Over a 9-month period, 8 of 40 nonduplicate isolates of Enterobacter spp. producing extended-spectrum ␤-lactamase (ESBL) were detected for the first time from two hospitals in Lagos, Nigeria. Microbiologic and molecular analysis confirmed the presence of ESBL. Only four isolates transferred ESBL resistance as determined by the conjugation test, and pulsed-field gel electrophoresis showed genetically unrelated isolates.

Foodborne bacteria are often associated with human infections; these infections can become more complicated to treat if the bacteria are also resistant to antimicrobials. In this study, prevalence, antimicrobial resistance, and genetic relatedness of Escherichia coli among food producing animals from Lagos, Nigeria, was investigated. From December 2012 to June 2013, E. coli were isolated from fecal samples of healthy cattle, chicken, and swine. Antimicrobial susceptibility testing against 22 antimicrobials was performed using broth microdilution with the Sensititre™ system. Clonal types were determined by pulsed-field gel electrophoresis (PFGE). From the analysis, 211/238 (88.7%), 170/210 (81%), and 136/152 (89.5%) samples from cattle, chicken, and swine, respectively, were positive for E. coli. A subset of those isolates (n=211) selected based on β-lactamase production was chosen for further study. Overall, E. coli exhibited the highest resistance to tetracycline (124/211; 58.8%), trimethoprim/sulfamethoxazole (84/211; 39.8%), and ampicillin (72/211; 34.1%). Approximately 40% of the isolates were pan-susceptible, and none of the isolates were resistant to amikacin, cefepime, ceftazidime, ertapenem, meropenem, or tigecycline. Among the resistant isolates, 28 different resistance patterns were observed; 26 of those were characterized as multi-drug resistant (MDR; resistance to ≥2 antimicrobials). One isolate was resistant to 13 different antimicrobials representing five different antimicrobial classes. Using PFGE, MDR E. coli were genetically diverse and overall did not group based on source; identical PFGE patterns were detected among isolates from different sources. These results suggest that isolates cannot be attributed to specific sources, and some may be present across all of the sources. Results from this study indicate that food-producing animals in Nigeria are a reservoir of MDR E. coli that may be transferred to humans via the food chain.

Introduction: The emergence of multidrug resistance (MDR; resistance to ≥ 2 more antimicrobials) in Escherichia coli is of concern due to complications encountered in treatment. Methodology: In this study, prevalence, antimicrobial resistance, and genetic characteristics of MDR community isolates of E. coli from Lagos, Nigeria were determined. Urine and stool samples were obtained from outpatients attending Lagos State hospitals and from animal handlers in abattoirs, poultries, and open markets, from December 2012 to July 2013.Results: Approximately 50% of urine (200/394) and 88% of stool samples (120/136) were positive for E. coli. Based upon β-lactamase production, a subset of those isolates was selected for further study. Of the 22 antimicrobials tested, E. coli exhibited resistance to all antimicrobials except amikacin and piperacillin/tazobactam. The highest levels of resistance were to tetracycline (182/247; 73.7%), trimethoprim/sulfamethoxazole (152/247; 61.5%), and ampicillin (147/247; 59.1%). Resistance to the cephalosporins ranged from 1.6%-15% including the third-and fourth-generation cephalosporins, cefpodoxime (20/247; 8.1%) and cefepime (4/247; 1.6%), respectively. MDR was observed in 69.6% (172/247) of the isolates. Forty-eight E. coli resistant to at least five antimicrobials were selected for further analysis using pulsed-field gel electrophoresis; seven distinct clusters were observed among the diverse patterns. Of the 48 MDR E. coli, 30 different sequence types (ST) were detected using multilocus sequence typing, including four ST131. Conclusions: This study demonstrated circulating MDR E. coli in the Nigerian community. Monitoring of antimicrobial resistance in developing countries is necessary to optimize empiric treatment and the prudent use of antimicrobials.

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Emergence of bla CTX-M-15, qnrB1 and aac(69)-Ib-cr resistance genes in Pantoea agglomerans and Enterobacter cloacae from Nigeria (sub-Saharan Africa)Resistance of Enterobacter species to extended-spectrum cephalosporins is known to be mediated by hyperproduction of chromosomal AmpC b-lactamases. However, the additional expression of plasmid-encoded extended-spectrum b-lactamases (ESBLs) has become more prevalent worldwide in recent years (Ko et al., 2008). In Nigeria, ESBL production in Enterobacter species has been associated with TEM-and SHV-type ESBLs (Aibinu et al., 2003;Kasap et al., 2010). Other b-lactamase resistance determinants, conferring resistance to extendedspectrum cephalosporins, such as bla VEB , bla OXA and bla CMY , have recently been reported in Nigerian Providencia species strains (Aibinu et al., 2011). In addition, the worldwide spread of CTX-M-15 (Cantó n & Coque, 2006) has reached Nigeria, having being identified in Klebsiella species and Escherichia coli (Soge et al., 2006;Olowe et al., 2010). There is no documented report yet on ESBL production mediated by bla or the association of the spread of PMQR determinants in Enterobacter species from Nigeria. This study reports the phenotypic and genotypic characteristics of ten clinical isolates of Enterobacter species and one isolate of Pantoea agglomerans with respect to the occurrence of bla CTX-M and other resistance genes. The Enterobacter species, which consisted of Enterobacter asburiae (n51), Enterobacter aerogenes (n51) and Enterobacter cloacae (n58), and the Pantoea agglomerans isolate represented 9.5 % of all members of the Enterobacteriaceae isolated within a period of 6 months from October 2008 to March 2009 at Lagos University Teaching Hospital (LUTH), a tertiary hospital, in Nigeria. Enterobacter agglomerans was previously renamed Pantoea agglomerans to reflect its genetic distance from the genus Enterobacter (Sanders & Sanders, 1997).Bacterial species identification was performed using the VITEK 2 system (VITEK2 GN-card; bioMérieux). Antimicrobial susceptibility testing was determined according to the guidelines of the Clinical and Laboratory Standards Institute (CLSI, 2010) by the broth microdilution method and VITEK2 AST-N13 card. The quality control strain used was E. coli ATCC 25922 (Oxoid). Etest strips containing cefotaxime in combination with clavulanic acid, and the double disc synergy tests (ESBL/AmpC ID D68C; Mast Group), were used for phenotypic detection and differentiation of both ESBL and AmpC production. Broth mate conjugation assays were performed as described by Pfeifer et al. Phenotypic analysis of the 11 isolates in this study revealed that two of the isolates (Enterobacter cloacae 213K and P. agglomerans 69K) were ESBL-producers. The ESBL gene bla CTX-M-15 was identified in both isolates. P. agglomerans 69K was isolated from the blood culture of an adult male patient admitted for sepsis and diagnosed HIV type-1-positive on admission. The patient was treated empirically with ceftriaxone and was referred to a...

