High-level and novel mechanisms of carbapenem resistance in Gram-negative bacteria from tertiary hospitals in Nigeria

A systematic review and meta-analysis of carbapenem-resistant Enterobacteriaceae in West Africa

BACKGROUND

In Africa, the problem of carbapenem-resistant Enterobacteriaceae (CRE) is aggravated by many factors. This systematic review attempted to describe the current status of the molecular epidemiology of carbapenem resistance in West Africa (WA).

METHODS

Articles published from 16 West African countries on the molecular epidemiology of carbapenem resistance were reviewed. An extensive literature search was carried out in PubMed, Scopus, Web of Science, and African Journals Online (AJOL) using specific keywords. The meta-analysis and forest plots of major pathogens and carbapenem resistance genes were done using the Open Meta-Analyst, Task Order # 2 software. The data were analysed in binary random model effects by the DerSimonian-Laird method at a 95% confidence interval.

RESULTS

Of the 431 articles found in our initial search, 60 (13.92%) were considered suitable for inclusion. Only seven of the 16 West African countries formed part of the analysis, Nigeria (23/60), Ghana (19/60), Burkina Faso (7/60), Senegal (6/60), Benin (2/60), Mali (2/60), and Togo (1/60). Also, 80% (48/60) of the studies used clinical samples, 16.67% (10/60) used environmental samples, and 3.33% (2/60) used animal samples. The average prevalence was highest in Acinetobacter baumannii (18.6%; 95% CI = 14.0-24.6, I2 = 97.9%, p < 0.001), followed by Pseudomonas aeruginosa (6.5%; 95% CI = 3.1-13.4, I2 = 96.52%, p < 0.001), Klebsiella pneumoniae (5.8%; 95% CI = 4.2-7.9, I2 = 98.06%, p < 0.001) and Escherichia coli (4.1%; 95% CI = 2.2-7.7, I2 = 96.68%, p < 0.001). The average prevalence of the blaNDM gene was 10.6% (95% CI = 7.9-14.3, I2 = 98.2%, p < 0.001), followed by 3.9% (95% CI: 1.8-8.3, I2 = 96.73%, p < 0.001) for blaVIM and 3.1% (95% CI: 1.7-5.8, I2 = 91.69%, p < 0.001) for blaOXA-48.

CONCLUSION

In West Africa, K. pneumoniae, E. coli, A. baumannii, and P. aeruginosa are the main CRE with blaNDM, blaVIM, and blaOXA-48 being the predominant carbapenem resistance genes. In view of these results, ongoing CRE surveillance combined with antimicrobial stewardship improved, laboratory detection methods, and adherence to infection control practices will be needed to control the spread of CRE.

Carbapenemase producing Gram negative bacteria: Review of resistance and detection methods

Gram negative bacilli that are carbapenem resistant have emerged and are spreading worldwide. Infections caused by carbapenem resistant isolates posses a significant threat due to their high morbidity and mortality rates. Carbapenemases production by multi-drug resistant pathogens severely restricts treatment choices for illnesses caused by bacteria that are resistant to both carbapenems and majority of β-lactam antibiotics. Various phenotypic and genotypic methods for identification can distinguish between different classes of carbapenemase and identify pathogens that are resistant to carbapenems. The establishment of a quick, accurate and reliable test for identifying the clinical strains that produce the carbapenemase enzyme is essential for optimum diagnosis of microbial pathogens and management of the global rise in the prevalence of carbapenemase producing bacterial strains. The aim of this review was to summarize the mechanisms of carbapenem resistance and to provide an overview of different carbapenemase detection methods for carbapenem resistant Gram negative bacilli.

The Importance of Carbapenemase-Producing Enterobacterales in African Countries: Evolution and Current Burden

Antimicrobial resistance (AMR) is a worldwide healthcare problem. Multidrug-resistant organisms (MDROs) can spread quickly owing to their resistance mechanisms. Although colonized individuals are crucial for MDRO dissemination, colonizing microbes can lead to symptomatic infections in carriers. Carbapenemase-producing Enterobacterales (CPE) are among the most important MDROs involved in colonizations and infections with severe outcomes. This review aimed to track down the first reports of CPE in Africa, describe their dissemination throughout African countries and summarize the current status of CRE and CPE data, highlighting current knowledge and limitations of reported data. Two database queries were undertaken using Medical Subject Headings (MeSH), employing relevant keywords to identify articles that had as their topics beta-lactamases, carbapenemases and carbapenem resistance pertaining to Africa or African regions and countries. The first information on CPE could be traced back to the mid-2000s, but data for many African countries were established after 2015-2018. Information is presented chronologically for each country. Although no clear conclusions could be drawn for some countries, it was observed that CPE infections and colonizations are present in most African countries and that carbapenem-resistance levels are rising. The most common CPE involved are Klebsiella pneumoniae and Escherichia coli, and the most prevalent carbapenemases are NDM-type and OXA-48-type enzymes. Prophylactic measures, such as screening, are required to combat this phenomenon.

