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Profile of outer membrane proteins of carbapenem-resistant Gram-negative bacilli in Ghana

BMC Research Notes volume 18, Article number: 49 (2025) Cite this article

Abstract

Objective

Carbapenem resistance is a major global health threat, but insights on its molecular determinants are scanty in sub-Saharan Africa, the predominant global antimicrobial resistance hotspot. This study aimed to profile outer membrane proteins (OMPs) of 111 carbapenem-resistant Gram-negative bacteria recovered from a broad spectrum of clinical specimens from Ghana.

Results

The OMPs of Pseudomonas aeruginosa produced decreased amounts of OprD or the porin was completely lost, except in 5.9% (n = 3) of the isolates which had high-level porins. For Acinetobacter baumannii, 96.8% (n = 30) expressed loss of OprF. One carbapenemase non-PCR-positive isolate with high-level porin expression was observed. In A. baumannii, the major and significant band on SDS-PAGE was ~ 35 kDa. There were substantial numbers of unrelated porin expression among the isolates. Particularly, OmpC/F or OmpK35/37 expression was deficient. Sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE) analysis for Escherichia coli, Klebsiella aerogenes, Klebsiella pneumoniae, and other Enterobacterales had OmpC and OmpF absent or markedly reduced compared to the control strains. Overall, porin loss was a major mechanism underlying carbapenem resistance among the isolates, suggesting that in carbapenem-resistant organisms that seem to lack known carbapenem resistance genes, porin loss may be the underlying carbapenem resistance mechanism.

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Introduction

Carbapenem-resistant Gram-negative bacteria (CR-GNB) have emerged as major public health threats worldwide, leading to increased morbidity, mortality, and healthcare costs [1,2,3]. In sub-Saharan Africa, the predominant global hotspot for antimicrobial resistance (AMR), AMR surveillance studies have rarely evaluated carbapenem resistance, which has become prevalent in the region [4,5,6]. Most of the few that have done so merely reported on carbapenem resistance prevalence, with little information on the molecular basis of the resistance [7, 8]. Those that studied the molecular epidemiology of carbapenem resistance mainly focused on the occurrence of carbapenemase genes among the isolates [1,2,3]. The involvement of outer membrane proteins (OMPs) in the resistance traits, although important, have been largely overlooked in these studies.

OMPs, also known as porins, are major cell wall components of Gram-negative bacteria [9]. Among other things, they help maintain bacterial membrane integrity, facilitate adhesion to host mucosa, biofilm formation, and passage of molecules (including iron and antibiotics) across the bacterial cell membranes [10,11,12,13]. They are also crucial to perpetuation of AMR in Gram-negative bacteria, through gene expression- and structural rearrangement-induced reduced permeability [14,15,16]. Besides, owing to their abundance on the bacterial surface, outer membrane proteins could be exploited in the design of vaccines and novel and improved antimicrobials [17].

The goal of the current study was to characterise OMPs of CR-GNB recovered from a broad spectrum of 3,840 clinical specimens collected in a three-year multicentre AMR surveillance in Ghana [1]. We have previously reported on AMR profiles and distribution of carbapenemase genes [1], as well as genetic relatedness [2] among these isolates. Thus, this study adds an underexplored angle to the discussion on carbapenem resistance from an AMR-affected region where sparse insights on carbapenem resistance have emanated from.

Materials and methods

Details of the CR isolates and previous analyses

In total, 3,840 clinical specimens collected from four major hospitals (Volta Regional Hospital [in the Volta Region], AngloGold Mines Hospital [in the Ashanti Region], Effia-Nkwanta Hospital [in the Western Region], and the Korle Bu Teaching Hospital [in the Greater Accra Region]) were evaluated for AMR and screened for beta-lactamase and carbapenemase genes and beta-lactamase and carbapenemase production [1].