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Background The COVID-19 pandemic, caused by SARS-CoV-2, continues to impact health systems throughout the world with serious medical challenges being imposed on many African countries like Nigeria. Although emerging studies have identified lymphopenia as a driver of cytokine storm, disease progression, and poor outcomes in infected patients, its immunopathogenesis, as well as environmental and genetic determinants, remain unclear. Understanding the interplay of these determinants in the context of lymphopenia and COVID-19 complications in patients in Africa may help with risk stratification and appropriate deployment of targeted treatment regimens with repurposed drugs to improve prognosis. Objective This study is designed to investigate the role of vitamin D status, vasculopathy, apoptotic pathways, and vitamin D receptor (VDR) gene polymorphisms in the immunopathogenesis of lymphopenia among African people infected with SARS-CoV-2. Methods This cross-sectional study will enroll 230 participants, categorized as “SARS-CoV-2 negative” (n=69), “COVID-19 mild” (n=32), “hospitalized” (n=92), and “recovered” (n=37), from two health facilities in Lagos, Nigeria. Sociodemographic data, travel history, and information on comorbidities will be obtained from case files and through a pretested, interview-based structured questionnaire. Venous blood samples (5 mL) collected between 8 AM and 10 AM and aliquoted into EDTA (ethylenediaminetetraacetic acid) and plain tubes will be used for complete blood count and CD4 T cell assays to determine lymphopenia (lymphocyte count <1000 cells/µL) and CD4 T lymphocyte levels, as well as to measure the concentrations of vitamin D, caspase 3, soluble vascular cell adhesion molecule-1 (sVCAM-1), and soluble Fas ligand (sFasL) using an autoanalyzer, flow cytometry, and ELISA (enzyme-linked immunosorbent assay) techniques. Genomic DNA will be extracted from the buffy coat and used as a template for the amplification of apoptosis-related genes (Bax, Bcl-2, BCL2L12) by polymerase chain reaction (PCR) and genotyping of VDR (Apa1, Fok1, and Bsm1) gene polymorphisms by the PCR restriction fragment length polymorphism method and capillary sequencing. Total RNA will also be extracted, reverse transcribed, and subsequently quantitated by reverse transcription PCR (RT-PCR) to monitor the expression of apoptosis genes in the four participant categories. Data analyses, which include a test of association between VDR gene polymorphisms and study outcomes (lymphopenia and hypovitaminosis D prevalence, mild/moderate and severe infections) will be performed using the R statistical software. Hardy-Weinberg equilibrium and linkage disequilibrium analyses for the alleles, genotypes, and haplotypes of the genotyped VDR gene will also be carried out. Results A total of 45 participants comprising 37 SARS-CoV-2–negative and 8 COVID-19–recovered individuals have been enrolled so far. Their complete blood counts and CD4 T lymphocyte counts have been determined, and their serum samples and genomic DNA and RNA samples have been extracted and stored at –20 °C until further analyses. Other expected outcomes include the prevalence and distribution of lymphopenia and hypovitaminosis D in the control (SARS-CoV-2 negative), confirmed, hospitalized, and recovered SARS-CoV-2–positive participants; association of lymphopenia with CD4 T lymphocyte level, serum vitamin D, sVCAM-1, sFasL, and caspase 3 levels in hospitalized patients with COVID-19; expression levels of apoptosis-related genes among hospitalized participants with COVID-19, and those with lymphopenia compared to those without lymphopenia; and frequency distribution of the alleles, genotypes, and haplotypes of VDR gene polymorphisms in COVID-19–infected participants. Conclusions This study will aid in the genotypic and phenotypic stratification of COVID-19–infected patients in Nigeria with and without lymphopenia to enable biomarker discovery and pave the way for the appropriate and timely deployment of patient-centered treatments to improve prognosis. International Registered Report Identifier (IRRID) DERR1-10.2196/21242

Here, we present the draft genome sequences of nine multidrug-resistant Escherichia coli strains isolated from humans (n = 6) and chicken carcasses (n = 3) from Lagos, Nigeria, in 2013. Multiple extended-spectrum β-lactamase (ESBL) genes were identified in these isolates.