenem (99.4%), piperacillin (98.2%), gentamycin (98.2%), meropenem (97.7%), ceftazidime (95.4%), amikacin (95.4%), and trimethoprim-sulfamethoxazole (90.8%). All strains showed multidrug resistance to the tested antibiotics. The distribution analysis of integrons genes revealed that 90.2, 72.4, and 12.1% of the isolates carried intI1, intI2, and intI3 genes, respectively. Moreover, two types of prevalent gene cassettes, including aad and dfr, were detected in class 1 integron-carrying strains. Conclusions: The current study showed the high prevalence of A. baumannii isolates harboring integrons in our investigated medical center, which may indicate the distribution of multidrug resistance events. The different gene cassette arrays in the present study highlight the remarkable role of geographical issues in disseminating multidrug-resistant isolates. This could be attributed to distinct therapeutic interventions in different areas. The results demonstrate the necessity of continuous surveillance to prevent the distribution of multidrug resistance among A. baumannii strains in Iran.

The Occurrence and Characterization of Class I, II, and III Integrons Among Carbapenemase-Producing Clinical Strains of Acinetobacter baumannii in Tehran, Iran

Background: Acinetobacter baumannii has emerged as a critical pathogen with high morbidity and mortality in long-term hospitalized patients who stay in intensive care units. Carbapenemases and integrons are two critical DNA elements that contribute to the emergence of multidrug-resistant (MDR) A. baumannii. Objectives: The current study aimed at characterization and molecular detection of class 1, 2, and 3 integrons among carbapenemase-producing A. baumannii strains recovered from a clinical setting in Tehran, Iran. Methods: A total of 65 non-replicated clinical strains were considered in this study. Class 1, 2, and 3 carbapenemase genes and clonal relatedness of the isolates were investigated by PCR assay. Results: The prevalence of carbapenemases was as follows: blaOXA23 (92.31%), blaVIM (69.23%), and blaNDM (1.54%). In addition, PCR sequencing confirmed the presence of gene cassette arrays consisting of aacA4-catB8-aadA1 (12/46, 26.09%), aadB-aadA1 (26.09%, 12/46), arr2-cm1A5 (30.43%, 14/46), and dfrA1-aadA1 (7.39%, 8/46) in class 1 integron and dfrA1-sat2 (52.94%, 9/17), and sat2-aadA1 (47.06%, 8/17) in class 2 integron. Sequence-based typing of both blaOXA-51-like and ampC revealed the following distribution of three different clone types among isolates: clonal complex (CC) 10 (46.15%, 30/65), CC2 (40%, 26/65), and CC3 (13.85%, 9/65). Statistical analysis showed that the presence of the intI1, blaOXA23, blaVIM, or blaNDM genes can significantly increase the acquiring MDR phenotypes in A. baumannii isolates. Conclusions: High prevalence of carbapenemase-producing A. baumannii harboring integrons is alarming public health. It seems that class 1 integron can be served as a predictive biomarker for the presence of MDR phenotypes in the clinical setting. However, integrons do not carry carbapenemases in these strains.

Molecular Characterization of Multiple Antibiotic-Resistant Acinetobacter baumannii Isolated from Egyptian Patients

Acinetobacter baumannii is an opportunistic microorganism commonly found in intensive care units (ICUs), and it is responsible for a broad span of hospital-acquired infections. Persistence of nosocomial infection caused by multidrug-resistant (MDR) A. baumannii is an alarming health care issue in Egypt, and at present, colistin remains the treatment of choice for the management of MDR A. baumannii infections. A. baumannii possesses great capacity to develop and acquire resistance to a broad range of antibiotics. The acquisition and dissemination of antibiotic-resistant determinants in A. baumannii strains are mediated by integrons, especially class I integrons. This study focuses on the characterization of some genetic mechanisms underlying the multidrug-resistant phenotypes of A. baumannii isolates in Egypt. Forty-eight A. baumannii specimens were isolated from different hospitalized patients; least resistance was observed against amikacin and tigecycline, with 60% and 58.5% of the isolates resistant, respectively, whereas 62.5% of the isolates were resistant to imipenem and meropenem. The highest sensitivity was found for colistin. Genetic analysis revealed that blaoxa-51 was detected in all isolates, the blaoxa-23-like gene was detected in 80% of the isolates, and blaoxa-24 and blaoxs-58 were not detected in any isolate. Finally, PCR analysis revealed that 6.6% of isolates carried the class I integron gene.

Genetic Diversity Analysis of Mupirocin-Resistant Staphylococcus aureus Clinical Isolates in Tehran Hospitals, Iran

Few studies describe the molecular characterization of mupirocin resistance in Staphylococcus aureus strains. In this study, we evaluated the characteristics of mupirocin resistance in S. aureus isolates for 1-year period in Tehran, Iran. In a cross-sectional study, we collected 51 unique mupirocin-resistant strains obtained from 648 S. aureus isolates. High- and low-level resistance were determined by minimum inhibitory concentration with broth microdilution method. Presence of the genes for resistance to antibiotics and toxins was detected by polymerase chain reaction assays. Genotyping was performed by S. aureus protein A (spa) and staphylococcal cassette chromosome mec (SCCmec) typing, whereas clones were determined by multilocus sequence typing. Among mupirocin-resistant isolates, methicillin-resistant S. aureus (MRSA) 23 (45.1%) and 28 (54.9%) isolates were classified as high- and low-level mupirocin resistance, respectively. Among the 51 tested strains 25 (49%) isolates were positive for mupA genes. Seven different clones were detected in this study. High-level mupirocin-resistant (HLMUPR) strains belonged to ST8-SCCmec IV/t064 (n = 10, 19.6%), ST5-SCCmec IV/t002 (n = 5, 9.8%), ST8-SCCmec IV/t008 (n = 4, 7.8%), and ST239-SCCmec III/t631 (n = 4, 7.8%) clones, while low-level mupirocin-resistant (LLMUPR) strains belonged to ST22-SCCmec IV/t790 (n = 11, 21.6%), ST239-SCCmec III/t860 (n = 9, 17.7%), and ST15-SCCmec IV/t084 (n = 8, 15.7%) clones. Two strains belonged to ST22-SCCmec IV/t790 clone, despite carrying mupA gene, and demonstrated LLMUPR phenotype. One ST8-SCCmecIV/t008 strain with HLMUPR was confirmed as Vancomycin-intermediate S. aureus strain. Our data demonstrated the need for thorough epidemiological monitoring and a routine mupirocin testing program to prevent and detect mupirocin resistance in MRSA.