The specimens yielded 111 CR isolates, mainly Pseudomonas aeruginosa (51), Acinetobacter baumannii (31), Escherichia coli (12), Pseudomonas putida (7), Klebsiella pneumoniae (3), Enterobacter cloacae (3), and one each of Sphingomonas paucimobilis, Shigella sonnei, Providencia stuartii, and Cronobacter sakazakii; the OMP profiles of these were evaluated in this study.

Outer membrane protein analysis of the CR isolates

In total, 111 non-duplicated CR isolates from 55 male and 56 female patients aged between 3 days and 91 years were investigated. A recent study by Sugawara & Nikaido [18] claimed that the major proteins in the outer membrane of Acinetobacter baumannii, a non-fermenter isolate that belongs to the low-permeability trimeric porin group, but has been found to equate to Escherichia coli OmpF/OmpC, and also shares close homology to Pseudomonas aeruginosa OprF and Escherichia coli OmpA. Therefore, in-house MBL-positive (VIM-positive) and wild-type Pseudomonas aeruginosa control strains from the Sheffield Hallam University (SHU) collection were included and used for the study analysis of OMPs. Two methods, with some modifications, were employed separately for organisms in the Enterobacteriaceae family and Acinetobacter species [19], and for Pseudomonas species [20], due to structural differences. Briefly, bacterial cultures were grown aerobically at 37 °C in Mueller-Hinton broth for six hours, then harvested by centrifugation. The pellet was resuspended in phosphate-buffered saline with lysozyme, sonicated to disrupt the cells, and centrifuged multiple times to remove whole cells and cell debris. The supernatant was then centrifuged to pellet the cell membranes, which were resuspended in a detergent solution to extract the outer membrane vesicles. The OMPs were harvested by centrifugation, washed to remove the detergent, and stored at -20 °C for later use.

Sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE)

Resolving gels were made at a 12% concentration of acrylamide. Polymerisation of acrylamide was prepared by adding 16 µl N, N,N’,N’-tetramethylethylenediamine (TEMED) (Bio-Rad); the gel solution was cast between two glass plates in the apparatus and then layered with isopropanol equilibrated with saturated aqueous sodium chloride. Once gel polymerisation was complete, the saturated isopropanol was removed and the area at the top of the gel was dried with filter paper. The stacking gels were made containing 6% acrylamide concentration. Acrylamide polymerisation was initiated by adding 10 µl TEMED; the gel solution was overlaid on the resolving gel, and 15-well comb was pushed into the gel to create sample wells. After complete polymerisation, the gel apparatus was assembled in the appropriate tank and covered in 1x SDS-PAGE running buffer made from 10x tris-glycine-SDS buffer in 500 ml of deionised water at pH 8.3; Tris base 15.0 g, Glycine 72.0 g, SDS 5.0 g. The crude OMP samples were mixed with SDS-PAGE loading buffer at a 6:1 ratio, boiled for 5–10 min, and loaded into the wells created in the gel. Electrophoresis was set at 130 volts per centimetre until the blue colour in the loading dye in the sample buffer had reached the end of the gel (approximately 45 to 60 min). OMPs were visualised by staining the gel for 1 h with Coomassie brilliant blue R solution, and then destained with destain solution overnight and 2 other changes of destain solution over 2 to 3 h until the gel was clear. OMP bands were compared with standard pre-stained protein ladder (Thermo-Scientific, Leicestershire, UK).

The analysis of the OMPs on SDS-PAGE of all the CR isolates were specifically compared with Pseudomonas aeruginosa control strains with or without OprD (~ 44 kDa) expression which affects susceptibility to carbapenems.

Table 1 Carbapenem MIC levels and major porins in carbapenem-resistant isolates
Full size table

Ethical approval

The study was approved by the Ethical Committee of the School Biomedical & Allied Health Sciences, College of Health Sciences, University of Ghana (Identification Number: SAHS-ET/SAHS/PSM/ML/05/AA/26A/2012–2013). The data and the bacteria were analysed anonymously, and hence informed consent was not applicable.

