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Genomic transmission analysis
of multidrug-resistant Gram-
negative bacteria within a
newborn unit of a Kenyan
tertiary hospital: A four-month
prospective colonization study
David Villinger
1,2,3
†
, Tilman G. Schultze
1,2,3
†
,
Victor M. Musyoki
4
†
, Irene Inwani
5
, Jalemba Aluvaala
5
,
Lydia Okutoyi
6
, Anna-Henriette Ziegler
1
, Imke Wieters
2,7
,
Christoph Stephan
2,7
, Beatrice Museve
8
,
Volkhard A. J. Kempf
1,2,3
*and Moses Masika
4
*
1
Institute of Medical Microbiology and Infection Control, University Hospital Frankfurt, Frankfurt am
Main, Hesse, Germany,
2
University Center of Infectious Diseases, University Hospital Frankfurt,
Frankfurt am Main, Hesse, Germany,
3
University Center of Competence for Infection Control,
Frankfurt, Hesse, Germany,
4
Department of Medical Microbiology, University of Nairobi,
Nairobi, Kenya,
5
Pediatrics Department, Kenyatta National Hospital, Nairobi, Kenya,
6
Quality Health
Department, Kenyatta National Hospital, Nairobi, Kenya,
7
Center of Internal Medicine/Infectious
Diseases Unit, University Hospital Frankfurt, Frankfurt am Main, Hesse, Germany,
8
Department of
Laboratory Medicine, Kenyatta National Hospital, Nairobi, Kenya
Objective: Multidrug-resistant organisms (MDRO), especially carbapenem-
resistant organisms (CRO), represent a threat for newborns. This study
investigates the colonization prevalence of these pathogens in a newborn
unit at a Kenyan tertiary hospital in an integrated approach combining routine
microbiology, whole genome sequencing (WGS) and hospital surveillance data.
Methods: The study was performed in the Kenyatta National Hospital (KNH) in
2019 over a four-month period and included 300 mother-baby pairs. A total of
1,097 swabs from newborns (weekly), mothers (once) and the hospital
environment were taken. Routine clinical microbiology methods were
applied for surveillance. Of the 288 detected MDRO, 160 isolates were
analyzed for antimicrobial resistance genes and phylogenetic relatedness
using whole genome sequencing (WGS) and bioinformatic analysis.
Results: In maternal vaginal swabs, MDRO detection rate was 15% (n=45/300),
including 2% CRO (n=7/300). At admission, MDRO detection rate for neonates
was 16% (n=48/300), including 3% CRO (n=8/300) with a threefold increase for
MDRO (44%, n=97/218) and a fivefold increase for CRO (14%, n=29/218) until
discharge. Among CRO, K. pneumoniae harboring bla
NDM-1
(n=20) or bla
NDM-5
(n=16) were most frequent. WGS analysis revealed 20 phylogenetically related
Frontiers in Cellular and Infection Microbiology frontiersin.org01
OPEN ACCESS
EDITED BY
Milena Dropa,
Faculty of Public Health, University of
São Paulo, Brazil
REVIEWED BY
Sameh AbdelGhani,
Beni-Suef University, Egypt
Chaitra Shankar,
Christian Medical College & Hospital,
India
Mariana Andrea Papalia,
Facultad de Farmacia y Bioquı
´mica,
Universidad de Buenos Aires,
Argentina
*CORRESPONDENCE
Volkhard A. J. Kempf
volkhard.kempf@kgu.de
Moses Masika
mosmasika@uonbi.ac.ke
†
These authors have contributed
equally to this work and share
first authorship
SPECIALTY SECTION
This article was submitted to
Clinical Microbiology,
a section of the journal
Frontiers in Cellular and
Infection Microbiology
RECEIVED 08 March 2022
ACCEPTED 05 August 2022
PUBLISHED 25 August 2022
CITATION
Villinger D, Schultze TG, Musyoki VM,
Inwani I, Aluvaala J, Okutoyi L,
Ziegler A-H, Wieters I, Stephan C,
Museve B, Kempf VAJ and Masika M
(2022) Genomic transmission analysis
of multidrug-resistant Gram-negative
bacteria within a newborn unit of a
Kenyan tertiary hospital: A four-month
prospective colonization study.