Characterization of Beta-Lactamase and Fluoroquinolone Resistance Determinants in Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa Isolates from a Tertiary Hospital in Yola, Nigeria

Infections due to antimicrobial resistant gram-negative bacteria cause significant morbidity and mortality in sub-Saharan Africa. To elucidate the molecular epidemiology of antimicrobial resistance in gram-negative bacteria, we characterized beta-lactam and fluoroquinolone resistance determinants in Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa isolates collected from November 2017 to February 2018 (Period 1) and October 2021 to January 2022 (Period 2) in a tertiary medical center in north-eastern Nigeria. Whole genome sequencing (WGS) was used to identify sequence types and resistance determinants in 52 non-duplicate, phenotypically resistant isolates. Antimicrobial susceptibility was determined using broth microdilution and modified Kirby-Bauer disk diffusion methods. Twenty sequence types (STs) were identified among isolates from both periods using WGS, with increased strain diversity observed in Period 2. Common ESBL genes identified included blaCTX-M, blaSHV, and blaTEM in both E. coli and K. pneumoniae. Notably, 50% of the E. coli in Period 2 harbored either blaCTX-M-15 or blaCTX-M-1 4 and phenotypically produced ESBLs. The blaNDM-7 and blaVIM-5 metallo-beta-lactamase genes were dominant in E. coli and P. aeruginosa in Period 1, but in Period 2, only K. pneumoniae contained blaNDM-7, while blaNDM-1 was predominant in P. aeruginosa. The overall rate of fluoroquinolone resistance was 77% in Period 1 but decreased to 47.8% in Period 2. Various plasmid-mediated quinolone resistance (PMQR) genes were identified in both periods, including aac(6')-Ib-cr, oqxA/oqxB, qnrA1, qnrB1, qnrB6, qnrB18, qnrVC1, as well as mutations in the chromosomal gyrA, parC and parE genes. One E. coli isolate in Period 2, which was phenotypically multidrug resistant, had ESBL blaCTX-M-15, the serine carbapenemase, blaOXA-181 and mutations in the gyrA gene. The co-existence of beta-lactam and fluoroquinolone resistance markers observed in this study is consistent with widespread use of these antimicrobial agents in Nigeria. The presence of multidrug resistant isolates is concerning and highlights the importance of continued surveillance to support antimicrobial stewardship programs and curb the spread of antimicrobial resistance.

Genotypic Characterization of Carbapenem-Resistant Klebsiella pneumoniae Isolated from an Egyptian University Hospital

Globally, Klebsiella pneumoniae (K. pneumoniae) has been identified as a serious source of infections. The objectives of our study were to investigate the prevalence of multidrug-resistant (MDR) K. pneumoniae in Tanta University Hospitals, Gharbia Governorate, Egypt; characterize their carbapenem resistance profiles; and identify their different capsular serotypes. We identified and isolated 160 (32%) K. pneumoniae from 500 different clinical samples, performed antimicrobial susceptibility testing, and then used multiplex PCR to detect carbapenemase genes and capsular serotypes K1, K2, K3, K5, K20, K54, and K57. We detected phenotypic carbapenem resistance in 31.3% (50/160) of the isolates; however, molecular assays revealed that 38.75% (62/160) of isolates were carrying carbapenemase-encoding genes. Generally, blaOXA-48 was the prevalent gene (15.5%), followed by blaVIM (15%), blaIMP (7.5%), blaKPC (4%), and blaNDM (3.8%). BlaVIM and blaOXA-48 correlated with phenotypic resistance in 91.67% and 88% of the isolates that harbored them, respectively. Capsular typing showed that the most prevalent pathotype was K1 (30.6%), followed by K57 (24.2%), K54 (19.35%), K20 (9.67%), and K2 (6.45%). A critical risk to community health is posed by the high incidence of multidrug-resistant (MDR) virulent K. pneumoniae isolates from our hospital, and our study examines this pathogen's public health and epidemiological risks.

