Carbapenamase-Producing Acinetobacter baumannii in China, Latin America and the Caribbean: A Systematic Review and Meta-Analysis

Haiyang Yu

Pedro Kourí Tropical Medicine Institute (IPK), Cuba

Guillermo Ezpeleta-Lobato

Bizkaia International Vaccination Center, España

Xu Han

Pedro Kourí Tropical Medicine Institute (IPK), Cuba

Yenisel Carmona-Cartaya

Pedro Kourí Tropical Medicine Institute (IPK), Cuba

Dianelys Quiñones-Pérez

Pedro Kourí Tropical Medicine Institute (IPK), Cuba

The genus Acinetobacter (Acinobacter spp.) is made up of several species. These gram-negative bacilli are among the most common nosocomial pathogens worldwide. Acinetobacter baumannii is the most clinically relevant species, due to its ability to develop various mechanisms that lend themselves to antibiotic resistance.[1] A member of the beta-lactam class (the same class of antibiotics as penicillins and cephalosporins), carbapenemic antibiotics are the last resort in treating A. baumannii infections.

There has been a worldwide increase in carbapenem resistance observed in clinical isolates of A. baumannii.[2] The Latin American Antimicrobial Resistance Surveillance Network found A. baumannii to have high resistance to carbapenems in 15 countries in the region during 2014–2016. The percentage of resistant isolates varied from 8% to 89%.[3] In China in 2016, 71.4% of A. baumannii isolates were resistant to carbapenems.[4] WHO published a list of priority pathogens in 2017, including A. baumannii, Pseudomonas aeruginosa, and carbapenem-resistant Enterobacteriacae spp. as critical priorities.[5]

The main mechanism of carbapenem resistance in A. baumannii (CRAB) strains is carbapenemases production. The most common of these are Ambler’s class D oxacillinases (OXAs).[2] Six subgroups of OXAs have been identified in A. baumannii: the species’ intrinsic carbapenemase OXA-51–like, and the acquired carbapenemases OXA-23–like, OXA-24–like, OXA-58–like, OXA-143–like, and OXA-235–like.[6] Class B metallobetalactamases (MBLs) are also a major threat because they are often located in mobile genetic elements, easily transferable between bacteria. Four types of MBLs are frequently detected in A. baumannii: imipenemase (IMP), Verona imipenemase (VIM), Seoul imipenemase (SIM), and New Delhi beta-lactamase (NDM).[7]

Molecular characterization of A. baumannii isolates is very useful in identifying the source of an outbreak and in helping to control its spread. Multilocus sequence typing (MLST) is highly discriminative and has been applied successfully to several bacterial pathogens, including A. baumannii. Additionally, this typing allows for comparisons between laboratories and provides a powerful tool for conducting epidemiological studies worldwide.[8]

The emergence of carbapenem-resistant forms of A. baumannii is a complex global problem, difficult to manage both clinically and therapeutically. Monitoring carbapenemase genotypes and molecular epidemiology studies contribute to more effective control measures. However, comparative analyses of circulating forms in different geographies are scarce. This work is a systematic review of published information on carbapenemase production and sequence types characterized in A. baumannii isolates in China, Latin America and the Caribbean (LAC).

We followed the SPIDER scheme in preparing this study.[9] We carried out a systematic review of all relevant publications in 2015–2020, adjusted according to recommendations contained in PRISMA guidelines (Preferred Reporting Items for Systematic Reviews and Meta-Analyses.)[10]

Search strategy and article selection The search was carried out in the following databases: PubMed (Medline), BVS (Regional Portal, Virtual Health Library), and CNKI (Chinese database). We used the following keyword combinations: “carbapenem resistance” OR “carbapenemase producing” combined with “Acinetobacter baumannii” combined with the names of the following countries: “Argentina”, “Bahamas”, “Belize”, “Bolivia”, “Brazil”, “Chile”, “China”, “Columbia”, “Costa Rica”, “Cuba”, “Ecuador”, “Guatemala”, “Guyana”, “Haiti”, “Honduras”, “Jamaica”, “Mexico”, “Nicaragua”, “Panama”, “Paraguay”, “Peru”, “Salvador”, “Surinam”, “Trinidad”, “Uruguay”, and “Venezuela”. We selected articles in three stages: by title, by abstract content, and finally, according to information contained in the full text.

Inclusion criteria We included studies with the following characteristics: 1) observational studies with a cross-sectional design; 2) analysis of A. baumannii clinical isolates in adult populations; 3) reports on CRAB; 4) detection of class A, B and D carbapenemases by molecular methods such as reverse-transcriptase polymerase chain reaction testing (RT-PCR) or MLST; 5) carbapenemase genotype analysis in LAC or China published in 2015–2020 in English, Spanish or Chinese.