Front. Cell. Infect. Microbiol. 12:892126.
doi: 10.3389/fcimb.2022.892126
TYPE Original Research
PUBLISHED 25 August 2022
DOI 10.3389/fcimb.2022.892126
transmission clusters (including five CRO clusters). In environmental samples,
the MDRO detection rate was 11% (n=18/164), including 2% CRO (n=3/164).
Conclusion: Our study provides a snapshot of MDRO and CRO in a Kenyan
NBU. Rather than a large outbreak scenario, data indicate several independent
transmission events. The CRO rate among newborns attributed to the spread of
NDM-type carbapenemases is worrisome.
KEYWORDS
multidrug resistance, colonization, sub-Sahara, whole genome sequencing,
NDM, carbapenemase
Introduction
Neonatal mortality rates in sub-Sahara Africa, including
Kenya, continue to be among the highest worldwide (Gage
et al., 2021) and severe newborn infections are accountable for
37% of these deaths (Ahmed et al., 2018). Due to limited medical
infrastructure, reduced treatment options and high patient
vulnerability (Laxminarayan and Bhutta, 2016), patients in
newborn units (NBU) are at high risk for infections with
multidrug-resistant organisms (MDRO). A WHO-report of
2017 classifies certain Gram-negative bacteria as critical
priority (World Health Organization, 2017) with carbapenem-
resistant Acinetobacter baumannii, carbapenem-resistant or 3rd
generation-cephalosporin resistant Enterobacteriaceae and
carbapenem-resistant Pseudomonas aeruginosa as highest
concern. Especially, carbapenem-resistant A. baumannii and
Enterobacteriaceae are prone to cause long-lasting outbreaks in
hospital settings (Khalid et al., 2020). Methicillin-resistant
Staphylococcus aureus (MRSA) are other pathogens often
involved in hospital-acquired infections (Schuetz et al., 2021).
Surveillance data of MDRO, MRSA and their transmission
routes is scarce in low-and middle-income countries (Huynh
et al., 2015) but knowledge about it is essential to initiate
appropriate infection control measures. In this study, we
identified clusters of MDRO and carbapenem-resistant
organisms (CRO) at the NBU of the Kenyatta National
Hospital (KNH) in Nairobi, Kenya, by an integrated approach
combining patient data, routine microbiology results, bacterial
genome sequences and infection epidemiology analysis.
Material and methods
Study design
This was a prospective study conducted in a newborn unit at
KNH between January and April 2019. Rectal swabs from
newborns, vaginal swabs from mothers and environmental
samples from surfaces and medical equipment (on study days
d55-57 and d89) were taken over a period of four months. These
samples were analyzed for the presence of MDRO (Department
of Medical Microbiology, University of Nairobi (UoN) and the
Department of Laboratory Medicine, KNH). For a subset of
MDRO, whole-genome-sequencing was performed, and
phylogenetic relatedness of the bacterial isolates was assessed
(Institute of Medical Microbiology and Infection Control,
University Hospital Frankfurt am Main, Germany). Clusters
were analyzed by integrated metadata analysis (sampling,
location within the hospital).
Study participants
In this study, 300 mother-newborn pairs over a period of 110
days were included. Inclusion criteria were (i) admission to the
NBU and (ii) given informed consent. Exclusion criteria was any
given medical or ethical contradiction to rectal swabs of
newborns or vaginal swabs of mothers. Ethical approval was
given by KNH –UoN Ethics & Research Committee (KNH/
UoN-ERC: P208/04/2018; University of Nairobi, Kenya, College
of Health Sciences, July 11th, 2018) and by the Ethics Committee
of the Medical Faculty Goethe University Frankfurt am Main,
Germany (FKZ 01KA1772; 15/05/2018).