Antibiotic resistance genes in the gut microbiota of mothers and linked neonates with or without sepsis from low- and middle-income countries

Early development of the microbiome has been shown to affect general health and physical development of the infant and, although some studies have been undertaken in high-income countries, there are few studies from low- and middle-income countries. As part of the BARNARDS study, we examined the rectal microbiota of 2,931 neonates (term used up to 60 d) with clinical signs of sepsis and of 15,217 mothers screening for bla_CTX-M-15, bla_NDM, bla_KPC and bla_OXA-48-like genes, which were detected in 56.1%, 18.5%, 0% and 4.1% of neonates’ rectal swabs and 47.1%, 4.6%, 0% and 1.6% of mothers’ rectal swabs, respectively. Carbapenemase-positive bacteria were identified by MALDI-TOF MS and showed a high diversity of bacterial species (57 distinct species/genera) which exhibited resistance to most of the antibiotics tested. Escherichia coli, Klebsiella pneumoniae and Enterobacter cloacae/E. cloacae complex, the most commonly found isolates, were subjected to whole-genome sequencing analysis and revealed close relationships between isolates from different samples, suggesting transmission of bacteria between neonates, and between neonates and mothers. Associations between the carriage of antimicrobial resistance genes (ARGs) and healthcare/environmental factors were identified, and the presence of ARGs was a predictor of neonatal sepsis and adverse birth outcomes.

Analysis of gut microbiota of mothers and its neonates—as part of the BARNARDS study—reveals associations between β-lactamase gene carriage and neonatal sepsis risk in low-income settings.

Beta-lactamase resistance genes in Enterobacteriaceae from Nigeria

Background

Beta-lactamase genes are one of the most important groups of antimicrobial resistance genes in human and animal health. Therefore, continuous surveillance of this group of resistance genes is needed for a better understanding of the local epidemiology within a country and global dissemination.

Aim

This review was carried out to identify different beta-lactamase resistance genes reported in published literature from Nigeria.

Methods

Systematic review and meta-analysis was carried out on eligible Nigerian articles retrieved from electronic literature searches of PubMed^®, African Journals Online, and Google Scholar published between January 1990 and December 2019. The Preferred Reporting Items for Systematic Reviews and Meta-Analyses method was adopted to facilitate clarity and transparency in reporting review findings.

Results

Fifty-seven articles were included. All beta-lactamases reported were detected from Gram-negative bacteria, particularly from Enterobacteriaceae. Thirty-six different beta-lactamase genes were reported in Nigeria. These genes belong to the narrow-spectrum, AmpC, extended-spectrum and carbapenemase beta-lactamase resistance genes. The pooled proportion estimate of extended-spectrum beta-lactamase genes in Nigeria was 31% (95% confidence interval [CI]: 26% – 36%, p < 0.0001), while the estimate of the bla_CTX-M-15 gene in Nigeria was 46% (95% CI: 36% – 57%, p < 0.0001). The proportion estimate of AmpC genes was 32% (95% CI: 11% – 52%, p < 0.001), while the estimate for carbapenemases was 8% (95% CI: 5% – 12%, p < 0.001).

Conclusion

This study provides information on beta-lactamase distribution in Nigeria. This is necessary for a better understanding of molecular epidemiology of clinically important beta-lactamases, especially the extended-spectrum beta-lactamases and carbapenemases in Nigeria.

Genetic support of carbapenemases: a One Health systematic review and meta-analysis of current trends in Africa

Antimicrobial resistance (AMR) is a public health threat globally. Carbapenems are β-lactam antibiotics used as last-resort agents for treating antibiotic-resistant infections. Mobile genetic elements (MGEs) play an important role in the dissemination and expression of antimicrobial resistance genes (ARGs), including the mobilization of ARGs within and between species. The presence of MGEs around carbapenem-hydrolyzing enzymes, called carbapenemases, in bacterial isolates in Africa is concerning. The association between MGEs and carbapenemases is described herein. Specific plasmid replicons, integrons, transposons, and insertion sequences were found flanking specific and different carbapenemases across the same and different clones and species isolated from humans, animals, and the environment. Notably, similar genetic contexts have been reported in non-African countries, supporting the importance of MGEs in driving the intra- and interclonal and species transmission of carbapenemases in Africa and globally. Technical and budgetary limitations remain challenges for epidemiological analysis of carbapenemases in Africa, as studies undertaken with whole-genome sequencing remained relatively few. Characterization of MGEs in antibiotic-resistant infections can deepen our understanding of carbapenemase epidemiology and facilitate the control of AMR in Africa. Investment in genomic epidemiology will facilitate faster clinical interventions and containment of outbreaks.

