Clones and Clusters of Antimicrobial-Resistant Klebsiella From Southwestern Nigeria.

BACKGROUND: Klebsiella pneumoniae is a World Health Organization high-priority antibiotic-resistant pathogen. However, little is known about Klebsiella lineages circulating in Nigeria. METHODS: We performed whole-genome sequencing (WGS) of 141 Klebsiella isolated between 2016 and 2018 from clinical specimens at 3 antimicrobial-resistance (AMR) sentinel surveillance tertiary hospitals in southwestern Nigeria. We conducted in silico multilocus sequence typing; AMR gene, virulence gene, plasmid, and K and O loci profiling; as well as phylogenetic analyses, using publicly available tools and Nextflow pipelines. RESULTS: Phylogenetic analysis revealed that the majority of the 134 K. pneumoniae and 5 K. quasipneumoniae isolates from Nigeria characterized are closely related to globally disseminated multidrug-resistant clones. Of the 39 K. pneumoniae sequence types (STs) identified, the most common were ST307 (15%), ST5241 (12%), ST15 (~9%), and ST25 (~6%). ST5241, 1 of 10 novel STs detected, is a single locus variant of ST636 carrying dfrA14, tetD, qnrS, and oqxAB resistance genes. The extended-spectrum ß-lactamase (ESBL) gene blaCTX_M-15 was seen in 72% of K. pneumoniae genomes, while 8% encoded a carbapenemase. No isolate carried a combination of carbapenemase-producing genes. Four likely outbreak clusters from 1 facility, within STs 17, 25, 307, and 5241, were ESBL but not carbapenemase-bearing clones. CONCLUSIONS: This study uncovered known and novel K. pneumoniae lineages circulating in 3 hospitals in Southwest Nigeria that include multidrug-resistant ESBL producers. Carbapenemase-producing isolates remain uncommon. WGS retrospectively identified outbreak clusters, pointing to the value of genomic approaches in AMR surveillance for improving infection prevention and control in Nigerian hospitals.

National health insurance scheme improves access and optimization of antimicrobial use in the Obafemi Awolowo University Teaching Hospitals Complex, Ile-Ife, Nigeria.

BACKGROUND: Nigeria instituted the National Health Insurance Scheme (NHIS) for universal health coverage. This study compared the NHIS and out-of-pocket (OOP) antibiotic prescribing with the World Health Organization (WHO) optimal values. METHODS: A total of 2190 prescription forms from the NHIS and OOP were included in this study conducted at Obafemi Awolowo University Teaching Hospitals Complex, Nigeria from January 2021 to December 2022 and analysed using WHO drug prescribing guidelines. RESULTS: The average number of drugs per encounter was higher in the NHIS prescribing (χ2=58.956, p=0.00) than in OOP prescribing. The percentage of encounters with an antibiotic prescribed is higher in NHIS prescribing (χ2=46.034, p=0.000) than in OOP prescribing. The percentage of parenteral antibiotic prescribing is higher in OOP prescribing (χ2=25.413, p=0.000) than in NHIS prescribing. The percentage of antibiotic prescribed from the National Essential Medicine List is higher in NHIS prescribing (χ2=8.227, p=0.000) as well as the antibiotics prescribed from the Access category of the WHO Access, Watch and Reserve (AWaRe) Classification of antibiotics (χ2=23.946, p=0.000) when compared with OOP prescribing. CONCLUSIONS: Prescribing indicators show better performances with NHIS antibiotic prescribing and are closer to the WHO-recommended optimal values than in OPP prescribing. Hence NHIS prescribing can be an easy target for hospital antibiotic stewardship intervention for optimal antibiotic prescribing.

Lest we forget: Odunbaku Oguntona Sapara William (1895-1935) beyond the demystification of deity.

Oguntola Odunbaku Sapara Williams (born Alexander Johnson Williams, 1861-1935) was a Fellow of the Royal Institute of Public Health. This paper attempts to highlight the effort of an African doctor to fight disease outbreaks during the African colonial era. His uninterrupted 32 years career as a colonial medical officer in one of the British colonies in West Africa, provided superintendence for the eradication of smallpox as a result of this, he was credited with the demystification of metaphysical involvement in the smallpox epidemic and thus eradication of smallpox in the Lagos colony. He also provided leadership for the control of bubonic plague, and tuberculosis epidemics and pioneered initiatives to reduce maternal and infant mortality by vaccination, enactment of public health law, environmental sanitation, and health education in Southwest Nigeria.

Rectal carriage of extended-spectrum ß-lactamase-producing Enterobacteriales among neonates admitted into a special care baby unit, southwest Nigeria.