Study site
At KNH NBU, 200 to 300 newborns per month receive
medical care. NBU is organized into nine sub-units. At
admission, newborns are examined in the admission room.
Medicalcareisprovidedinnewbornintensivecareunits
(NICU1, NICU2, NICU3), in nurseries (nursery B1, nursery
B2, nursery B3) or in an isolation room. Nursery D is reserved
for newborns with improved health condition. The delivery
Villinger et al. 10.3389/fcimb.2022.892126
Frontiers in Cellular and Infection Microbiology frontiersin.org02
ward is separated from NBU by two floors. Mothers stay in
different post-natal wards and visit the NBU every three hours to
(breast-)feed their babies.
Sample collection
Vaginal swabs (MK Plast, New Delhi, India) were collected
from mothers once at the day their newborns were admitted
(according to the ethics proposal KNH/UoN-ERC: P208/04/
2018). Rectal swabs of newborns were taken at the day of
admission, weekly during their stay at NBU and at discharge
from the NBU. Due to ethical reasons, no sample was taken from
deceased newborns. Environmental samples were categorized as
(i) medical devices (e.g., ventilators, ultrasound transducer), (ii)
near patient (e.g., cots, incubators), (iii) far from patient (e.g.,
desks, computer equipment) or (iv) unclean areas (e.g., surfaces,
sinks), and were taken on d55-57 and d89.
Routine microbiology testing
Bacterial cultures were incubated for 24 hours at 35-37°C on
selective chromogenic ESBL agar (CHROMagar, Mast, Paris,
France). Identification (ID) and antimicrobial susceptibility
testing (AST) was done via VITEK-2 (bioMerieux SA, Marcy-
l’E
toile, France) using GN83 and P580 cards and imipenem E-
test strips (Liofilchem, Roseto degli Abruzzi, Italy) according to
Clinical Laboratory Standards Institute (CLSI) guidelines
(Clinical and Laboratory Standards Institute (CLSI), 2019).
Each ID and AST included a purity control on Columbia
blood agar. All MDRO isolates were stored at -80°C in
CRYOBANK™medium (Mast).
Sequencing
Due to the agreements of the ethics proposal (KNH/UoN-
ERC: P208/04/2018), 160 bacterial isolates (including 51/63
CRO) were selected from 288 detected MDRO for whole
genome sequencing (WGS) prioritized by the following
criteria: (i) carbapenem-resistant phenotype, (ii) culturable
bacterial status upon arrival in Germany and (iii) likeliness of
transmission onto or among newborns. Isolates were shipped on
dry ice in CRYOBANK medium to Frankfurt am Main,
Germany and were phenotypically re-assessed upon arrival
using routine microbiology methods. Identification and AST
were confirmed using Vitek-2, ID MALDI-ToF MS (bioMerieux
SA, Nürtingen, Germany) according to European Committee on
Antimicrobial Susceptibility Testing (EUCAST) guidelines
version 8.0 (accessible via https://www.eucast.org/clinical_
breakpoints/). Lateral flow assays (Hardy, Santa Maria, USA)
were used to detect the following carbapenemases: NDM, KPC,
OXA-48, VIM and IMP. All laboratory testing was performed
under strict quality control criteria (laboratory accreditation
according to ISO 15189:2011 standards) at the Institute for
Medical Microbiology and Infection Control, University
Hospital Frankfurt am Main, Germany. Isolates with
inconsistent AST, unclear documented origin and copy strains
(meaning that the same pathogen was detected in the same
newborn multiple times) were excluded from further analysis.
