Distribution of drug resistance genes and clinical characteristics of Acinetobacter baumannii isolated from the University Medical Center at Ho Chi Minh City

Abstract

Background: Infections resulting from A. baumannii in hospitals lead to numerous severe consequences as its antibiotic resistance, particularly to carbapenems, continues to rise. Given that resistance characteristics undergo constant changes due to mutations and gene transfer between species and strains, monitoring the real-time circulation of resistant strains is essential.

Methods: A descriptive cross-sectional method with analysis and experimentation were applied in this study. All strains of A. baumannii were isolated at the University Medical Center at Ho Chi Minh City from May 2020 to May 2021, then underwent antimicrobial susceptibility testing. Real-time PCR was performed to identify resistance genes, including blaOXA-51, blaOXA-23, blaOXA-48, blaOXA-58, and blaNDM-1. The patient’s information was collected by using the designated clinical research form.

Results: The study included 76 A. baumannii isolates. The resistance rates to imipenem and meropenem were 93.4%. Additionally, A. baumannii exhibited resistance to most of the other antibiotics investigated, with rates exceeding 80%. There was low resistance to Cefoperazone/sulbactam (6.1%) and colistin (5.3%). The distribution of resistance genes showed the prevalence of blaOXA-51 (100%), blaOXA-23 (88.2%), blaOXA-48 (43.4%), blaOXA-58 (2.6%), and blaNDM-1 (6.6%). The blaOXA-23 gene exhibited a statistically significant difference between carbapenem-susceptible A. baumannii (CSAB) and carbapenem-resistant A. baumannii (CRAB) (p < 0.001) and across different types of patient samples (p = 0.004). The distribution of the blaNDM-1 gene showed a statistically significant difference based on the clinical department sending the sample types (p = 0.029). There was a significant association between carbapenem resistance and the distribution of gene combinations (p < 0.001).

Conclusion: The carbapenem resistance rate was 93.4% for imipenem and meropenem, while it was low for cefoperazone/sulbactam (6.1%) and colistin (5.3%). blaOXA-51 holds significant importance in the identification of A. baumannii bacteria, and blaOXA-23 (88.4%) plays a decisive role in carbapenem resistance in A. baumannii at this hospital.

INTRODUCTION

In Vietnam, A. baumannii stands out as a prominent pathogen in nosocomial infections, imposing significant economic and public health burdens. Recent reviews for Southeast Asia and East Asia indicate a prevalence of carbapenem-resistant bacteria in Vietnam ranging from 43% to 92% 1 . The resistance mechanisms of A. baumannii to carbapenems are diverse, with particular emphasis on the β-lactamase mechanism, specifically β-lactamases of classes B and D. Notably, class D bla _OXA genes ( bla _OXA-51 , bla _OXA-23 , bla _OXA-58 , bla _OXA-48 ) and Metallo-β-lactamase enzymes are controlled by the highly concerning class B gene, bla _NDM-1 . These genes, situated on the chromosomes and/or plasmids of bacteria, not only have the potential to be passed on to the next generation but also exhibit horizontal inheritance, spreading resistance to other bacteria. This phenomenon exacerbates the severity of Carbapenem resistance in A. baumannii , escalating it into an increasingly serious problem.

The prevalence of hospital infections attributed to A. baumannii is on the rise in many hospitals in Viet nam 2 , 3 , 4 , 5 , 6 , 7 , 8 . Given the ever-changing resistance characteristics resulting from mutations and gene transfers among species and strains, it is crucial to continuously monitor the circulation of resistant strains in real-time. Additionally, investigating clinical characteristics such as A. baumannii -caused infections, specimen type, department, and the type of medical interventions becomes imperative to understand their relationship with the distribution of the aforementioned resistance genes.

MATERIALS AND METHODS

Materials

All strains of A. baumannii were isolated at HCMC University Medical Center from May 2020 to May 2021.

Inclusion criteria: Microbiological culture-positive with A. baumannii from one of the following clinical specimens: blood, sputum/ bronchial fluid, pus/wound fluid, urine.

Exclusion Criteria: Samples have duplicate information previously taken; samples do not have access to medical records of treated patients whose samples have results of A. baumanni isolates from 05/2020-05 2021 at HCMC University Medical Center.