BACKGROUND: The intestinal microbiota of neonates can be colonised by extended-spectrum ß-lactamase-producing Enterobacteriales (ESBL-PE) with the risks of subsequent infections. The antimicrobial resistance profile of the gut flora of neonates is not well defined in Nigeria. This study determined the burden of rectal carriage of ESBL-PE among neonates. METHODS: We conducted a prospective longitudinal study among neonates admitted into a tertiary hospital from September 2019 to November 2019. Stools were sampled at admission and weekly until exit and processed by standard laboratory methods including polymerase chain reaction to identify ESBL genes. The ESBL-PE colonisation period prevalence at admission and acquisition rate were determined. RESULTS: The period prevalence of the ESBL-PE colonisation and acquisition rate were 46.5% (59/127) and 34.6% (36/104), respectively. Prolonged rupture of the amniotic membrane (PROM; >24 h; p=0.004, odds ratio [OR] 0.297), number of neonates on admission in the same room (p<0.001, OR 0.053) and presence of an ESBL-PE colonisers (p=0.004, OR 0.272) were independent risk factors for ESBL-PE rectal colonisation. ESBL-PE colonisation did not correlate with mortality (Fisher's exact test 1.342, p=0.196). CONCLUSIONS: The rate of ESBL-PE neonatal rectal colonisation is high in our settings and this underscores the need for a review of neonatal admission protocols, embracing of antibiotic stewardship in the management of PROM, resistance surveillance and implementation of infection prevention and control in the neonatal unit.

Clinical and bacteriological profiles of neonatal sepsis in a tertiary hospital, south-western Nigeria.

Introduction: Antibiotic-resistant bacteria complicate treatment options in neonatal sepsis, especially in developing countries. This study determined the epidemiology and bacteriological characteristics of neonatal sepsis at a tertiary hospital, in southwest Nigeria. Methods: This was a cross-sectional study from December 2017 to April 2019 among admitted babies with clinical neonatal sepsis. Blood culture was performed by semi-automated system, sepsis biomarker assay (serum procalcitonin) by a semi-quantitative kit while proforma was used to capture clinico-demographic data. Bacterial identification, antibiotic susceptibility patterns, determination of genetic elements mediating resistance, were performed by standard methods and polymerase chain reaction protocols, respectively. Quantitative data were expressed as frequencies, mean; bivariate and multivariate analyses were performed by Chi-square or Fishers' exact test and logistic regression. Results: Of the 192 cases of neonatal sepsis enrolled, 42.7% (82/192) were blood culture positive. Factors associated with blood culture positivity included respiratory rate ≥60 bpm (60/82; p<0.03), lethargy/unconsciousness (59/82; FE=7.76; p<0.001), grunting respiration (54/82; p=0.04), meconium passage before birth (17/82; p=0.03) and prolonged rupture of membranes ≥24 hours (50/82; FE=6.90; p=0.01). On the other hand, mortality in the neonates was associated with elevated serum procalcitonin assay (>0.5 ng/mL) χ2=13.58; p=0.03] and Gram-negative bacteremia (χ2=24.64; p<0.001). The most common bacterial isolates were Staphylococcus aureus (42/82), coagulase-negative Staphylococcus spp. (17/82), Enterobacter spp. (8/82), and Acinetobacter spp. (6/82). Methicillin resistance was present in 85.7% (36/42) of Staphylococcus aureus and 52.9% (9/17) of coagulase-negative Staphylococcus, while extended-spectrum beta-lactamase (ESBL) and AmpC enzymes were present in (21.1%; 4/19) of the Gram-negative bacilli. Conclusions: Almost half of the cases of clinically diagnosed neonatal sepsis have bacterial etiologic confirmation of sepsis. Gram-negative bacteremia and high serum procalcitonin predict mortality in neonatal sepsis. There was high resistance to common antibiotics for the treatment of neonatal sepsis in our settings.

An ST131 clade and a phylogroup A clade bearing an O101-like O-antigen cluster predominate among bloodstream Escherichia coli isolates from South-West Nigeria hospitals.

Escherichia coli bloodstream infections are typically attributed to a limited number of lineages that carry virulence factors associated with invasiveness. In Nigeria, the identity of circulating clones is largely unknown and surveillance of their antimicrobial resistance has been limited. We verified and whole-genome sequenced 68 2016-2018 bloodstream E. coli isolates from three sentinel sites in South-Western Nigeria and susceptibility tested 67 of them. Resistance to antimicrobials commonly used in Nigeria was high, with 67 (100 %), 62 (92.5 %), 53 (79.1 %) and 37 (55.2 %) showing resistance to trimethoprim, ampicillin, ciprofloxacin and aminoglycosides, respectively. Thirty-five (51 %) isolates carried extended-spectrum ß-lactamase genes and 32 (91 %) of these were multidrug resistant. All the isolates were susceptible to carbapenems and colistin. The strain set included globally disseminated high-risk clones from sequence type (ST)12 (2), ST131 (12) and ST648 (4). Twenty-three (33.8 %) of the isolates clustered within two clades. The first of these consisted of ST131 strains, comprising O16:H5 and O25:H4 sub-lineages. The second was an ST10-ST167 complex clade comprising strains carrying O-antigen and capsular genes of likely Klebsiella origin, identical to those of avian pathogenic E. coli Sanji, and serotyped in silico as O89, O101 or ONovel32, depending on the tool used. Four temporally associated ST90 strains from one sentinel were closely related enough to suggest that at least some of them represented a retrospectively detected outbreak cluster. Our data implicate a broad repertoire of E. coli isolates associated with bloodstream infections in South-West Nigeria. Continued genomic surveillance is valuable for tracking clones of importance and for outbreak identification.