DNA of cultured bacteria was extracted using DNeasy
UltraClean 96 Kit (Qiagen, Venlo, Netherlands). Library
preparation and sequencing was performed by a commercial
service provider (Novogene, Cambridge, UK) using Illumina
chemistry. Sequencing was carried out on a NovaSeq 6000
flow cell using a paired-end sequencing strategy of 2x150 bp.
Details for in silico-sequenceanalysisisdescribedinthe
Supplementary Information.
Software/Statistics
Research Electronic Data Capture software (REDCap,
Vanderbilt University, Nashville, USA) was used to capture
and store sample metadata (e.g., sample type, sampling date
and time, location) and resistance phenotype (including ID, AST
and subcultures). Confidence intervals (CI) were calculated
using Newcombe-Wilson (Newcombe, 1998) method and the
Relative Risk (RR) was determined using the Armitage -Berry
Methods (Armitage et al., 2008).
Results
Sample collection and phenotypic
determination of antimicrobial resistance
A total of 300 mother-newborn pairs were included in this
study. The median age of the mothers was 27 years, and the
range of newborn gestation age was between 25 weeks+6 days to
42 weeks+0 days. These newborns were admitted to the NBU at
the day of delivery (or immediately after referral from
other hospitals).
In total, 1,097 swabs were obtained, including 164
environmental samples (Figure 1A). Among the 288 detected
MDRO, the most frequent species was K. pneumoniae (n=155)
followed by E. coli (n=83) and A. baumannii (n=7). Multidrug-
resistant P. aeruginosa isolates were not detected in any sample.
Furthermore, 63 bacterial isolates were identified as CRO
(K. pneumoniae: n=35; E. coli: n=13; A. baumannii: n=5).
At admission to NBU (after delivery or after referral from
another hospital), MDRO were detected from 16% of newborns
(n=48/300; 16%; CI 12-21%), including 3% CRO (n=8/300; 3%;
CI 1-5%). Among mothers, a 15% MDRO rate (n=45/300; 15%;
CI 11-19%), including 2% CRO (n=7/300; 2%; CI 1-5%) was
Villinger et al. 10.3389/fcimb.2022.892126
Frontiers in Cellular and Infection Microbiology frontiersin.org03
observed. The rates for mothers and newborns at admission
were similar (MDRO: RR 0.94; CI 0.65-1.36; CRO: RR 0.88; CI
0.32-2.38). For newborns, the rate of MDRO increased from
admission to discharge from 16% to 44% (n=97/218; 44%; CI 38-
51%), and for CRO from 3% to 14% (n=29/218; 14%; CI 9-18%)
indicating that 49 newborns became colonized with MDRO and
of these, 21 newborns with CRO. This represents a three-fold
increase of MDRO and a five-fold increase of CRO (MDRO: RR
2.78; CI 2.06-3.75; CRO: RR 4.99 CI 2.33-10.70). The highest
increase was observed in the first week after admission to NBU
(see Figure 1B).
MDRO and CRO isolates were obtained from medical devices
(n=9), unclean areas (n=6) and near patient areas (n=3). Rates in
NBU-environmental samples were 11% (n=18/164; 11%; CI 7-
17%) for MDRO and 2% (n=3/164; 2%; CI 1-5%) for CRO.
Genomic characterization and
phylogenetic analysis of MDRO and CRO
Of all sequenced Enterobacteriaceae, 89% (n=137/154)
harbored an extended spectrum b‐lactamase (ESBL) type
bla
CTX-M-15
. For 42/51 sequenced CRO, a bla
NDM
-type
carbapenemase gene was identified. These were distributed
among K. pneumoniae (n=25; bla
NDM-1
: n=14, bla
NDM-5
: n=10,
bla
NDM-7
: n=1), E. coli (n=11; bla
NDM-5
: n=6, bla
NDM-7
: n=5) and
other Enterobacteriaceae (n=6; all harboring bla
NDM-1
). For all
four A. baumannii isolates, a bla
OXA‐23
carbapenemase was
detected; one of those additionally harbored bla
OXA‐66
,two
others bla
OXA‐69
and one bla
OXA‐365
. Other detected
carbapenemases include bla
OXA‐232
and bla
OXA‐181
(each found
in one K. pneumoniae isolate, respectively). Detailed information
regarding sequence type and antimicrobial resistance genes is
given in Supplementary Table 1.