Research procedure: A. baumannii strains were isolated, identified, and subjected to antibiotic susceptibility testing on the Vitek 2 system according to the hospital's standardized procedure. DNA extraction was then performed by using QIAamp DNA Microbiome Kit of QIAGEN, the quality and quantity checking by using Nanodrop spectrophotometer, followed by Real time PCR (real time PCR machine eppendorf) to detect and classify the carbapenem resistance genes: bla _OXA-51 , bla _OXA-23 , bla _OXA-48 , bla _OXA-58 , bla _NDM-1 . The real-time PCR reactions to identify these carbapenem resistance genes have been optimized with specific primer pairs, and the PCR reactions are quality-controlled by including internal positive and negative controls.

Statistical methods

Statistical analyses were conducted using Stata software(version 14.1). Pearson’s Chi-square or Fisher’s exact test with a level of confidence of 95% was used for categorical variables. Variables are: carbapenem resistance, carbapenem resistance genes, specimen type, type of A. baumannii infections, discharge outcomes, clinical departments sending specimens.

Ethical consideration

This study was reviewed and approved by the Ethics Committee of the University of Medicine and Pharmacy at Ho Chi Minh City (decision number 10/HĐĐĐ-ĐHYD on January 13, 2022).

RESULTS

A study was conducted on 76 strains of A. baumannii isolated at the University Medical Center at Ho Chi Minh City from May 2020 to May 2021. The average age of the patients with A. baumannii infection was 71.8 ± 18.7 years, with the youngest being 20 years old and the oldest being 98 years old. Among the subjects, 44 (57.9%) were male and 32 (42.1%) were female.

Meropenem is the strongest antibiotic after vancomycin. Meropenem (Merrem, Meronem) is an antibacterial specialist of the carbapenem family with a wide scope of use. It has proven to be the definitive course of treatment before the causative organism has been identified. Meanwhile imipenem là kháng sinh carbapenem có phổ kháng khuẩn rộng hơn và hiệu lực cao hơn các kháng sinh beta-lactam khác. Both imipenem and meropenem belong to a group of antibiotics called carbapenems. Carbapenems are potent members of the β-lactam family that inhibit bacterial cell-wall biosynthesis inhibitors. They are highly effective against Gram-negative and Gram-positive drug-resistant infections. As such, carbapenems are typically reserved as an antibiotic of last resort. Therefore, we are interested in the proportion of A. baumannii strains resistant to these two antibiotics compared to the strains still sensitive to them among the total strains included in this study.

Figure 1 . The proportion of imipenem- and meropenem-resistant A. baumannii strains compared to the sensitive strains among the total samples included in the study.

The rate of A. baumannii resistance to imipenem and meropenem was quite high, both of which were 93.4%. Statistical results regarding the strains indicated that when there is resistance to imipenem, there is also resistance to meropenem, and vice versa.

Afterwards, we surveyed the frequency of occurrence of the genes of interest, and the results are depicted in Figure 2 .

Figure 2 . The frequency of occurrence of the target genes among the isolated strains of A. baumannii .

We want to determine if there is a correlation between the presence of the genes we are investigating and the antibiotic resistance of A. baumannii . Therefore, statistical calculations have been conducted, and the results are presented in Table 1 .

Table 1 Relationship between genes and carbapenem resistance

Only the blaOXA-23 gene was significantly different between the CRAB and CSAB groups.

Table 2 Gene distribution according to clinical departments sending specimens

Only the blaNDM-1 gene distribution significantly differed according to the clinical department that sent the specimen (p=0.029).

Table 3 Gene distribution according to specimen type

The distribution of blaOXA-23 was significantly different for different types of patient samples (p=0.004).

Table 4 Gene distribution according to the type of A. baumannii infection

There was no statistically significant association between gene distribution and the type of A. baumannii infection.

Table 5 Gene distribution according to discharge outcome

There was no statistically significant association between gene distribution and discharge outcome.

Table 6 Gene combinations

The two-gene combination accounted for the largest proportion (51.3%), followed by the three-gene combination. There are few blaNDM-1 and blaOXA-58 genes, and they do not appear alone but rather in combination with other genes.

Table 7 Relationship between gene combination distribution and carbapenem resistance

There was a statistically significant difference between carbapenem resistance and the distribution of gene combinations (p < 0.001).