Exclusion criteria Studies with one or more of the following characteristics were excluded: 1) contained no information on CRAB; 2) studied isolation in pediatric populations; 3) did not report on class A, B and D carbapenemase classes; 4) duplicated other research; and 5) studies that reported experiments in non-human subjects or were review articles, conference abstracts, meta-analyses or systemic reviews.

Review articles and meta-analyses were only considered in this review’s discussion section. Screening for inclusion was carried out individually by two team members. When there were differences of opinion, these were discussed with the principal investigator. Endnote X9 and Excel were used to manage references.

Study quality evaluation Study quality was evaluated by two researchers using the JBI Critical Appraisal Tools for Prevalence Studies.[11] This tool includes nine items, each of which was scored as either ‘Yes’ (when the requirement was met), as ‘No’ (when the requirement was not met) or as ‘Not Clear’ (if it was unknown whether the requirement was met) or as ‘Not Applicable’.[11] Studies were considered high quality when their score was ≥80% of the maximum possible score (8 or more items scored “Yes”), average quality when their score was 70%–79% (6–7 items scored ‘Yes’), and low quality when their score was <70% (6 or fewer items scored ‘Yes’).

Data extraction Two team members carried out data selection and extraction individually, as well as bias risk analysis. We organized data on carbapenemase genotypes in China, Latin America and the Caribbean into a matrix (Table 1).

Data analysis and statistics We carried out a quantitative study (meta-analysis) on A. baumannii carbapenemase genotypes and a qualitative study (qualitative descriptive synthesis) for sequence types, due to the great diversity of sequence types and differences between geographical areas. Two investigators undertook data analysis for the quantitative study. Statistical analysis was performed using the Metaprop module of Stata version 15 (StataCorp LLC U.S.A),[12] and obtained estimates of the combined prevalence of predominant A. baumannii carbapenemases in different regions, as well as their 95% confidence intervals (95% CI), which are represented in corresponding forest graphs (Figure 2).

We used either fixed-effect or random-effect models according to statistical heterogeneity between studies, which was assessed using the Cochran I2 statistic (a value of 0% indicates no heterogeneity; 25%, 50% and 75% are considered to have low, medium and high heterogeneity, respectively). Egger’s weighted linear regression test, combined with a funnel plot, was used to assess publication bias. An assessment of ‘no publication bias’ was made when the regression line started from the origin of the ordinate axis (Y) (publication bias increases as the line moves away from the Y coordinate’s origin). Statistical significance was assessed at 0.1 and not 0.05.[13]

Table 1
Table 1: Data extraction characteristics

CRAB Carbapenem-resistant A. baumannii; MLST: Multilocus sequence typingRT-PCR Reverse-transcriptase polymerase chain reaction

Literature search, selection and validation We initially selected 334 articles, which were reduced to 318 after eliminating duplicates. Of these, 261 were excluded for failure to meet inclusion criteria or because they were outside the scope of this review. Finally, we fully reviewed a total of 57 articles, and 29 were selected that met all established criteria, which were then included in the meta-analysis (Figure 1).

Medium-high scores were obtained upon evaluation of the cross-sectional observational studies (Table 2). In this study, 95% is used as expected prevalence in calculating sample size, as carbapenemase production is the CRAB’s dominant cause. Considering three studies on molecular isolate typing in hospitals,[14–16] the confidence level equal to 95% and precision equal to 5%, the estimated minimum CRAB sample size was 73. Consequently, we excluded 14 articles due to small sample size. Another 14 studies on carbapenemase genoptyping were excluded for only reporting detection of Class D carbapenemases.

Carbapenemase characteristics Of the 29 studies included in this systematic review, 12 were from LAC, involving 11 countries and 17 were from 11 Chinese provinces. OXA-type carbapenemases were detected in all studies. In LAC, OXA-23, OXA-24, OXA-58 and OXA-72 genotypes were predominant, with respective prevalences of 0.73 (0.54–0.89), 0.06 (0.00–0.17), 0.03 (0.01–0.06) and 0.02 (0.00–0.06). In China, OXA-23, OXA-24 and OXA-72 were the most common, with respective prevalences of 0.91 (0.84–0.96), 0.03 (0.01– 0.08), 0.02 (0.00–0.05).

Metallobetalactamases were less frequent than OXAs and were detected in only two countries in the Latin American and Caribbean region, with NDM 0.01 (0.00–0.01) as the predominant genotype, and in six Chinese provinces, with four predominant genotypes: NDM 0.02 (0.00–0.04), VIM 0.07 (0.00–0.21), IPM 0.02 (0.00–0.06) and SIM 0.01 (0.00–0.03) (Table 3). Only one clinical isolate Class A carbapenemase producer (KPC) was found, and it was isolated in Colombia.