Results

Results summary of previous investigations on the CR isolates

Among the 111 isolates, 58% (n = 64) were meropenem-resistant, 66.7% (n = 74) were imipenem-resistant, and 75% (n = 83) were doripenem-resistant, with 58% (n = 64) of the isolates having ≥ 32 mg/mL minimum inhibitory concentration (MIC) levels [1]. Also, 23.4% (n = 26) of the isolates were demonstrated as carbapenemase-positive by polymerase chain reaction (PCR), and the highest carbapenemase gene prevalence was from Acinetobacter spp. (9 NDM-1-positives) and P. aeruginosa (2 postive for NDM-1 and 7 positive for VIM-1), followed by E. coli (3 positive for NDM-1), K. pneumoniae (2 positive for OXA-48), one VIM-1-positive P. putida isolate, and one each NDM-1-positive P. stuartii and S. sonnei, respectively [1].

Porin expression in the CR isolates

There were different expressions of porins for all CR isolates investigated (Fig. 1). The OMPs of Pseudomonas aeruginosa produced decreased amounts of OprD or the porin was completely lost, except the 5.9% (3/51) with high levels of porin in them (Table 1). Most of the isolates which had loss of porins were among the presumptive carbapenemase non-PCR positives.

For Acinetobacter baumannii, 96.8% (30/31) expressed loss of OprF in them, which included the NDM-1-positive producers. One carbapenemase non-PCR-positive isolate with high-level expression of porin was observed. Of all the Acinetobacter baumannii isolates analysed, the major and significant band on SDS-PAGE was ~ 35 kDa.

There were substantial numbers of unrelated porin expression. In particular, OmpC/F or OmpK35/37 expression was deficient. SDS-PAGE analysis for Escherichia coli, Klebsiella aerogenes, Klebsiella pneumoniae, and others in the Enterobacteriaceae group had OmpC and OmpF absent or markedly reduced at Bands 35 kDa and 37 kDa, respectively, compared to control strains.

Fig. 1
figure 1

Representative outer membrane proteins of control strains and carbapenem-resistant isolates on SDS-PAGE. Note M = Protein marker in kDa; C1 = Control SHU 2048 VIM-positive Pseudomonas aeruginosa strain; C2 = Control SHU 2054 MBL-negative Pseudomonas aeruginosa strain; 85–111 represent sample numbers; OprM/J (48/49 kDa) = Major intrinsic multidrug efflux proteins; OprD (44 kDa) = Specific for β-lactam imipenem resistance; OprF (35 kDa) = Major porin for structural stabilisation of peptidoglycan; OprH/G (22/23 kDa) = Polycationic antimicrobial uptake and putatively in iron uptake. Full-length gels are presented in Supplementary Fig. 1

Full size image

Discussion

This study profiled OMPs among a collection of carbapenem-resistant isolates from Ghana. OMPs of the Pseudomonas aeruginosa isolates produced decreased amounts of OprD or the porin was completely lost, except for 5.9% (3 out of 51) which had high levels of porin in them. The majority of the isolates which had loss of porins were among the presumptive carbapenemase non-PCRpositives. It is worth mentioning that the effect of OprD reduction or loss could be one of the mechanisms that explain the ease with which Pseudomonas aeruginosa is known to become resistant. High-level production of β-lactamase activity by nitrocefin assays were prevalent in all the CR isolates studied. The effect and presence of these non-plasmid determinant enzymes may contribute significantly to carbapenem resistance coupled with the loss of OprD gene [21].