DISCUSSION

*Carbapenem resistance: Since carbapenem-resistant A. baumannii was identified in 1991, there has been a worldwide surge in the prevalence of A. baumannii strains exhibiting resistance to these antibacterial antibiotics. This phenomenon poses a public health threat in Europe, as well as in South and Southeast Asia, particularly within intensive care units (ICUs) 2 . A. baumannii was 93.4% resistant to both carbapenems tested in this study (imipenem and meropenem). In other words, the carbapenem susceptibility rate of A. baumannii is less than 10%. According to the following comparison table from recent years, the resistance rate is quite high, above 90%; there are also studies where this rate is up to 100% 3 . This rate is similar to that reported in some recent studies and is also consistent with predictions that the rate of resistance to antibiotics in this group will increase in previous years.

Table 8 Comparison of carbapenem resistance of A. baumannii in several domestic and foreign studies

* Distribution of resistance genes in the study

Survey of 5 resistance genes in 76 strains of A. baumannii using real-time PCR. Our results are similar to those of many other domestic and foreign studies, and blaOXA genes, especially blaOXA-23 , are the most common carbapenemase-encoding genes in A. baumannii worldwide.

Table 9 Comparison of gene distribution rates

BlaOXA-51 : The results of this study are consistent with those of all the abovementioned domestic studies. One hundred percent of A. baumannii strains carry the blaOXA- 51 gene. This gene is the natural intrinsic gene of A. baumannii , and research has also used this gene in combination to identify A. baumannii 12 . The blaOXA-51 gene is located on the chromosome, which usually does not lead to carbapenem resistance due to poor hydrolysis; however, in the presence of the upstream ISAba1 insertion sequence, the blaOXA-51 gene can provide a promoter that allows overproduction and overexpression of this gene 14 .

BlaOXA-23 : Among the carbapenem-resistant strains, the blaOXA-23 gene carrier accounted for 93.0% (66/71), similar to the findings of the Luu Thi Vu Nga study (2016) 12 , Reza Beigverdi (2019) 15 , and Hoang Quoc Cuong et al. (2019) 7 . Looking for an association between blaOXA-23 and carbapenem resistance, the difference was statistically significant (p=0,001), which may demonstrate that the findings of this study are consistent and reinforce the finding that blaOXA-23 is the main gene affecting carbapenem resistance in A. baumannii 16 . Reviewing the distribution of the blaOXA-23 gene by specimen type revealed statistically significant differences (p=0.004) other characteristics, such as the clinical department sending samples, infectious pathology or discharge status, did not show statistically significant differences.

BlaOXA-48 : This gene was first identified in a strain of Klebsiella pneumoniae from Turkey 17 . In our study, 43.4% of the strains of A. baumannii carried this gene however, this percentage is quite low compared to that reported in Tarafdar F's study in Iran (92%) 4 . In contrast, many early studies have not detected this gene in A. baumannii . BlaOXA -48 is located on the plasmid, and previous studies have not detected this gene in A. baumannii, as there is likely no transverse inheritance through this plasmid, and the rapid spread of this β-lactamase may have occurred in recent years. In Vietnam, no studies of the blaOXA-48 gene have been conducted in strains of A. baumannii . Although the activity of carbapenemase is lower than that of other class D β-lactamases, blaOXA-48 is reported to undergo faster hydrolysis of imipenem than meropenem 16 . In this study, the distribution of the blaOXA-48 gene did not significantly differ between the CRAB and CSAB groups, perhaps due to the coemergence of multiple variants in the study or due to interactions with other carbapenemases without seeing the above differences. Because studies of this gene in A. baumannii are limited, we do not have data to compare and investigate conformity with other studies.

BlaOXA-58 : The detection rate of this gene was the lowest among the survey genes (2.6%). In the CRAB group, this rate was 7.7%, and this gene only appeared in the CRAB group. This rate is also consistent with that of blaOXA-58 , which is usually the lowest gene identified in many studies, but our results were significantly lower than those of several other studies, such as those of Hoang Quoc Cuong (10.3%) 7 , Luu Thi Vu Nga (5,6%) 12 , Udomluk Leungtongkam (6.5%) 18 , and Hou Cheng (5.3%) 13 ; in particular, in the study of Le Nu Xuan Thanh, this rate reached 27.9% 11 . According to a study in China, until 2008, blaOXA-58 was the most common gene (more than blaOXA-23 ) in this country until the replacement of blaOXA-23 in 2009, and the resistance level of blaOXA-58 was also lower than that of blaOXA-23 . 19 More recently, in Vietnam, research has indicated that when blaOXA-58 has increased expression of imipenem resistance in the presence of ISAba3 insertion sequences, this combination may make blaOXA-58 worrisome 20 .

