Genomic features of an isolate of Empedobacter falsenii harbouring a novel variant of metallo-ß-lactamase, blaEBR-4 gene.

Empedobacter falsenii is an emerging opportunistic pathogen that has been occasionally implicated in various human infections. In this study, we described the genomic features of a multidrug resistant E. falsenii Q1655 obtained from a patient attending a public hospital in Sokoto, northwest Nigeria. The isolate, E. falsenii Q1655, was isolated from the stool sample of a patient in Sokoto, Nigeria. The identity of the isolate was confirmed by MALDITOF-MS. The disc diffusion test and modified Carba-NP test were used for phenotypic antibiotic susceptibility test and carbapenemase enzyme production test, respectively. The whole genome of the strain was sequenced using the Illumina MiSeq technique. Resistome analysis was done by annotation of the WGS against the ARG-ANNOT database. The isolate was resistant to all ß-lactam antibiotics with the exception of cefepime. The MICs of imipenem and ertapenem as determined by E-test were 12 µg/ml and 2 µg/ml, respectively. Modified Carba NP test showed that the strain was carbapenemase producing. Resistome analysis revealed the presence of a novel metallo-ß-lactamase, a chromosomal blaEBR-4, which exhibited 94.92% and 97.02% nucleotide and protein sequence identities respectively with blaEBR-3 gene of E. falsenii 174,820. Seven and eight amino-acid substitutions were observed with the blaEBR-1 and blaEBR-2, respectively. We reported the first isolation and genomic description of an extensively drug resistant isolate of Empedobacter falsenii in Nigeria. This report broadens our knowledge of carbapenem resistance in E. falsenii and it will serve as a useful guide in the development of antibiotic use policy.

Bhargavaea massiliensis sp. nov. and Dietzia massiliensis sp. nov., Novel Bacteria Species Isolated from Human Urine Samples in Nigeria.

Two novel bacteria species designated Marseille-Q1000T and Marseille-Q0999T were isolated from urine samples of patients in Sokoto, Northwest-Nigeria. They were Gram-positive bacteria and belong to two different genera, Bhargavaea and Dietzia. The genome size and G + C content of Marseille-Q1000T and Marseille-Q0999T were 3.07 and 3.51 Mbp with 53.8 and 71.0 mol% G + C content, respectively. The strains exhibited unique phenotypic and genomic features that are substantially different from previously known bacterial species with standing in nomenclature. On the basis of the phenotypic, phylogenetic and genomic characteristics, strains Marseille-Q0999T (= CSURQ0999 = DSM 112394) and Marseille-Q1000T (= CSURQ1000 = DSM 112384) were proposed as the type strains of Bhargavaea massiliensis sp. nov., and Dietzia massiliensis sp. nov., respectively.

Prevalence, risk-factors, and antimicrobial susceptibility profile of methicillin-resistant Staphylococcus aureus (MRSA) obtained from nares of patients and staff of Sokoto state-owned hospitals in Nigeria.

Aim: The aim of the study was to determine the prevalence of methicillin-resistant Staphylococcus aureus (MRSA) obtained from the nasal cavity of participants and investigate the antibiotic resistance profiles of the isolates from Sokoto state, Nigeria. Methods: Nasal swabs of both nares were obtained from 378 participants across three study centers within the six-month study period. The Staphylococcus aureus isolates recovered were characterized, and their resistance phenotype determined in conjunction with MRSA prevalence. Results: Phenotypic screening of isolates obtained in this study revealed a total of 131 (17.3%) coagulase-positive Staphylococci out of 756 samples. Of this number, there were 81 (61.8%) S. aureus, 36 (27.5%) Staphylococcus intermedius, 6 (4.5%) Staphylococcus hyicus, and 8 (6.1%) Staphylococcus schleiferi. Conclusion: This study found a prevalence of 61.8% and 46.9% of S. aureus and MRSA among the studied hospitals in Sokoto state, thus demonstrating that the nares of the hospital populace are not free from S. aureus and MRSA colonization.

First whole genome sequence of Paenalcaligenes suwonensis bearing blaVIM-5 Metallo-ß-lactamase: A clinical isolate responsible for acute gastroenteritis.