Essentially, in most multidrug-resistant Pseudomonas aeruginosa, isolates chromosomally encode resistance mechanisms in association with hyperexpression of AmpC, overproduction of the MexAB efflux system, or both, without harbouring a carbapenem resistance gene that could inactivate the OprD gene. The effect of these resistance mechanisms and the presence of β-lactamase enzymes may have resulted in the high number of carbapenemase non-PCR positives. According to Yang et al. [22], porins play a significant role in increasing Gram-negative bacterial resistance to carbapenems. Importantly, presence of ESBL- or AmpC-type enzymes is an essential element for resistance among Enterobacteriaceae and non-fermenting Pseudomonas species. This recognition was also observed in CR isolates in this study. Thus, all the 7 VIM-1-producing Pseudomonas aeruginosa isolates were carriers of TEM-1 and SHV-1 enzymes; 6 carbapenemase non-PCR positives out of 7 Pseudomonas putida isolates including the only VIM-1-positive isolate had reduced OprD or loss of porin by the SDS-PAGE assessment in this study. Pirnay et al. [23] emphasised that the major determinant of resistance to imipenem, particularly, in Pseudomonas aeruginosa in the absence of MBL could be mutational change in the oprD gene. It is worth noting that most Pseudomonas aeruginosa carbapenemase non-PCR positives, including other CR isolates, showed decreased production of the oprD gene, which could be mutation-driven resistance. This phenomenon was observed on the electrophoretic patterns of the SDS-PAGE analysis with a reduction or loss of outer membrane porin D.

A study by Fusté et al. [24], also on multidrug-resistant Pseudomonas aeruginosa, revealed a similar reduction of the OprD, the main uptake of carbapenems, while in another study from Brazil [25], markedly reduced OprD expressions were observed in MBL-negative Pseudomonas isolates. This is in agreement with this present study, which has demonstrated that OprD loss and VIM-1 production could be one of the possible mechanisms emerging in MBL negative Pseudomonas aeruginosa from Ghanaian hospitals.

For Acinetobacter baumannii, 96.8% expressed OprF loss, which included the NDM-1-positive producers. One carbapenemase non-PCR positive isolate with high-level porin expression was observed, although the mechanism of resistance remains unclear. It should be mentioned that the selectivity of the outer membrane permeability barrier is different for organisms such as Acinetobacter species or Pseudomonas aeruginosa compared with those in the Enterobacteriaceae group. The OmpAb of ~ 40 kDa, an OMP of Acinetobacter baumannii accounts for approximately 30–40% of the total OMPs [26], as compared to that of Pseudomonas aeruginosa. Li et al. [27] emphasised that these organisms do not produce the classical Escherichia coli-type trimeric porins that provide an increased influx of small drugs. The main nonspecific porin in these organisms is a homology of Escherichia coli OmpA, which functions by adding structural fitness usually connected to the outer membrane underlying peptidoglycan [27]. Acinetobacter baumannii has a close homology to Escherichia coli OmpA, an antibiotic selection and permeant porin [28] and Pseudomonas aeruginosa OprF, which is the major OMP [18]. Of all the Acinetobacter baumannii isolates, the major and significant band on SDS-PAGE was ~ 35 kDa, strongly suggesting that the outer membrane of Acinetobacter baumannii contains reduced amounts of low-permeability porins, a situation similar to the OprF of Pseudomonas aeruginosa.

The deficiency in OmpC/F or OmpK35/37 expression could be due to mutation and the presence of a large collection of non-fermenters highly resistant to cephalosporins and carbapenems studied, mainly, Pseudomonas aeruginosa and Acinetobacter baumannii isolates. These organisms have mutational complexities, structural differences, diminishing permeability or altered porin expressions compared to Escherichia coli and Klebsiella pneumoniae which were relatively few in numbers in this study.

Other membrane proteins were analysed and also compared with the Pseudomonas aeruginosa control strains since the porins are closely related to the absence or presence of OmpA, OmpAb, OmpC, and OmpF porins which have similar resistance to β-lactams and other antimicrobials. The SDS-PAGE analysis for Escherichia coli, Klebsiella aerogenes, Klebsiella pneumoniae, and others in the Enterobacteriaceae group had OmpC and OmpF absent or markedly reduced at Bands 35 kDa and 37 kDa, respectively, compared to control strains. The presence of OmpA in most of the Enterobacteriaceae group, for instance, in Klebsiella aerogenes, is the major source of stabilisation within the bacterial membrane, which leads to a reduction in the expression of OmpC and OmpF porins, and eventually a reduced susceptibility to β-lactams and other antimicrobials [29, 30]. Previous studies explained that the level of expression of OmpC and OmpF porins may not necessarily control the permeability of the outer membrane to nitrogen and glucose uptake under nutrient restriction, but may also be due to differential control by the concentration of certain antimicrobials within the environment [31, 32]. These studies are in agreement with this present study analysis which accounted for the high number of carbapenemase non-PCR positives.

