Molecular characterization of invasive Enterobacteriaceae from pediatric patients in Central and Northwestern Nigeria

Abstract

Background Bacteremia is a leading cause of mortality in developing countries, however, etiologic evaluation is infrequent and empiric antibiotic use not evidence-based. Here, we evaluated the patterns of ESBL resistance in children enrolled into a surveillance study for community acquired bacteremic syndromes across health facilities in Central and Northwestern Nigeria. Method Blood culture was performed for children aged less than 5 years suspected of having sepsis from Sept 2008-Dec 2016. Blood was incubated using the BACTEC 00AE system and Enterobacteriacea identified to the species level using Analytical Profile Index (API20E ® ). Antibiotic susceptibility profile was determined by the disc diffusion method. Real time PCR was used to characterize genes responsible for ESBL production. Result Of 21,000 children screened from Sept 2008-Dec 2016, 2,625(12.5%) were culture-positive. A total of 413 Enterobacteriaceae available for analysis were screened for ESBL. ESBL production was detected in 160 Enterobacteriaceae , high resistance rates were observed among ESBL-positive isolates for Ceftriaxone (92.3%), Aztreonam (96.8%), Cefpodoxime (96.3%), Cefotaxime (98.8%) and Trimethoprim/sulfamethoxazole (90%), while 87.5%, 90.7%, and 91.9% of the isolates were susceptible to Imipenem, Amikacin and Meropenem respectively. Frequently detected resistance genes were bla TEM—83.8% (134/160), and, bla CTX-M 83.1% (133/160) followed by bla SHVgenes 66.3% (106/160). Co-existence of bla CTX-M, bla TEM and bla SHV was seen in 94/160 (58.8%), bla CTX-M and bla TEM in 118/160 (73.8%), bla TEM and bla SHV in 97/160 (60.6%) and bla CTX-M and bla SHV in 100/160 (62.5%) of isolates tested. Conclusion Our results indicate a high prevalence of bacteremia from ESBL Enterobacteriaceae in this population of children. These are resistant to commonly used antibiotics and careful choice of antibiotic treatment options is critical. Further studies to evaluate transmission dynamics of resistance genes could help in the reduction of ESBL resistance in these settings.

Multi-drug resistance and high mortality associated with community-acquired bloodstream infections in children in conflict-affected northwest Nigeria

“…The 20% blood culture positivity rate identified in our study is similar to those obtained in the few available studies from hospitalized children < 5 years of age in Nigeria, ranging between 11 and 30% [21][22][23] . Half of the bacteria implicated in confirmed CA-BSI in this study were GNB.…”

“…This is similar to the results from a recent metaanalysis of pediatric CA-BSI that included six studies from African hospitals where 54.8% (CI95% 45.1-64.4) of infections were due to GNB. ESBL producing bacteria were identified in 22% of the GNB isolates which is higher than the 6% of ESBL producing Enterobacterales isolated in Enugu (Nigeria) in 2019 24 but closer to the 39% of ESBL positive GNB reported from central and northwest Nigeria in 2020 in similar patient groups 22 . It has been shown that malnourished children have an increased risk for acquisition of ESBL producing Enterobacterales when exposed to amoxicillin 25 .…”

Bacterial Blood Isolates in Children: Conventional vs. Bactec Automated Blood Culture System in a Tertiary Health Centre in Gombe, North East Nigeria

“…This differentiation can be accurately done by the semiautomated systems now available years [60] [61] [62]. This easier identification systems may have contributed to the increasing reports of Alcaligenes spp in recent years In this study Citrobacter constituted the third most common isolate by Bactec method with greater detection rate over the manual method.…”

An ST131 clade and a Phylogroup A clade bearing a novel Escherichia coli O-antigen cluster predominate among bloodstream E. coli isolates from southwest Nigeria hospitals

“…Although studies conducted in Africa and other low-and middle-income countries (LMICs) have shown the abundance of invasive E. coli [9,10], these studies are too few and far between so that ExPEC and AMR epidemiology are poorly understood [7,11]. In Nigeria, there is sparse molecular information on ExPEC, but a few studies point to likely clonal expansion of resistant lineages and local presence of pandemic clones of concern [12][13][14][15][16]. These studies provide valuable information but represent an insufficient picture of ExPEC clones in Nigeria with few data available from South.…”

“…Escherichia coli isolates were often misidentified as Klebsiella pneumoniae (n = 8) or Citrobacter freundii (n = 6) at the sentinel laboratories, while the VITEK2 system misidentified E. coli as Klebsiella pneumoniae (n = 3) or Enterobacter aerogenes (n = 1).Phylogroups, Serotypes, and Sequence Types of E. coli bloodstream isolatesE. coli sent from all three hospital sentinel laboratories spanned all E. coli phylogroups, with18,15,19,8,2, 1, and 5 E. coli genomes classified within phylogroups A, B1, B2, C, D, E, and F, respectively. The most common sequence types (ST) among the 33 identified STs include; ST131 (n = 12), ST156 (n = 5), and 4 each of ST10, ST167 ST410, ST648, and ST90.…”