Carbapenemase-producing Alcaligenes species has been described in only few studies, with none so far from the African continent. Here, we report the whole genome sequence of Peanalcaligenes suwonensis bearing blaVIM-5 metallo-ß-lactamase and first detection of carbapenemase producing Alcaligenes faecalis isolated from patients attending tertiary healthcare facilities in Nigeria. The isolates were identified by MALDI-TOF Mass Spectrometry. Antibiotic susceptibility assay, modified Carba NP test and genomic investigation revealed that two isolates of Alcaligenes faecalis and an isolate of Paenalcaligenes suwonensis harboured blaVIM-5 gene. The genome sequence analysis of the P. suwonensis 191B isolate, responsible for acute gastroenteritis, reveal the presence of 18 antibiotic resistance genes coding for resistance to five different classes of antibiotics. Three of the genes (blaOXA-368, blaCARB-4 and blaVIM-5) codes for resistance to ß-lactam antibiotics. To our best knowledge, we describe here the first genome sequence of P. suwonensis species and the first detection of class B carbapenemase blaVIM-5 in a clinical isolate of P. suwonensis species and Alcaligenes faecalis in Nigeria. The finding of this study is of concern, as lateral dissemination of the genes into clinically important Gram-negative pathogens is highly likely.

A systematic review on the prevalence of extended-spectrum beta lactamase-producing Gram-negative bacteria in Nigeria.

OBJECTIVE: There are numerous reported cases of extended-spectrum beta-lactamases (ESBLs) producing Enterobacteriaceae in Nigeria. Yet, there are regions in Nigeria where cases of ESBL were under-reported. The review aims to assess the prevalence of ESBL-producing Gram-negative bacteria in Nigeria and the genes involved. METHODS: An extensive literature search was carried out through an electronic database including PubMed, Scopus, Google Scholar and African Journals Online (AJOL). Articles published between January 2004 and November 2019 were included in the study. The titles and abstracts of the retrieved articles were reviewed, and then the full texts of the selected articles were reviewed. Articles were divided according to geopolitical zones. RESULTS: Among the 217 articles identified, 60 studies (10 from north-central, 4 from northeast, 7 from the northwest, 17 from the southeast, 10 from south-south, and 12 from southwest Nigeria) were included. The highest prevalence recorded was 82.3%, while the lowest was 7.5%. The genes TEM, SHV, and CTX-M were the predominant variant commonly found. The most frequently used phenotypic detection method is the double disc synergy test (DDST). CONCLUSION: ESBL-producing Gram-negative bacteria in hospital and community settings in Nigeria were commonly found. The prevalence of ESBL is very high, with one of the geopolitical zones under-reported. Future research should be conducted in these zones where there are scant studies, and a holistic approach involving the clinicians, researchers, laboratory scientists, and patients will go a long way in reducing the dissemination of this resistance mechanism.

Molecular detection of chloramphenicol-florfenicol resistance (cfr) genes among linezolid resistant MRSA isolates in Sokoto State, Nigeria / Detecção molecular de genes de resistência ao cloranfenicol-florfenicol (cfr) entre isolados de MRSA resistentes a linezolida no estado de Sokoto, Nigéria

Objective: we investigated previous literatures for documentation of the trend in Sokoto, Nigeria and found none. We deemed it fit to determine the frequency of linezolid resistance mediated by cfr gene among MRSA isolates from Sokoto State-owned hospitals. Methods: Bacterial species identification was carried out with Microgen™ Staph-ID System kit (Microgen, Surrey, UK). Disc agar diffusion method (Modified Kirby-Bauer's) following Clinical and Laboratory Standards Institute (CLSI 2018) guidelines was used in antimicrobial susceptibility testing. The results were interpreted and managed using WHONET 5.6 software (WHO, Switzerland). Oxacillin resistant screening agar base (ORSAB) culture was used to determine phenotypic methicillin resistance. Polymerase chain reaction (PCR) was carried out to determine the presence of cfr-gene. Results: A total of 81 S. aureus isolates were phenotypically identified. Of this number, 46.91% (38/81) were MRSA; Healthcare workers (39.5%), Outpatient (28.9%), In patient (21%), Security men and Cleaners (5.3% each). Importantly linezolid resistance rate among the MRSA isolates was 44.7%. Analysis of antimicrobial susceptibility profile also showed a multiple antibiotics resistance burden of MDR (5.9%), possible XDR (47.1%), XDR (41.1%) and PDR (5.9%) amongst LR-MRSA. About 52.9% (9/17) of LR-MRSA harbored the cfr gene. Conclusions: This is the first report to document cfr gene in LR-MRSA strains in Sokoto. The cfr gene was found among the studied LR-MRSA strains and if cfr-mediated linezolid resistance is not properly checked, its phenotypic expression may result in an outbreak of multiple antibiotic resistant strains.