Concurrent Resistance to Carbapenem and Colistin Among Enterobacteriaceae Recovered From Human and Animal Sources in Nigeria Is Associated With Multiple Genetic Mechanisms

Resistance to last resort drugs such as carbapenem and colistin is a serious global health threat. This study investigated carbapenem and colistin resistance in 583 non-duplicate Enterobacteriaceae isolates utilizing phenotypic methods and whole genome sequencing (WGS). Of the 583 isolates recovered from humans, animals and the environment in Nigeria, 18.9% (110/583) were resistant to at least one carbapenem (meropenem, ertapenem, and imipenem) and 9.1% (53/583) exhibited concurrent carbapenem-colistin resistance. The minimum inhibitory concentrations of carbapenem and colistin were 2–32 μg/mL and 8 to >64 μg/mL, respectively. No carbapenem resistant isolates produced carbapenemase nor harbored any known carbapenemase producing genes. WGS supported that concurrent carbapenem-colistin resistance was mediated by novel and previously described alterations in chromosomal efflux regulatory genes, particularly mgrB (M1V) ompC (M1_V24del) ompK37 (I70M, I128M) ramR (M1V), and marR (M1V). In addition, alterations/mutations were detected in the etpA, arnT, ccrB, pmrB in colistin resistant bacteria and ompK36 in carbapenem resistant bacteria. The bacterial isolates were distributed into 37 sequence types and characterized by the presence of internationally recognized high-risk clones. The results indicate that humans and animals in Nigeria may serve as reservoirs and vehicles for the global spread of the isolates. Further studies on antimicrobial resistance in African countries are warranted.

Characterization of carbapenem-resistant gram-negative bacterial isolates from Nigeria by whole genome sequencing

This study characterized the mechanisms of carbapenem resistance in gram-negative bacteria isolated from patients in Yola, Nigeria. Whole genome sequencing (WGS) was performed on 66 isolates previously identified phenotypically as carbapenem-non-susceptible. The patterns of beta-lactamase resistance genes identified were primarily species-specific. However, bla_NDM-7 and bla_CMY-4 were detected in all Escherichia coli and most Providencia rettgeri isolates; bla_NDM-7 was also detected in 1 Enterobacter cloacae. The E. coli and E. cloacae isolates also shared bla_OXA-1, while bla_OXA-10 was found in all P. rettgeri, one Pseudomonas aeruginosa and 1 E. coli. Except for Stenotrophomonas maltophilia isolates, which only contained bla_L1, most species carried multiple beta-lactamase genes, including those encoding extended-spectrum beta-lactamases, AmpC and OXA in addition to a carbapenemase gene. Carbapenemase genes were either class B or class D beta-lactamases. No carbapenemase gene was detected by WGS in 13.6% of isolates.

Prevalence of pathogenic Klebsiella pneumoniae based on PCR capsular typing harbouring carbapenemases encoding genes in Uganda tertiary hospitals

BACKGROUND

Klebsiella pneumoniae is an opportunistic pathogen that has been implicated as one of commonest cause of hospital and community acquired infections. The K. pneumoniae infections have considerably contributed to morbidity and mortality in patients with protracted ailments. The capacity of K. pneumoniae to cause diseases depends on the presence of an array virulence factors. Coexistence and expression of virulence factors and genetic determinants of antibiotic resistance complicates treatment outcomes. Thus, emergence of pathogenic MDR K. pneumoniae poses a great threat to the healthcare system. However, the carriage of antibiotic resistance among pathogenic K. pneumoniae is yet to be investigated in Uganda. We sought to investigate the carbapenem resistance profiles and pathogenic potential based on capsular serotypes of K. pneumoniae clinical isolates.

METHODS

This was a cross sectional study involving use of archived Klebsiella pneumoniae isolates collected between January and December, 2019 at four tertiary hospitals in Uganda. All isolates were subject to antimicrobial susceptibility assays to determine phenotypic antibiotic resistance, pentaplex PCR to detect carbapenemases encoding genes and heptaplex PCR to identify capsular serotypes K1, K2, K3, K5, K20, K54 and K57.

RESULTS

The study found an overall phenotypic carbapenem resistance of 23.3% (53/227) and significantly higher genotypic resistance prevalence of 43.1% (98/227). Over all, the most prevalent gene was blaOXA-48-like (36.4%), followed by blaIMP-type (19.4%), blaVIM-type (17.1%), blaKPC-type (14.0%) and blaNDM-type (13.2%). blaVIM-type and blaOXA-48-like conferred phenotypic resistance in all isolates and 38.3% of isolates that harbored them respectively. Capsular multiplex PCR revealed that 46.7% (106/227) isolates were pathogenic and the predominantly prevalent pathotype was K5 (18.5%) followed by K20 (15.1%), K3 (7.1%), K2 (3.1%) and K1 (2.2%). Of the 106 capsular serotypes, 37 expressed phenotypic resistance; thus, 37 of the 53 carbapenem resistant K. pneumoniae were pathogenic.

