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.

A multicenter survey of asymptomatic cryptococcal antigenemia among patients with advanced HIV disease in Nigeria.

As of 2018, cryptococcal antigen (CrAg) screening in patients with advanced human immunodeficiency virus (HIV) disease (AHD) was not routinely implemented in Nigeria despite being recommended in the national HIV treatment guidelines. Our aim was to determine the prevalence and risk factors for asymptomatic cryptococcal antigenemia in adult people living with HIV (PLHIV) in Nigeria to advocate for the implementation of routine CrAg screening. A descriptive cross-sectional study and CrAg screening of consecutive adult PLHIV with CD4 counts ≤200 cells/µL was conducted from April 2018 to April 2019 at HIV clinics in eleven tertiary hospitals spread across Nigeria's six geopolitical regions. Prevalence of asymptomatic cryptococcal antigenemia was estimated by facility and geopolitical zone. Logistic regression was conducted to identify risk factors for cryptococcal antigenemia. In total, 1,114 patients with AHD were screened. The overall prevalence of asymptomatic cryptococcal antigenemia was 3.9% with wide variation across facilities (range: 0/75 [0%]- 15/122 [12.3%]) and geopolitical zones (range: 0/75 [0%]-19/279 [6.8%]). Prevalence of antigenemia was highest in the South-West (19/279 [6.8%]) and lowest in the North-East (0/75 [0%]). Prevalence was 5.2% (26/512) and 3.2% (18/561) in patients with CD4<100 and CD4 of 101-200, respectively. Of all patients with antigenemia, 50% were on antiretroviral therapy (ART) at the time of having a positive CrAg test. In adjusted analysis, cryptococcal antigenemia was significantly less in patients on ART and patients who had completed any formal education. The survey showed a high overall burden of cryptococcal antigenemia in Nigeria, with variable prevalence across geopolitical regions. We provided valuable evidence for implementing routine CrAg screening of AHD patients in Nigeria which has commenced in selected centres.

Standardization of Aspergillus IgG diagnostic cutoff in Nigerians.

BACKGROUND AND OBJECTIVES: Commercial Aspergillus IgG antibody assays have become pivotal in the current diagnosis of chronic pulmonary aspergillosis (CPA). However, diagnostic cutoffs have been found to vary from manufactures' recommendations in different settings. This study aimed to establish the Aspergillus IgG reference range among Nigerians and determine a diagnostic cutoff for CPA. METHODS: Sera from 519 prospectively recruited healthy blood donors and 39 previously confirmed cases of CPA were analysed for Aspergillus IgG levels using the Bordier test kit (Bordier Affinity Products SA, Crissier, Switzerland). Accuracy versus cutoff profile and receiver operating characteristics (ROC) curve were analysed for both CPA cases and controls using the R-Studio (2020), (Window desktop, version 4.0.2 software with R packages "nnet" and "ROCR"). RESULTS: Among healthy blood donors, 141 (27.2%) were aged 16-25 years with median (interquartile range, IQR) of 22 (20-24) years; 304 (58.6%) were aged 26-40 years with median (IQR) of 32 (29-36) years; while 74 (14.2%) were aged 41-60 years with median (IQR) of 46 (44-49.75). Median IgG level in respective age groups were 0.069 (0.009-0.181), 0.044 (0.014-0.202) and 0.056 (0.01-0.265) with no significant difference found in the three age categories (p = 0.69). The overall diagnostic cutoff for the diagnosis of CPA was 0.821 with an accuracy of 97.1% and area under the curve (AUC) = 0.986. CONCLUSION: The optimal diagnostic cutoff for diagnosing CPA in Nigerians using the Bordier kit was 0.821 which is lower than the manufacturer's recommended cutoff of 1.0. The determination of this cutoff among Nigerians will significantly enhance accurate identification of CPA and assessment of its true burden in Nigeria.

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, blaNDM-7 and blaCMY-4 were detected in all Escherichia coli and most Providencia rettgeri isolates; blaNDM-7 was also detected in 1 Enterobacter cloacae. The E. coli and E. cloacae isolates also shared blaOXA-1, while blaOXA-10 was found in all P. rettgeri, one Pseudomonas aeruginosa and 1 E. coli. Except for Stenotrophomonas maltophilia isolates, which only contained blaL1, 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.

A mini- national surveillance study of resistance profiles of Staphylococcus Aureus isolated from clinical specimens across hospitals in Nigeria.

BACKGROUND: Infections with Staphylococcus aureus cause significant morbidity and mortality worldwide. Resistant strains of S. aureus to commonly used antibiotics are being increasingly encountered in clinical practice, necessitating the need to determine the resistance pattern in Nigeria. METHODS: Antibiotic susceptibility testing was performed on 360 S. aureus isolates from clinical specimen from seven hospitals across the six geo-political regions of Nigeria using Kirby Bauer disc diffusion technique, and E-test for vancomycin. Cefoxitin 30 µg disc was used to determine methicillin resistance, and D-test for inducible clindamycin resistance. RESULTS: Methicillin-resistant S. aureus was confirmed in 176 (48.9%) of the isolates, 346 (96%) for penicillin G and 311 (86.4%) for trimethoprim. 175 (99.4%) of the 176 resistant to methicillin were susceptible to vancomycin. Linezolid, tigecycline, chloramphenicol and clindamycin had susceptibilities of 341 (94.7%), 332 (92.2%), 298 (82.8%) and 290 (80.6%) respectively. Inducible clindamycin resistance was elucidated in 25 (29.1%) of the 86 isolates. Generally, MRSA isolates were more resistant than methicillin-sensitive S. aureus (MSSA) to all antibiotics tested. CONCLUSION: Staphylococcus aureus rates of resistance are high and call for urgent action such as antibiotic stewardship programmes and periodic surveillance to enhance clinical outcomes. While targeted therapy is preferred, options for empiric treatment include chloramphenicol, clindamycin, linezolid or vancomycin.

Characterisation of carbapenem-resistant Gram-negative organisms from clinical specimens in Yola, Nigeria.

OBJECTIVES: This study aimed to identify carbapenem-resistant Gram-negative bacteria from clinical specimens of patients in Yola, Nigeria. METHODS: Routine clinical specimens were screened for the presence of carbapenem-resistant Gram-negative bacteria using chromogenic agar plates. Susceptibility of all presumptive isolates to carbapenems was tested by MIC and disk diffusion methods. Real-time PCR was used to test for the presence of carbapenemase genes. RESULTS: Screening of 1741 clinical specimens yielded 119 (6.8%) presumptive carbapenem-resistant Gram-negative bacteria. Antimicrobial susceptibility testing confirmed carbapenem resistance in 105 of these isolates. New Delhi metallo-ß-lactamase (blaNDM) gene was detected in 26 isolates and Verona integron-encoded metallo-ß-lactamase (blaVIM) gene was detected in four. The mechanism of resistance could not be identified in approximately two thirds of the carbapenem-resistant isolates. CONCLUSION: While blaNDM and blaVIM accounted for 28.6% of the resistance seen, further molecular-based studies are needed to characterise the other mechanisms of carbapenem resistance in these isolates.