A phylogenetic analysis of the 160 selected isolates was carried
out. Copy strains (n=17) were excluded once confirmed by
sequence analysis. Results revealed 20 clusters of closely related
isolates, including five CRO clusters. Of these, 19 were formed by
K. pneumoniae (CRO clusters: n=4) and one cluster was formed
by E. coli (see Figure 2 and Supplementary Table 2).
Among these clusters, cluster I and II as well as cluster VI,
VII and VIII consist of isolates of the same sequence type. The
median difference between isolates of cluster VI and VII is 132
SNVs (min: 130; max: 133), of cluster VI and VIII 182 SNVs
(min: 175; max: 184) and of cluster VII and VIII 191 SNVs (min:
183; max: 193), respectively. Similarly, cluster I and II both
belong to ST39, with a median difference between the isolates of
2,380 SNVs (min: 2,380, max: 2,384). These results demonstrate
that these clusters VI, VII and VIII are distinguishable within ST
17 and clusters I and II within ST 39.
Cluster I, which consist of K. pneumoniae ST39 with
bla
CTX-M-15
, represents the largest cluster (n=15). The isolates
spanned the complete investigated period (d14 until d106) and
were obtained from 15 neonates in seven of the nine NBU-
subunits (except isolation room and NICU3).
Cluster VIII, formed by K. pneumoniae isolates of ST17
carrying bla
NDM-5
, was the largest CRO cluster (Figure 3). The
respective isolates derived from nine different newborns and
were obtained from three different subunits (Supplementary
Figure 1). The initial isolate was sampled on Nursery B3 on
d46. Six isolates were detected in Nursery D (on d74 (n=2), d82,
d85 (n=2) and d96) and two in NICU2 on d90 and
d95, respectively.
Clusters indicating transmissions among mothers and
newborns were rarely found (only cluster XIII and XIV). Only
in three cases, bacteria of the same species (K. pneumoniae with
MDRO status) were detected in mothers and their respective
newborns but none of these bacteria were phylogenetically
BA
FIGURE 1
Results of the surveillance study. (A) Study design including the respective sample numbers (MDRO, multidrug-resistant organisms; CRO,
carbapenem-resistant organisms). (B) Total prevalence of the identified bacteria grouped by sample type. “Admission”and “discharge”refer to
the particular hospital stays of patients. Column sizes indicate absolute numbers, while percentages of MDRO and CRO are given next to the
respective columns.
Villinger et al. 10.3389/fcimb.2022.892126
Frontiers in Cellular and Infection Microbiology frontiersin.org04
closely related (pairwise SNP distance: 16,780, 16,583 and >133k
SNPs, respectively) excluding vertical transmission from mother
to child. Clusters consisting of isolates obtained from the NBU-
environment and among newborn samples (cluster IX) as well as
clusters consisting exclusively of samples from mothers (cluster
XIX) were detected. Besides the already mentioned ST39 (n=26;
cluster I: n=15, cluster II: n=9; no cluster: n=2), ST17 (n=17;
including the NDM-5-positive cluster VIII: n=9) and ST348
(n=13; no carbapenemase detected) were the most frequently
found K. pneumoniae sequence types.
Plasmid MLST analysis and genomic assessment of those
regions flanking carbapenemase genes indicate that transmission
of bacteria rather than plasmid hospitalism is the dominant
mechanism for the spread of carbapenemases and the occurrence
of CRO (see Supplementary Figure 2,Supplementary Figure 3).