Objetivo: avaliar a incidência de resistência linezolida cfr-mediada entre os isolados de MRSA dos hospitais do Estado de Sokoto. Métodos: A identificação das espécies bacterianas foi realizada com Microgen™ Staph-ID System kit (Microgen, Surrey, UK). Método de difusão em ágar de disco (Kirby-Bauer modificado) seguindo as diretrizes do Clinical and Laboratory Standards Institute (CLSI 2018). O resultado foi interpretado e gerido com WHONET 5.6 (OMS, Suíça) software. A cultura ORSAB (Oxacillin resistant screening agar) foi utilizada para determinar a resistência fenotípica à meticilina. A PCR foi realizada para determinar a presença de cfr-gene. Resultados: um total de 81 isolados de S. aureus foi identificada fenotipicamente. Desse número, 46,91% (38/81) eram de MRSA; Profissionais de saúde (39,5%), Ambulatoriais (28,9%), Em paciente (21%), Homens de segurança e Limpadores (5,3% cada). A taxa de resistência linezolida entre os isolados de MRSA foi de 44,7%. A análise do perfil de sensibilidade antimicrobiana também mostrou uma carga de resistência a antibióticos múltiplos de MDR (5,9%), possível XDR (47,1%), XDR (41,1%) e PDR (5,9%) entre LR-MRSA. Um total de, 52,9% (9/17) da LR-MRSA abrigava o gene cfr. Conclusões: Este é o primeiro relatório a documentar o cfr-gen nas estirpes LR-MRSA em Sokoto. O gene cfr está presente entre as cepas estudadas de LR-MRSA, e se a resistência cfr-mediated linezolida não for adequadamente verificada, sua expressão fenotípica pode resultar em um surto de múltiplas cepas resistentes a antibióticos.

High prevalence of multidrug-resistant Gram-negative bacterial infections in Northwest Nigeria.

INTRODUCTION: There is limited data on the prevalence and antibiotic susceptibility profile of Gram-negative bacteria in northwest Nigeria. This study thus aimed to investigate the prevalence of multidrug resistant Gram-negative bacterial infections among patients in two healthcare facilities in Sokoto, northwest Nigeria. METHODS: A total of 735 non-duplicate clinical bacterial isolates were collected between January and July 2019, from among specimens processed by the diagnostic microbiological laboratory of the two hospitals. The isolates were identified using MALDI-TOF mass spectrometry and tested against a panel of sixteen (16) antibiotics using the current EUCAST guidelines. RESULTS: Of the 735 randomly selected bacterial isolates, 397 (54.0%) yielded Gram-negative bacteria. In the two hospitals, E. coli 104 (26.2%) and Klebsiella spp. 58 (14.6%) were the most common Gram-negative pathogens implicated in all infections. Overall, the isolates exhibited moderate to high resistance to all tested antibiotics, the lowest was observed against amikacin (7.1%). The phenotypic test for ESBL and carbapenemase enzymes showed that 48 (24.6%) and 15 (32.6%) of the isolates were positive, with 88.9% of the isolates being multidrug resistant. CONCLUSIONS: The study documents prevalent high multidrug resistant Gram-negative bacterial infections, predominantly caused by E. coli and K. pneumoniae in Sokoto, northwest Nigeria. The isolates were mostly MDR and exhibited ESBL and carbapenemase activities. The findings of this study call for urgent implementation of infection control measures and antibiotic stewardship in our hospitals so as to limit the spread of antibiotic-resistant bacteria in our healthcare facilities.

Epidemiology of surgical site infections in Nigeria: A systematic review and meta-analysis.

INTRODUCTION: Surgical site infection (SSI) is a major patient safety concern in hospitals. Unlike most developed countries, Nigeria does not yet have an established national system to monitor the occurrence of this infection. This meta-analysis was thus designed to determine the pooled cumulative incidence of SSIs and various determinants of its occurrence in Nigeria. METHODS: The electronic databases were systematically searched for articles reporting the occurrence and risk factors associated with SSIs in Nigeria from January 2000 to December 2018. The eligible articles were evaluated using a set of pre-defined criteria. The extracted data were analysed using the comprehensive meta-analysis software. The Begg and Egger's regression tests were used to assess the risk of bias of the included publications. RESULTS: Thirty-two articles emanating from the six geopolitical regions of Nigeria were included in this meta-analysis. The pooled cumulative incidence of SSIs was 14.5% (95% confidence interval [CI]: 0.113-0.184) with the highest incidence reported in the north-eastern region (27.3%, 95% CI: 0.132-0.481) of the country. It was also found to occur more predominantly following colorectal and abdominal surgeries, among elderly patients and in patients with co-morbid conditions. The most frequently reported was the superficial incisional SSIs occurring in 62.5% (95% CI: 0.333-0.848). Higher preponderance was also observed among patients with dirty wounds (52.7%, 95% CI: 0.367-0.682). CONCLUSION: This meta-analysis documents for the first time the national burden of SSIs in Nigeria. Control measures geared towards its reduction should be strengthened and a national policy on SSI surveillance, prevention and control developed.