CONCLUSION

The high prevalence of virulent and antibiotic resistant K. pneumoniae among clinical isolates obtained from the four tertiary hospital as revealed by this study pose a great threat to healthcare. Our findings underline the epidemiological and public health risks and implications of this pathogen.

Epidemiology and prevalence of extended-spectrum β-lactamase- and carbapenemase-producing Enterobacteriaceae in humans, animals and the environment in West and Central Africa

Extended-spectrum β-lactamase-producing Enterobacteriaceae (ESBL-E) and carbapenemase-producing Enterobacteriaceae (CPE) are widespread. Here we used the 'One Health' approach to determine knowledge gaps on ESBL-E and CPE in West and Central Africa. We searched all articles on ESBL-E and CPE in these African regions published in PubMed, African Journals Online and Google Scholar from 2000 onwards. Among the 1201 articles retrieved, we selected 165 studies (West Africa, 118; Central Africa, 47) with data from 22 of the 26 West and Central Africa countries. Regarding the settings, 136 articles focused only on humans (carriage and/or infection), 6 articles on humans and animals, 13 on animals, 1 on humans and the environment, 8 on the environment and 1 on humans, animals and environments. ESBL-E prevalence ranged from 11-72% in humans and 7-79% in aquatic environments (wastewater). In animals, ESBL-E prevalence hugely varied: 0% in cattle, 11-36% in chickens, 20% in rats, 21-71% in pigs and 32-75% in dogs. The bla_CTX-M-15 gene was the predominant ESBL-encoding gene and was associated with plasmids of incompatibility groups F, H, K, Y, N, I1 and R. CPE were studied only in humans. Class B metallo-β-lactamases (NDM) and class D oxacillinases (OXA-48 and OXA-181) were the most common carbapenemases. Our results show major knowledge gaps, particularly on ESBL and CPE in animals and the environment, that might limit antimicrobial resistance management in these regions. The results also emphasise the urgent need to improve active surveillance programmes in each country and to support antimicrobial stewardship.

Carbapenem-resistant Enterobacteriaceae (CRE) and gram-negative bacterial infections in south-west Nigeria: a retrospective epidemiological surveillance study

Background

Carbapenem-resistant Enterobacteriaceae (CRE) are often responsible for severe, life-threatening infections and they represent a critical threat to the available antibiotic agents and to global health. An understanding of the epidemiology of these infections will be indispensable to the development of appropriate case management as well as infection prevention and control (IPC) measures in any healthcare setting.

Objectives

The objective of this study was to investigate and describe the epidemiology of carbapenem-resistant Enterobacteriaceae (CRE) and other gram-negative bacteria in a tertiary hospital in south west Nigeria using routinely collected microbiological laboratory data.

Methods

A retrospective collection of microbiological laboratory records from the January to June 2018 was performed. All culture and antimicrobial susceptibility test results of patients who required laboratory tests were collected. Other information collected include: patient demographics, clinical specimen types and the requesting hospital department. The data was analyzed using SPSS Windows version 24. Comparison between categorical variables was done using chi-square tests while independent sample t-test was used to determine significant mean differences between groups. A p < 0.05 was taken to be statistically significant.

Results

The prevalence of carbapenem-resistance among Enterobacteriaceae and gram-negative bacteria isolates was 22% (n = 39/177). Of these, 35.9% (n = 14) were Klebsiella pneumonia, 30.8% (n = 12) were Pseudomonas aeruginosa and 15.4% (n = 6) were Klebsiella oxytoca. 87.2% (n = 34) of these were also multi-drug resistant, with a mean total resistance score of 3.92 (SD = ± 1.44). There were differences observed in proportion of carbapenem-resistance across clinical specialties and age groups; however, these differences were not statistically significant. Independent sample t-test revealed that carbapenem-resistant isolates exhibited more drug resistance than carbapenem-sensitive isolates (3.93 vs. 2.30; p < 0.001).

Conclusion

Carbapenem resistance is an important threat to the current antibiotic armory. Active surveillance, particularly in the healthcare setting is required to identify high risk groups, inform better treatment options and infection prevention and control measures.