According to the I2 values, high heterogeneity was observed among studies and we consequently used a random-effects model for the meta-analysis. Egger tests (p >0.1) and funnel plots show the characteristic shape of the asymmetric dispersion (Table 3 and Figure 2).

Molecular typing characteristics In 17 of the 29 studies, MLST was performed on CRAB isolates. In total, 41 sequence types (STs) were identified: 16 in LAC and 26 in China. Clear geographical differences were observed in predominant ST frequencies: ST79, ST25, ST1 and ST15 were more common in LAC; while ST195, ST208, ST191, ST368 and ST369 were found more frequently in China. ST2 was found in both (Table 2 and Figure 3).

Carbapenemase types Antibiotic overuse has led to an increase in multi-drug–resistant Acinetobacter. More than 50% of Acinetobacter spp. isolates in the United States, South America, India and China are resistant to carbapenem antiobiotics.[46] This study verifies the high prevalence of OXAs in CRAB isolates in China, Latin America and the Caribbean. OXA-51–like carbapenemases (including OXA-51, 64, 65, 66, 68, 69, 70, 71, 78, 79, 80 and 82) occur naturally in A. baumannii.[47] OXA-24–like carbapenemases (including OXA-24, 25, 26, 40 and 72) have been found in both plasmid and chromosomal structures; OXA-58–like and OXA-23–like carbapenemases are encoded by plasmids,[48] which increases the probability of horizontal transmission. The plasmid-encoded carbapenemases OXA-23, OXA-24 and OXA-58 were the most frequently isolated carbapenemases in the two regions analyzed in this study. These results justify the non-inclusion of OXA-51 type carbapenemases, as their resistance to CRAB is intrinsic, and thus has little impact on amplifying carbapenem resistance in this species.

Carbapenemase OXA-72 was first identified in 2004 in an A. baumannii isolate from Thailand,[49] and subsequently detected in Brazil, Mexico, Ecuador, Peru, China and Europe.[27,43,45,50,51] PXA-231 and OXA-253 were identified in Brazil and Peru, respectively. Both belong to the OXA-143–like group. OXA-231 and OXA-253 were reported the first time in A. baumannii isolates from Brazil (in 2007 and 2014, respectively) and still appear mainly in that country.[52,53] The dissemination of this subgroup requires monitoring, as it has been described more recently in Iran (2017), Colombia (2017) and Peru (2018).[45,54,55]

Figure 1
Figure 1: Literature selection results (PRISMA)

CRAB: Carbapenemase resistant Acinetobacter baumannii; MDR: Multi-drug resistant; PRISMA: Preferred Reporting Items for Systematic Reviews and Meta-Analyses; XDR: Extensively drug-resistant

The data obtained in this review show that MBLs have a very low prevalence and are mainly of the NDM, VIM and IPM types. Five Chinese provinces reported MBLs; Hu Nan and Jian Xi provinces, in particular, have very high prevalence of this type of carbapenemases. In LAC, only Cuba and Colombia detected MBLs, both of which had very low prevalence rates. A meta-analysis of Iranian isolates reported a prevalence of 21.9% and 6.2% of OXA-24 and OXA-58 carbapenemase isolates, respectively, and higher prevalences of MBLs (IMP, 16.7%; VIM, 12.3% and NDM, 2.7%)[56] than those found in LAC and China. A study in Egypt reported a prevalence of 95.7% IMP, 7,1% VIM and 42.9% GIM in A. baumannii isolates.[57] The emergence and spread of MBL-producing A. baumannii strains has been reported in the United States, Canada, Europe, Japan, Australia, Africa and the Middle East.[58] The differences in OXA and MBL prevalence between countries is likely due to pressures of antimicrobial selection, horizontal transfer of carbapenemase genes by mobile genetic elements (plasmids) between species, propagation of clones carrying these genes or to a combination of all these factors.

Detected sequence types MLST is considered the gold standard for detecting bacterial sequence types and is highly useful in epidemiology. This review includes 17 studies based on MLST. Due to the great diversity in sequence types and the differences between countries and provinces, we only carried out a descriptive qualitative study on these articles (Figure 3). In the case of LAC, these studies mainly originated in South America (namely in Brazil, Peru, Argentina, Colombia, Chile, Bolivia, Ecuador, Paraguay and Uruguay). The most common sequence types in the region were ST79, ST25, ST1 and ST15. ST79 had the widest geographic spread, and was detected in Ecuador, Peru, Brazil, Paraguay, Uruguay and Argentina,[34,35,39,43,45] which implies greater current dissemination than had been reported earlier (in a review carried out in 2018).[59] ST25 was detected in Bolivia, Paraguay, Uruguay and Argentina,[39,43] and had been previously identified in Honduras (2012) and Brazil (2013).[60,61] ST1 was found in isolates from Peru, Brazil and Argentina,[39,44,45] and was the predominant Argentinian isolate. ST15 was detected in Ecuador, Chile and Brazil; it was associated with carbapenemase production (mainly OXA-23–like carbapenemases), and has had rapid dissemination, mainly in South America.[62]