Discussion
This report focusses on MDRO colonization prevalence
among newborns in a tertiary hospital in Kenya with a special
emphasis on carbapenem resistance. Data revealed a five-fold
increase of CRO from 3% at admission to 14% at discharge
underlining the need for appropriate infection control actions.
Genomic analysis revealed 20 MDRO clusters and, in particular,
five heterogeneous CRO clusters (clusters: VIII: n=9 isolates; XV:
n=5; IV: n=3; XX: n=3; XIII: n=2; see Supplementary Table 2)
within the relatively short study period. These results indicate not
one ongoing outbreak scenario but several individual
transmissions and emphasize a need for multiform
counteractions which are not easy to implement in clinical
routine patient care.
BC
A
FIGURE 2
Phylogenetic analysis of the 160 sequenced isolates. Phylogenetic analysis revealed 20 clusters (I-XX) depicted as circles. (A) K. pneumoniae,
(B) E. coli,(C) A. baumannii. Circle areas represent the number of patients and environmental samples forming the cluster, while the circle color
indicates the respective sample types (rose, maternal; light blue, neonatal; green, environmental). Multilocus sequence types (ST) of clusters are
shown below each cluster. Non-typable sequence types are designated as “ST-”. Sequence types of all particular isolates are given in
Supplementary Table 1.
Villinger et al. 10.3389/fcimb.2022.892126
Frontiers in Cellular and Infection Microbiology frontiersin.org05
Data on MDRO colonization prevalence among NBUs in low-
and middle-income countries is limited (Huynh et al., 2015)and
studies are often focussed on clinical infections while the
colonisation status (a prerequisite for infection) is not reported.
The most prevalent sepsis-causing pathogens in NBUs in sub-
Saharan Africa are S. aureus,Klebsiella spp. and E. coli (Okomo
et al., 2019). In our study, screening did not detect any MRSA (data
not shown). While similar to our findings, a previous study from
two hospitals in Nairobi, Kenya (Omuse et al., 2015)reportedonly
a low MRSA prevalence (3.7%), in our study only vaginal and rectal
swabs were included, which are known to be of limited sensitivity
for MRSA detection (Bitterman et al., 2010). The absence of
multidrug-resistant P. aeruginosa in other sub-Saharan NBUs
(Ghana) is also consistent with our results (Labi et al., 2020).
An earlier Kenyan study reported ESBL colonization rates of
10% at admission to NBU with an incidence of acquisition of
21.4% per day resulting in more than half of the neonates to be
colonized with ESBL within the first three days upon admission
(Kagia et al., 2019). In Ghana (Labi et al., 2020), 75% of the
Klebsiella spp. from NBUs were ESBL positive and the carriage
rate of carbapenemase-producing Klebsiella spp. was 8%. This
shows that, the MDRO colonization rate among newborns in this
study is high but within the reported range from sub-Saharan
Africa (Kagia et al., 2019;Labi et al., 2020). In contrast, a study
from a German NBUs disclosed Denkel et al., 2014 (Rettedal et al.,
2015) found 2.9% of mothers to be colonized with ESBL.
The high rate of CRO-colonized newborns at discharge (14%)
is alarming but in range with results from other sub-Saharan studies
(8-9% in South Africa (Ballot et al., 2019)andGhana(Labi et al.,
2020)). Consistently, when looking at neonatal sepsis, an increase of
CRO from about 3% (2013) to 9% (2015) was detected in South
Africa due to NDM-producing K. pneumoniae (Ballot et al., 2019)
but the underlying NDM-subtype remained unreported. Also, high
CRO rates (e.g. 24% carbapenem resistance among K. pneumoniae)
in clinical isolates at KNH have been described earlier (Wangai
et al., 2019). These reports indicate that CRO represent a significant
threat for patients and, in particular, for newborns in Kenya and
other sub-Saharan African countries.
