Clones and Clusters of Antimicrobial-ResistantKlebsiellaFrom Southwestern Nigeria

Abstract

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.

Screening and Characterization of Multidrug-Resistant Enterobacterales among Hospitalized Patients in the African Archipelago of Cape Verde

“…Moreover, it has been associated with the global dispersion of OXA-48, OXA-181, OXA-232, and OXA-204 producers [ 21 ]. In the African continent, besides South Africa, ST307 was found to be predominant among ESBL-producing K. pneumoniae isolated between 2016 and 2018 from three sentinel surveillance hospitals in Nigeria [ 22 ]. In addition, a K. pneumoniae ST307 clinical isolate harboring the bla OXA-48 gene on an IncL-type plasmid was reported in Tunisia in the same period [ 23 ].…”

Genomic characterization of invasive typhoidal and non-typhoidal Salmonella in southwestern Nigeria

“…In this report we present the outcome of genomic characterization of invasive Salmonella infections from AMR surveillance in sentinel hospitals in Nigeria. The genomic characterization of invasive Salmonella isolates in this study was possible because these hospitals perform blood culture and are enrolled in Nigeria’s new antimicrobial resistance surveillance system, which offers genomic services at the National Reference Laboratory level [26]. Nonetheless, blood culture is available at very few institutions in Nigeria, a limitation still prevalent in many African settings that impacts the genomic surveillance of invasive Salmonella .…”

Establishing a national reference laboratory for antimicrobial resistance using a whole-genome sequencing framework: Nigeria’s experience

“…As many as 33/134 (25 %) of Klebsiellae submitted to the NRL before 2019 were misidentified at the sentinel level as other Enterobacteriaceae or, in a few cases, as Pseudomonas or Acinetobacter spp. [36]. The reference laboratory’s semi-automated biochemical identification by VITEK2 made it possible to correctly identify 18 (54.5 %) of these, but we would have required some other method to correctly speciate non-pneumoniae Klebsiella spp.…”

“…We have similarly identified likely outbreaks of temporally and spatially connected Acinetobacter , Klebsiella and Enterobacter spp. that would have otherwise been unrecognized and have been able to confirm Acinetobacter baumanii and Serratia marcescens outbreaks that were suspected by sentinel sites based on epidemiological information [36, 38] (and Chioma Osuagwu, Oyinlola O. Oduyebo, Anderson O. Oaikhena, Erkison E. Odih and co-workers, unpublished). Serratia spp.…”

“…that VITEK2 incorrectly identified as K. pneumoniae [36]. Some misidentifications were due to technical or resource limitations; for example, some of our sentinel laboratories can only afford the most inexpensive and minimal suites of biochemical reagents they require to operate and many of these cannot identify common pathogens below the genus level.…”