Occurrence of Surgical Site Infections at a Tertiary Healthcare Facility in Abuja, Nigeria: A Prospective Observational Study.

Surgical site infection (SSI) is one of the most frequent complications of surgical interventions. Several factors have been identified as major determinants of occurrence of SSIs. The present study determined the occurrence and possible risk factors associated with SSIs at a tertiary healthcare facility in Abuja, Nigeria. All patients scheduled for operation in the hospital during the study period and who consented to participate willingly in the study were observed prospectively for the occurrence of SSI based on criteria stipulated by the United States Centre for Disease Control and Prevention (CDC). Data on sociodemographic characteristics, lifestyle, surgical procedure and co-morbidity were collected into a pre-tested data collection tool and analysed using IBM SPSS Statistics software v.24. Predictors of SSIs were identified using multivariate logistic regression model and p-value less than 0.05 was considered statistically significant. Of the 127 surgical patients that met the inclusion criteria comprising 65 (51.2%) females and 62 (48.8%) males between 1 and 83 years with mean age of 25.64 ± 1.66 years, 35 (27.56%; 95% Confidence Interval (CI): 0.205⁻0.360) developed SSIs. Prolonged post-operative hospital stays (p < 0.05), class of wound (p < 0.0001) and some comorbid conditions were found to be significantly associated with higher SSI rate. The SSI rate was highest among patients that had Kirschner-wire insertion (75.0%), followed by an unexpectedly high infection rate among patients that had mastectomy (42.9%), while lower percentages (33.3%) were recorded among patients that had exploratory laparotomy and appendicectomy. The overall magnitude of SSIs in this facility is high (27.6%; 95% CI: 0.205⁻0.360). Several factors were found to be independent predictors of occurrence of SSI. The findings thus highlight the need for improved surveillance of SSIs and review of infection control policies of the hospital.

Molecular characterisation of extended-spectrum ß-lactamase-producing Gram-negative bacterial isolates from surgical wounds of patients at a hospital in North Central Nigeria.

OBJECTIVES: This study aimed to characterise extended-spectrum ß-lactamase (ESBL)-producing Gram-negative bacterial isolates from patients with surgical site infections (SSIs) at a tertiary healthcare facility in Abuja, Nigeria. METHODS: Consecutive, non-duplicate wound swabs were collected over a 3-month period from wounds of patients with SSI and were cultured appropriately. Bacterial isolates were identified using rapid identification kits. The modified agar disk diffusion method was used for antimicrobial susceptibility testing, and phenotypic ESBL activity of the isolates was determined using the double-disk synergy test (DDST). PCR was thereafter used for molecular characterisation of the isolates. RESULTS: A total of 57.1% (20/35) of the bacterial isolates were Gram-negative, with Pseudomonas aeruginosa (7/20; 35.0%) being the most prevalent. The isolates exhibited varying degree of antimicrobial resistance, with resistance as high as 100% for ampicillin and amoxicillin. Phenotypic ESBL production was observed in 65.0% (13/20) of the Gram-negative bacterial isolates. DNA analysis revealed that 61.5%, 53.8% and 38.5% of the isolates harboured blaSHV, blaCTX-M and blaTEM genes, respectively, with 30.8% of the isolates co-harbouring blaSHV and blaCTX-M. Similarly, 23.1% of the isolates harboured blaSHV and blaTEM, whilst 15.4% harboured blaCTX-M and blaTEM. However, none of the investigated isolates harboured a blaOXA gene. CONCLUSION: The prevalence of ESBL genes among Gram-negative SSI pathogens is high. This calls for an urgent need to review infection control policies and antimicrobial prescription patterns as well as increased surveillance of ESBLs as the possibility of an epidemic outbreak of multidrug-resistant pathogens in the hospital is high.