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.

Epizootiology and Molecular Identification of Trypanosome Species in Livestock Ruminants in the Gambia.

INTRODUCTION: African Animal Trypanosomiasis (AAT) or nagana in animals, is caused by the blood-borne parasitic protozoa called trypanosomes, and is potentially fatal. It is estimated that Africa loses $4‒5 billion annually due to the death of livestock to nagana in the tsetse belt. PURPOSE: Although The Gambia lies within this belt, there is scanty data regarding the epizootiology of nagana in The Gambia. Here, records of reported cases of nagana for the period 2010-2019 at the International Trypanotolerance Centre (ITC) in The Gambia were analyzed retrospectively. METHODS: For insights into the current prevalence of AAT, blood samples of 384 cattle, 42 goats, and 59 sheep from the Central River Region (CRR) and Lower River Region (LRR) were analyzed microscopically for parasite identification. Furthermore, trypanosomes were characterized by polymerase chain reaction (PCR) using a panel of primers that identify trypanosomes to the level of the species and subspecies by targeting a portion of the internally transcribed spacer-one (ITS-1) of the ribosomal RNA. RESULTS: The retrospective study indicates that Trypanosoma vivax (66%) and T. congolense (33.4%) were the predominant species. Based on the archive records of ITC, the villages Touba, Misera, and Sambel Kunda all in the CRR of the Gambia are the most burdened with AAT. Microscopic examination of blood samples from cattle showed a prevalence of 1.56%, whereas the PCR-based analysis gave a higher prevalence of 12.5%. The molecular analysis revealed the presence of T. vivax (3.65%), T. congolense kilifi (2.6%), T. b. brucei (1.3%), T. congolense savannah/forest (0.52%), T. b. gambiense (0.52%). Interestingly, 4.43% of mixed infections i.e. multiple trypanosome species in individual animals were recorded. In 18% of the mixed infection cases, T. godfreyi, T. simiae were coinfecting cattle alongside T. congolense. The molecular identification including the phylogenetic analysis implicated T. congolense as the most predominant trypanosome species infecting animals in The Gambia. CONCLUSION: The incidence of nagana in The Gambia is documented and the prevalent trypanosomes identified to be T. vivax, different types of T. congolense, and T. brucei including the gambiense subspecie. Finally, nagana is less profound in sheep and goats compared to cattle, with seasonal and regional variations playing a significant role in the disease dynamics.

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.

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.

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.