Multicentre study of the burden of multidrug-resistant bacteria in the aetiology of infected diabetic foot ulcers.

BACKGROUND: Infected diabetic foot ulcer (IDFU) is a public health issue and the leading cause of non-traumatic limb amputation. Very few published data on IDFU exist in most West African countries. OBJECTIVE: The study investigated the aetiology and antibacterial drug resistance burden of IDFU in tertiary hospitals in Osun state, Nigeria, between July 2016 and April 2017. METHODS: Isolates were cultured from tissue biopsies or aspirates collected from patients with IDFU. Bacterial identification, antibiotic susceptibility testing and phenotypic detection of extended-spectrum beta-lactamase and carbapenemase production were done by established protocols. Specific resistance genes were detected by polymerase chain reaction. RESULTS: There were 218 microorganisms isolated from 93 IDFUs, comprising 129 (59.2%) Gram-negative bacilli (GNB), 59 (27.1%) Gram-positive cocci and 29 (13.3%) anaerobic bacteria. The top five facultative anaerobic bacteria isolated were: Staphylococcus aureus (34; 15.6%), Escherichia coli (23; 10.6%), Pseudomonas aeruginosa (20; 9.2%), Klebsiella pneumoniae (19; 8.7%) and Citrobacter spp. (19; 8.7%). The most common anaerobes were Bacteroides spp. (7; 3.2%) and Peptostreptococcus anaerobius (6; 2.8%). Seventy-four IDFUs (80%) were infected by multidrug-resistant bacteria, predominantly methicillin-resistant S. aureus and GNB producing extended-spectrum ß-lactamases, mainly of the CTX-M variety. Only 4 (3.1%) GNB produced carbapenemases encoded predominantly by bla VIM. Factors associated with presence of multidrug-resistant bacteria were peripheral neuropathy (adjusted odds ratio [AOR] = 4.05, p = 0.04) and duration of foot infection of more than 1 month (AOR = 7.63, p = 0.02). CONCLUSION: Multidrug-resistant facultative anaerobic bacteria are overrepresented as agents of IDFU. A relatively low proportion of the aetiological agents were anaerobic bacteria.

Antimicrobial use among hospitalized patients: A multi-center, point prevalence survey across public healthcare facilities, Osun State, Nigeria.

INTRODUCTION: In order to inform sub-national action plan for control of antimicrobial resistance (AMR) and benchmark interventions to improve antibiotic use, it is essential to define situations on antibiotic use using standardized tools. We sought to assess quality of antimicrobial prescription across all government healthcare facilities with capacities for in-patient care in the first of the 36 states in Nigeria as part of ongoing state-wide situation analysis on AMR. METHODS: A survey was conducted between 10-27 June 2019 using the WHO methodology for point prevalence survey on antibiotic use in hospitals. Data was collected from hospital administrators and records of hospitalized patients. Data analysis was done using Microsoft Excel 2010 (Redmond Washington). RESULTS: Prevalence of antibiotic use amongst all 321 included patients was 76.6% (246/321). Of all indications recorded, the highest was surgical prophylaxis (96/260, 36.9%) for which there were multiple doses beyond 24 hours in almost all cases (91/96, 94.8%). The largest volume of prescribing took place in the surgical wards, and the most common prescriptions were metronidazole (142/564, 25.2%), cefuroxime (104/564, 18.4%), and ceftriaxone (77/564, 13.7%). Overall, 46.3% of the antibiotics used belong to Access group, 53.5% to watch and only 0.2% to Reserve. Treatment in almost all instances 544/563 (96.6%) was empiric. CONCLUSIONS: The majority of patients received multiple antibiotics mostly without compliance to guidelines. There was low prescribing of Access antibiotics and excessive use of antibiotics in the Watch group. Antibiotics were used most commonly for surgical prophylaxis but inappropriately. Inappropriate use of antibiotics in this study underscores the crucial need for an action plan incorporating antimicrobial stewardship.