Limitation

The study is limited by the few number of isolates evaluated and the age of the data.

Conclusion

In all, porin loss was demonstrated as one of the possible major mechanisms underlying the carbapenem resistance trait of the investigated isolates. Thus, in carbapenem-resistant organisms that do not seem to harbour known carbapenem resistance genes, porin loss may be the underlying carbapenem resistance mechanism.

Data availability

The datasets used and/or analysed during the current study are not publicly available due to ethical restrictions, but are available from the corresponding author on reasonable request.

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Acknowledgements

We are grateful to the laboratories of the hospitals in Ghana that contributed bacterial isolates to this study as well as the technical support provided by the Microbiology Laboratory of Sheffield Hallam University. This study is in part based on work performed as part of F.S.C.’s doctoral research carried out at Sheffield Hallam University, UK, in collaboration with the University of Ghana and the Korle Bu Teaching Hospital in Accra, Ghana.

Funding

This research was supported with funds from the University of Ghana’s College of Health Sciences Endowment Fund.

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Authors and Affiliations

  1. Department of Medical Laboratory Sciences, School of Biomedical & Allied Health Sciences, College of Health Sciences, University of Ghana, Accra, Ghana

    Francis S. Codjoe

  2. Biomolecular Science Research Centre, Sheffield Hallam University, Sheffield, England, UK

    Francis S. Codjoe

  3. Department of Medical Microbiology, University of Ghana Medical School, Korle Bu, P. O. Box KB 4236, Accra, 00233, Ghana

    Fleischer C. N. Kotey & Eric S. Donkor

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  1. Francis S. Codjoe
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Contributions

Conceptualisation, F.S.C. and E.S.D.; methodology, F.S.C., F.C.N.K., and E.S.D.; software, F.S.C.; validation, E.S.D. and F.S.C.; formal analysis, F.S.C., F.C.N.K., and E.S.D.; investigation, F.S.C., F.C.N.K., and E.S.D.; resources, E.S.D. and F.S.C.; data curation, F.S.C., E.S.D., and F.C.N.K.; writing—original draft preparation, F.S.C., E.S.D., and F.C.N.K.; writing—review and editing, F.S.C., E.S.D., and F.C.N.K.; visualisation, F.S.C., E.S.D., and F.C.N.K.; supervision, E.S.D.; project administration, F.S.C. and E.S.D.; funding acquisition, F.S.C. and E.S.D. All authors have read and agreed to the published version of the manuscript.

Corresponding author

Correspondence to Eric S. Donkor.

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Ethics approval and consent to participate

The study was approved by the Ethical Committee of the School Biomedical & Allied Health Sciences, College of Health Sciences, University of Ghana (Identification Number: SAHS-ET/SAHS/PSM/ML/05/AA/26A/2012–2013). Consent to participate was not applicable in this study, as the studied bacteria and their associated dataset had been anonymised.

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The authors declare no competing interests.

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Codjoe, F.S., Kotey, F.C.N. & Donkor, E.S. Profile of outer membrane proteins of carbapenem-resistant Gram-negative bacilli in Ghana. BMC Res Notes 18, 49 (2025). https://doiorg.publicaciones.saludcastillayleon.es/10.1186/s13104-024-07070-6

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  • Published:

  • DOI: https://doiorg.publicaciones.saludcastillayleon.es/10.1186/s13104-024-07070-6

Keywords

BMC Research Notes

ISSN: 1756-0500

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