Contribution of NDM and OXA-type carbapenemases to carbapenem resistance in clinical Acinetobacter baumannii from Nigeria

Objective: Acinetobacter baumannii infections are rarely diagnosed in many hospitals in Nigeria due to a lack of capacity for the identification of the organism in spite of the clinical significance of this opportunistic nosocomial organism. We assembled a panel of presumptive isolates of A. baumannii from tertiary hospitals in Nigeria and analysed mechanisms of resistance phenotypically and by whole genome sequencing.Materials and methods: Twenty-one clinical isolates of A. baumannii identified using standard microbiological tests were tested for susceptibility to a panel of antibiotics by the agar dilution method, and production of ESBLs using phenotypic tests. Whole genome sequencing and comparative genomic analysis were used to determine the antimicrobial resistance genes, strain types, phylogenetic relationships and genetic context of resistance genes.Results: The MIC₅₀ and MIC₉₀ of most antibiotics were very high with no difference between MIC₅₀ and MIC₉₀ values apart for amikacin, meropenem and colistin where MIC₅₀ and MIC₉₀ ranged between 1-4 µg/ml and 64->64 µg/ml, respectively. Multiple resistance genes were detected in most of the isolates including bla_NDM-1, various bla_OXA-51 family alleles and bla_OXA-23. Interestingly, bla_NDM-1 carriage did not always result in phenotypic carbapenem resistance. Whole genome alignments typing showed strains belonged to three major clades. Strains within these clades had different resistance genes and resistance patterns.Conclusions: This report shows a high level of resistance to important antibiotics and carbapenem resistance in A. baumannii in Nigeria. We hope this work will serve as a reference for future study in the sub-Saharan region of Africa.

Carbapenem Resistant Enterobacteriaceae in Africa

Carbapenems are regarded as unique among the �-lactam antibiotics due to their broad spectrum of activity and ability to resist �-lactamase hydrolysis. Carbapenems are the only �-lactam antibiotics with efficacy in severe infections caused by extended-spectrum beta-lactamase (ESBL) producing bacteria. However, recent reports of carbapenem resistance particularly among members of Enterobacteriaceae that are responsible for diseases such as gastrointestinal infections, septicemia, pneumonia, meningitis, peritonitis as well as urinary tract infections, call for concerns. In Africa, the problem of carbapenem-resistant Enterobacteriaceae (CRE) is aggravated by factors such as the high rate of infections, poor diagnostic tools, sub-optimal disease surveillance, and abuse of antibiotics. Besides, the problem of CRE in Africa is understudied. This review distills available literature on the spread of CRE in Africa, CRE genes in circulation, and the need to pay attention to this emerging threat to lives in developing countries.

High proportion of carbapenemase-producing Escherichia coli and Klebsiella pneumoniae among extended-spectrum β-lactamase-producers in Nigerian hospitals

OBJECTIVES

Carbapenem-resistant Enterobacterales are a global problem, however little is known about the burden and origin of carbapenem resistance in Africa. The objectives of this study were to determine the proportion of carbapenem-resistant isolates among extended-spectrum β-lactamase-producing Enterobacterales (ESBL-E), to identify the underlying mechanisms of resistance and to assess the population structure of carbapenem-resistant isolates from Nigeria.

METHODS

ESBL-E isolates (n = 175) from infections were collected at four hospitals in Lagos, Nigeria, from July 2016 to January 2018 and were screened for carbapenem resistance using a VITEK®2 automated system. All carbapenem-resistant ESBL-E (CRE) were screened for bla_KPC, bla_CTX-M, bla_CMY-2, bla_NDM, bla_VIM, bla_IMP, bla_OXA-181 and bla_OXA-48 genes. Genotyping of randomly selected isolates was performed by whole-genome sequencing.

RESULTS

The isolates included Escherichia coli (n = 113; 64.6%) and Klebsiella pneumoniae (n = 62; 35.4%). Of the 175 ESBL-E isolates, 48 (27.4%) were resistant to carbapenems (15 E. coli and 33 K. pneumoniae). CRE isolates carried bla_NDM (n = 30; 62.5%), bla_NDM + bla_OXA-181 (n = 10; 20.8%), bla_OXA-181 (n = 2; 4.2%) and bla_NDM + bla_OXA-48 (n = 1; 2.1%); no carbapenemase gene was detected in 5 isolates (10.4%). The isolates showed low diversity and were mainly associated with multilocus sequence typing (MLST) sequence types ST410 for E. coli and ST395 and ST147 for K. pneumoniae.

CONCLUSION

Carbapenem resistance is frequent among ESBL-E in Nigeria and is mainly associated with bla_NDM. Genotyping suggested that the observed clones possibly originated from Southeast Asia.

