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 β-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.

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 β-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.

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.

Concentrations of polychlorinated biphenyl in indoor environment of public bars and its health implications

This study determined the indoor air levels of polychlorinated biphenyls (PCBs) in some selected public bars in Southern part of Nigeria. The result obtained was used to carry out health risk assessment of exposure to PCBs in these indoor environment.s. Air samples were obtained from the selected popular bars using polyurethane (PUF) passive samplers. PCB quantification was done using GC-MS operated in selected ionization mode (SIM). Health risk assessment from exposure of these pollutants was determining using toxicity equivalence quotient (TEQ), inhalation risk assessment (IRA), incremental life cancer risk (ILCR), and hazard quotient (HQ). The results showed the average concentration range of 0.15-0.17 µg/m³. The mean TEQ at various locations was 0.00050 ng WHO-TEQ/m³, while the calculated daily inhalation exposure values were 0.0004 ng TEQ kg^-1 day^-1 for adults and 0.0002 ng TEQ kg^-1 day^-1 for children. The values of IRA, ILCR for the children, and HQs for both adults and children were higher than the WHO permissible limits. The study revealed that both non-carcinogenic and carcinogenic risks associated with longtime exposure to PCBs in the indoor environment public bars.