BlaNDM-1 : The percentage in our study was 6.6%, which is similar to that reported in other studies 7 , 12 and higher than that reported in Iran (2.7%) 15 . Some studies of this topic, such as Le Nu Xuan Thanh et al. (2016) (11.8%) 11 and Udomluk Leungtongkam et al. 18 (9.2%), have reported higher rates. Although there are disparities, there are generally few such studies, and studies with higher rates often come from populations sampled from 2-4 hospitals in the region or in the country. Regarding the distribution of the blaNDM-1 gene according to some clinical features in the study, since the frequency of occurrence of the gene was quite small in the study, it is impossible to make a meaningful difference. However, in terms of characteristics such as resistance to carbapenems, 5/5 strains were found to carry the blaNDM-1 gene (100%) resistant to carbapenems (both imipenem and meropenem), and according to the clinical department’s results, there was a difference in the number of samples sent by the clinical department (p=0.026), which was mainly concentrated in 4/5 genes in the internal medicine department (one in the respiratory department, two in the neurology department, one in the Geriatric-Palliative Care Department), and one in the Neurosurgery Department. In terms of distribution by infectious disease, specimen type and discharge outcome did not significantly differ.

* Gene combinations

The occurrence of single-gene strains was only 3.9% (3 out of 76) with the blaOXA-51 gene, while the remaining 73 strains all carried more than one gene, with 54.0% having 2-gene combinations and 42.1% having 3-gene combinations. In both our research and the studies referenced above, all A. baumannii strains consistently exhibited 100% expression of the blaOXA-51 gene. Therefore, when encountering a single-gene strain, the blaOXA-51 gene is invariable. This study aligns with those referenced studies, albeit with a slightly lower percentage 7 , 9 , 12 . The appearance rate of the blaOXA-23 gene in this study is comparable to that in many previous studies, but it has the highest rate among the examined studies. In contrast, the aforementioned studies did not include a survey of the blaOXA-48 gene, which constituted 43.4% of the genes identified in our study. This difference may contribute to a reduction in the monogenic ratio of blaOXA-51 compared to findings in other studies. Additionally, the distribution of gene combinations showed a statistically significant association with carbapenem resistance (p < 0.001), implying that the increase in carbapenem resistance may be attributed to an increase in the number of combinations of resistance genes.

The 2-gene combinations used were blaOXA-51 + blaOXA-23 , blaOXA-51 + blaOXA-48 and blaOXA-51 + blaNDM-1 . In particular, the percentage of patients with the blaOXA-51 + blaOXA-23 gene combination was 94.9%. The 3-gene combinations used were blaOXA-51 + blaOXA-48 + blaNDM-1 and blaOXA-51 + blaOXA-23 + blaOXA-48 và blaOXA-51 + blaOXA-58 + blaNDM-1 . In our study, we did not have any findings containing 4 genes in the same survey strain, while the study of Hoang Quoc Cuong et al. showed that up to 2 strains had all 4 genes: blaNDM-1 + blaOXA-51 + blaOXA-23 + blaOXA-58 7 .

CONCLUSION

The occurrence rate of the blaOXA-23 gene in this study was comparable to that in many previous studies, but it had the highest rate among the examined studies. In contrast, the aforementioned studies did not include a survey of the blaOXA-48 gene, which constituted 43.4% of the genes identified in our study. This difference may contribute to a reduction in the monogenic ratio of blaOXA-51 compared to findings in other studies. Additionally, the distribution of gene combinations showed a statistically significant association with carbapenem resistance (p < 0.001), implying that the increase in carbapenem resistance may be attributed to an increase in the number of combinations of resistance genes.

Acknowledgments

We would like to sincerely thank the University of Medicine and Pharmacy at Ho Chi Minh City (UMP) and the University Medical Center (UMC) for their help and for creating the best conditions for us in research and completing the project.

Abbreviations

non

Author contributions

Duong Thi Hong Diep: conceived the idea, designed the study, collected specimens and patient information, and edited the manuscript.

Cao Thi Phung: performed experiments, performed statistical analysis, wrote the manuscript.

Funding

Duong Thi Hong Diep received the funding from the University of Medicine and Pharmacy at Ho Chi Minh City for this work.

Availability of data and materials

none

Competing interests

The authors declare that they have no competing interests.