Phenotypic and Genotypic Characterization of Carbapenem-Resistant Gram-Negative Bacilli Pathogens from Hospitals in Ghana

In Ghana, surveillance efforts on antibiotic resistance so far have not covered carbapenem resistance. In this study, our aim was to apply phenotypic and genotypic methods to identify and characterize carbapenem-resistant (CR) Gram-negative bacteria from the hospital environment in Ghana. A collection of 3840 isolates of Gram-negative bacilli infections from various clinical specimens was screened for carbapenem resistance by disc diffusion for imipenem, meropenem, and doripenem. Minimum Inhibitory Concentration (MIC) of the CR isolates was determined by E-test for the three carbapenems. All the CR isolates were further screened for carbapenemase activity by modified Hodge and boronic acid disc synergy tests. The CR isolates were investigated for the presence of carbapenemase and extended-spectrum beta-lactamase genes by PCR and confirmed by sequencing. The overall prevalence of CR isolates was 2.9% (111/3840). Based on the disc diffusion test, prevalence of resistance to carbapenems were doripenem (75%), imipenem (66.7%), and meropenem (58%). The highest measurable MIC levels (≥32 μg/mL) were observed in 56.8% of CR isolates with the nonfermenters, Pseudomonas aeruginosa (24.3%) and Acinetobacter species (18.9%), disproportionately represented. Phenotypic identification of carbapenamase activity occurred in 18.9% of the CR isolates by the modified Hodge test and 2.7% by Boronic acid disc synergy test; 21.6% exhibited carbapenemase production by both methods. All the CR isolates carried ESBL genes (blaTEM and blaSHV), whereas 23.4% were carriers of carbapenemase genes, of which 14.4% were blaNDM-1, 7.2% blaVIM-1, and 1.8% blaOXA-48. Phylogenetically, the CR isolates were diverse and showed limited relatedness to isolates from other geographical regions.

Detection of the carbapenemase gene blaVIM-5 in members of the Pseudomonas putida group isolated from polluted Nigerian wetlands

There are increasing concerns about possible dissemination of clinically relevant antibiotic resistance genes, including genes encoding for carbapenemases in the environment. However, little is known about environmental distribution of antibiotic resistance in Africa. In this study, four polluted urban wetlands in Nigeria were investigated as potential reservoirs of carbapenem-resistant bacteria (CRB). CRB were isolated from the wetlands, characterized by Blue-Carba test, MIC determinations and whole genome sequencing (WGS). Nine of 65 bacterial isolates identified as members of the Pseudomonas putida group (P. plecoglossicida and P. guariconensis, respectively) harboured the metallo-beta-lactamase gene bla_VIM-5. WGS revealed the bla_VIM-5 in three novel Tn402-like class 1 integron structures containing the cassette arrays aadB|bla_VIM-5|bla_PSE-1, aadB|bla_VIM-5|aadB|bla_PSE-1, and bla_VIM-5|aadB|tnpA|bla_PSE-1|smr2|tnpA, respectively. Strains carrying the aadB|bla_VIM-5|bla_PSE-1 cassette also carried an identical integron without bla_VIM-5. In addition_, the strains harboured another Tn402-like class 1 integron carrying bcr2, several multidrug resistance efflux pumps, and at least one of ampC, aph(3”)-lb, aph(6)-ld, tetB, tetC, tetG, floR, and macAB. This is the first report of a carbapenemase gene in bacteria from environmental sources in Nigeria and the first report of bla_VIM-5 in environmental bacteria isolates. This result underscores the role of the Nigerian environment as reservoir of bacteria carrying clinically relevant antibiotic resistance genes.

CTX-M-15 is Established in Most Multidrug-Resistant Uropathogenic Enterobacteriaceae and Pseudomonaceae from Hospitals in Nigeria

β-Lactam antibiotics are widely used to treat urinary tract infections in Nigeria. This study aimed to determine the presence and characteristics of extended spectrum β-lactamases in commonly isolated uropathogenic Gram-negative bacteria (GNB) in Nigeria. Fifty non-duplicate GNB isolates consisting of Escherichia coli, 19; Klebsiella pneumoniae, 21; and Pseudomonas aeruginosa, 10 were obtained from three tertiary hospitals in Nigeria. The antibiotic susceptibility testing of all isolates to a panel of antibiotics including minimum inhibitory concentrations (MICs) and extended spectrum β-lactamases was determined. Polymerase chain reactions and sequencing were used to detect β-lactam genes. Polymerase chain reactions and sequencing identified varying extended spectrum β-lactamases (ESBLs) encoding genes for 24 isolates (48.0%). Cefotaximase-Munich (CTX-M) 15 was the dominant gene with 20/24 of the isolates positive at 83.3%; multiple genes (2 to 6 ESBL genes) were found in 20 of the isolates. The isolates encoded other genes such as CTX-M-14, 33.3%; sulfhydryl variable (SHV) variants, 58.3%; oxacillinase (OXA) variants, 70.8%; OXA-10, 29.2%; and Vietnamese extended β-lactamase (VEB) 1, 25.0%. There was no difference between the MIC₅₀ and MIC₉₀ of all the isolates. The high-level multidrug resistance of uropathogens to third generation cephalosporins including other antibiotics used in this study is strongly associated with carriage of ESBLs, predominantly CTX-M-15, as well as CTX-X-M-14, OXA-10, and VEB-1.