Eight provinces in China conducted multilocus sequence studies using MLST; ST195 and ST208 were the most common. These two sequence types have been found in other regions of the world and tend to become the dominant STs once introduced.[63–65] A study of the clinical and molecular characteristics of CRAB-produced bacteremia in China showed clones ST195 and ST208 to be predominant, and bacteremia resulting from A. baumannii clone ST195 was associated with higher lethality.[66] Clones ST191, ST368 and ST369 are moderately prevalent in China and are more commonly found in Asia than the rest of the world. Hospital infection by A. baumannii clones ST191 and ST369 has also been reported in China and South Korea.[67,68] The STs that are the most common in China are rarely reported in LAC; only ST369 has been reported in Mexico in 2020.[69] This may be the result of differing clonal ancestries in both regions and selection pressure from different antimicrobial use habits.

ST2 was found in both regions (Peru in LAC and Liao Ning in China). ST2 is prevalent in some countries in Pacific Asia and Europe,[70–74] but has not been reported with any frequency in LAC in the last five years. Although this study found ST2 to be associated with OXA-72, other studies have described ST2 A. baumannii clones as mainly being producers of OXA-23.[74–76] ST2’s dissemination in LAC merits consideration.

This study has provided estimates of the prevalence of different types of carbapenemases in A. baumannii in LAC and China, and the geographical distribution of different circulating CRAB STs and supports adjustments to resistance surveillance programming and antimicrobial management.

Study limitations There were some Latin American and Caribbean countries and Chinese provinces that produced no studies that met our selection criteria. Consequently, there is no information on carbapenemase-producing CRAB strain genotypes in these regions. Additionally, most studies do not detect Class A carbapenemases. This exclusion may have led to an overrepresentation of other carbapenemase classes and this preferential study of certain classes may have introduced bias. Finally, while the Egger test in not statistically significant and publication bias is unlikely, there is considerable heterogeneity between studies, as suggested by the asymmetric and sparse shape of the funnel plots. This could be due to insufficient sample size in the included studies, or to some variation (either geographical or temporal) in the strains or other methodological aspects such as differences in sample inclusion and exclusion criteria, among other factors.

Table 2
Table 2: Studies included in the systematic review

All were cross-sectional studies

^& Quality criteria: 1. The sample was appropriate to address the target population, 2. The sample was obtained using an adequate method, 3. The sample size was adequate 4. Participants and the context are described in detail 5. Data analysis was carried out with sufficient coverage of the identified sample 6. Effective methods were used to identify diseases or health problems 7. The sample was measured using standard and reliable methods for all participants 8. The statistical analysis was appropriate 9. Response rate was adequate or low response rate was adequately managed.n number of times the sequence was foundN total isolates studiedNA Not applicable (detection not performed)ND Not detectedX did not meet the requirement– met the requirement

Table 3
Table 3: Meta-analysis of carbapenemase genotypes in China, Latin America and the Caribbean

MBLs Metallobetalactamasesn Number of isolates with the genotypeN Total number of carbapenem-resistant A. baumannii isolatesNumber of studies number of studies in which carbapenemases were identified

Figure 2
Figure 2: Forest plot and funnel plot for OXA-23 carbapenemase prevalence in China, Latin America and the Caribbean

A: OXA-23 carbapenemase prevalence in China

B: OXA-23 carbapenemase prevalence in Latin America and the Caribbean

Figure 3
Figure 3: Acinetobacter baumannii sequence type (ST) geographic distribution in China, Latin America and the Caribbean

A. baumannii resistance to carbapenem antibiotics is a global threat, and there is increasing diffusion of carbapenem-producing A. baumannii isolates and increasing geographic ST variation. Enzymes produced by regional isolates are generally very similar, while differences in STs are observed between China, Latin America and the Caribbean. Different regions have different epidemic CRAB strains, and it is important to consider local epidemiology in order to best tailor patient treatment. Studying circulating enzymes, clones and genetic lines facilitates understanding of region-specific resistance mechanisms.

Multidisciplinary collaboration is necessary (microbiologists, clinicians, epidemiologists and specialists in preventive medicine with experience in infection control), and will allow for early detection and study of resistance using molecular methods; adequate treatment, taking into consideration the patient’s clinical status, common circulating strains, and infection characteristics; and adoption of epidemiological measures aimed at multi-drug–resistant infection prevention and control, reducing transmission at community- and hospital levels. A multidisciplinary approach can provide better results in managing a complex, multifactorial problem with major implications for public health.

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