Molecular surveillance reveals widespread colonisation by carbapenemase and extended spectrum beta-lactamase producing organisms in neonatal units in Kenya and Nigeria

Abstract

Objectives Neonatal sepsis, a major cause of death amongst infants in sub-Saharan Africa, is often gut derived. Gut colonisation by Enterobacteriaceae producing extended spectrum beta-lactamase (ESBL) or carbapenemase enzymes can lead to antimicrobial-resistant (AMR) or untreatable infections. We sought to explore the rates of colonisation by ESBL or carbapenemase producers in two neonatal units (NNUs) in West and East Africa. Methods Stool and rectal swab samples were taken at multiple timepoints from newborns admitted to the NNUs at the University College Hospital, Ibadan, Nigeria and the Jaramogi Oginga Odinga Teaching and Referral Hospital, Kisumu, western Kenya. Samples were tested for ESBL and carbapenemase genes using a previously validated qPCR assay. Kaplan–Meier survival analysis was used to examine colonisation rates at both sites. Results In total 119 stool and rectal swab samples were taken from 42 infants admitted to the two NNUs. Colonisation with ESBL (37 infants, 89%) was more common than with carbapenemase producers (26, 62.4%; P = 0.093). Median survival time before colonisation with ESBL organisms was 7 days and with carbapenemase producers 16 days (P = 0.035). The majority of ESBL genes detected belonged to the CTX-M-1 (36/38; 95%), and CTX-M-9 (2/36; 5%) groups, and the most prevalent carbapenemase was blaNDM (27/29, 93%). Conclusions Gut colonisation of neonates by AMR organisms was common and occurred rapidly in NNUs in Kenya and Nigeria. Active surveillance of colonisation will improve the understanding of AMR in these settings and guide infection control and antibiotic prescribing practice to improve clinical outcomes.

The Importance of Carbapenemase-Producing Enterobacterales in African Countries: Evolution and Current Burden

“…In a 2023 study that also included Kenya, 20/24 Nigerian infants presented CPE colonization at some point during hospital admission. bla NDM was identified especially, but bla OXA-48 and bla VIM were also identified [22]. More noteworthy recent data were found in a study on Sub-Saharan countries described below [116].…”

“…Seven of eighteen (7/18) Kenyan infants tested positive for CPE colonization at some point during admission. The most prevalent gene was bla NDM , but bla OXA-48 and bla VIM were also identified [22].…”

“…It has been demonstrated that chronic carriers are prone to developing severe, hard-to-treat infections themselves, with significant morbidity and mortality rates, as some colonizing bacteria tend to express their pathogenicity factors and become virulent in particular circumstances, such as immunosuppression, imbalance of the bacterial flora, trauma, surgery, antimicrobial treatment, etc. [9,[18][19][20][21][22][23][24].…”

Gut colonization and subsequent infection of neonates caused by extended-spectrum beta-lactamase-producing Escherichia coli and Klebsiella pneumoniae

“…In this prospective study, it was revealed that upon admission to the HIMFG NICU, 27.6% (13/47) of patients were already colonized by ESBL-PEco and ESBL-PKpn. The percentage increased to 87% (41/47) by the end of the follow-up period, exceeding the reporting range, which typically ranged from 8% to 83% (Huerta-Garcıá et al, 2015;Folgori et al, 2018;Hagel et al, 2019;Edwards et al, 2023). Notably, the study by Huerta-Garcıá et al carried out in our country reported that during the second week of hospital stay, 81% of neonates were intestinally colonized by ESBL-PEco and ESBL-PKpn, while our study revealed 78.7% (37/47) colonization during the same week of hospitalization (Huerta-Garcıá et al, 2015).…”

Faecal carriage and risk factors of carbapenemase-producing gram-negative bacteria resistant to third-generation cephalosporins in hospitalized and non- hospitalized patients, Kenya

“…Gastrointestinal carriage of AMR bacteria may precede infection and, without active surveillance, can serve as a hidden reservoir for drug-resistant organisms' transmission in hospital environments [11] [12] [13]. Yet, few studies have focused on faecal carriage of MDR bacteria and risk factors for colonization in Kenya, including faecal carriage of CRE in adults and children (1%) [14], carbapenemase-producing organisms (62.4%) in hospitalized newborns [15], and ESBL Enterobacteriales among neonates before (10%) and after admission (55%) [13]. Some identi ed risk factors for colonization with antimicrobial-resistant bacteria are eating soil from the household yard, informal hand-washing stations [16], number of known carriers and participants in a ward [13].…”