Carbapenem-Resistant Enterobacteriaceae: A Strategic Roadmap for Infection Control

The incidence of carbapenem-resistant Enterobacteriaceae (CRE) has increased worldwide with great regional variability. Infections caused by these organisms are associated with crude mortality rates of up to 70%. The spread of CRE in healthcare settings is both an important medical problem and a major global public health threat. All countries are at risk of falling victim to the emergence of CRE; therefore, a preparedness plan is required to avoid the catastrophic natural course of this epidemic. Proactive and adequate preventive measures locally, regionally, and nationally are required to contain the spread of these bacteria. The keys to success in preventing the establishment of CRE endemicity in a region are early detection through targeted laboratory protocols and containment of spread through comprehensive infection control measures. This guideline provides a strategic roadmap for infection control measures based on the best available evidence and expert opinion, to enable preparation of a multifaceted preparedness plan to abort epidemics of CRE. Infect Control Hosp Epidemiol 2017;38:580-594.

New Hydrazones Bearing Thiazole Scaffold: Synthesis, Characterization, Antimicrobial, and Antioxidant Investigation

New series of hydrazones 5–18 were synthesized, in good yields, by reacting 4-methyl-2-(4-(trifluoromethyl)phenyl)thiazole-5-carbohydrazide with differently substituted benzaldehyde. The resulting compounds were characterized via elemental analysis, physico-chemical and spectral data. An antimicrobial screening was done, using Gram (+), Gram (−) bacteria and one fungal strain. Tested molecules displayed moderate-to-good growth inhibition activity. 2,2-Diphenyl-1-picrylhydrazide assay was used to test the antioxidant properties of the compounds. Monohydroxy (14–16), para-fluorine (13) and 2,4-dichlorine (17) derivatives exhibited better free-radical scavenging ability than the other investigated molecules.

The Molecular Epidemiology and Genetic Environment of Carbapenemases Detected in Africa

Research articles describing carbapenemases and their genetic environments in Gram-negative bacteria were reviewed to determine the molecular epidemiology of carbapenemases in Africa. The emergence of resistance to the carbapenems, the last resort antibiotic for difficult to treat bacterial infections, affords clinicians few therapeutic options, with a resulting increase in morbidities, mortalities, and healthcare costs. However, the molecular epidemiology of carbapenemases throughout Africa is less described. Research articles and conference proceedings describing the genetic environment and molecular epidemiology of carbapenemases in Africa were retrieved from Google Scholar, Scifinder, Pubmed, Web of Science, and Science Direct databases. Predominant carbapenemase genes so far described in Africa include the blaOXA-48 type, blaIMP, blaVIM, and blaNDM in Acinetobacter baumannii, Klebsiella pneumoniae, Enterobacter cloacae, Citrobacter spp., and Escherichia coli carried on various plasmid types and sizes, transposons, and integrons. Class D and class B carbapenemases, mainly prevalent in A. baumannii, K. pneumoniae, E. cloacae, Citrobacter spp., and E. coli were the commonest carbapenemases. Carbapenemases are mainly reported in North and South Africa as under-resourced laboratories, lack of awareness and funding preclude the detection and reporting of carbapenemase-mediated resistance. Consequently, the true molecular epidemiology of carbapenemases and their genetic environment in Africa is still unknown.

Isolation of multiple carbapenemase-producing Gram-negative bacilli from a patient recently hospitalized in Nigeria

A 29-year-old female transferred to a tertiary care hospital in Winnipeg, Canada, after a prolonged period of hospitalization in Nigeria was found to be colonized with a VIM-2-producing Pseudomonas aeruginosa, a NDM-1-producing Klebsiella pneumoniae, and an OXA-181-producing Escherichia coli. Detection of carbapenemase-producing organisms from a rectal swab was accomplished by screening with chromogenic media, followed by confirmation with the Rapid CARB Screen kit (Rosco Diagnostica, Taastrup, Denmark). This case illustrates the need for clinical microbiology laboratories to have a protocol in place to screen patients for carbapenemase producers, even in countries where these organisms are rarely encountered.