K. pneumoniae NDM-1 was initially detected in Nairobi in
the year 2007 (Poirel et al., 2011). Among more than 200 studies
from 2010 to 2019 analysing the prevalence of NDM in Africa,
NDM-1 was dominating by far (93%) with much lower rates for
NDM-5 (4%) and NDM-7 (2%) (Safavi et al., 2020).
Enterobacteriaceae from Kenyan hospitals were reported
earlier to harbor NDM-1 and NDM-5 and for A. baumannii
OXA-23 was found to be most prevalent (Musila et al., 2021).
This carbapenemase pattern is widely reflecting the distribution
of CRO characterized in our study.
MDRO outbreaks in NBUs are frequently reported and whole
genome sequence analysis has proven a powerful tool for outbreak
analysis (Mammina et al., 2007;Dramowski et al., 2017;Johnson
and Quach, 2017;Brinkac et al., 2019;Okomo et al., 2020). Usually,
FIGURE 3
Surveillance timeline of CRO over 110 study days. From 51 detected CRO, seven copy strains were excluded resulting in 44 unique isolates. In
separate rows, the K. pneumoniae clusters IV, VIII, XIII, XV and the E. coli cluster XX are displayed.
Villinger et al. 10.3389/fcimb.2022.892126
Frontiers in Cellular and Infection Microbiology frontiersin.org06
problems in basic hygiene and increased exposure to medical
procedures are significantly associated with MDRO infections
(Haller et al., 2015). Such basic hygiene problems (possibly
originating from medical staff or mothers, or visitors) are
reflected by the high rate of MDRO/CRO detections from
environmental samples (MDRO: n=18/164; CRO: n=3/164) and
are difficult to overcome.
Shortcomings in basic hygienecontributed,e.g.,toa
K. pneumoniae ST39 outbreak in Gambia (Okomo et al.,
2020) and this sequence type was also the prevalent among
MDRO isolates (cluster I and II; n=25) in our study. In KNH,
we found 20 different clusters suggesting several independently
occurring transmission eventsoverallNBUsubunits
with MDRO isolates from mothers and environmental
samples (see Supplementary Figure 1). Unfortunately, exact
transmission routes could not be reconstructed as this topic
was not part of the initial study protocol. Clearly, the high
MDRO entry by mothers (15% MDRO, 2% CRO) and
newborns (16% MDRO, 3% CRO) at admission is a challenge
for any infection control team.
To mitigate against this threat to newborns, staff at the KNH
NBU have implemented multiple infection control measures
(e.g., infection control team with weekly ward rounds, antibiotic
stewardship team with daily consultations) and supported the
analysis of the MDRO/CRO prevalence and transmission events
strongly. Also, transmission events were clearly detected at the
NBU, the successful work of the team is reflected by the fact that
56% of the newborns were not colonized with MDRO
at discharge.
The herein described MDRO and CRO prevalence at the
NBUs of KNH is worrisome and needs further attention (i) to
clarify transmission routes and (ii) to implement further
infection control measures. Generally, the limited MDRO
surveillance data from sub-Saharan Africa indicate an increase
of CRO infections in recent years but studies analysing
colonization rather than infections are scarce (Okomo et al.,
2019). It must be assumed that the extend of antibiotic resistance
in Kenya is underestimated.
Data availability statement
Sequence data generated in this study was deposited in the
NCBI Sequence Read Archive (SRA) under BioProject
accession PRJNA804332.
Ethics statement
Ethical approval was given by KNH –UoN Ethics &
Research Committee (KNH/UoN-ERC: P208/04/2018;
University of Nairobi, Kenya, College of Health Sciences, July
11th, 2018) and by the Ethics Committee of the Medical Faculty
Goethe University Frankfurt am Main, Germany (FKZ
01KA1772; 15/05/2018).
Authors contributions
General conceptualization: DV, VK, II, IW, and LO.
Concept design and project management: DV and MM. Data
collection and bacteriology: DV, MM, A-HZ, BM, VM, JA, IW,
and LO. Data analysis non-WGS: DV, VM, A-HZ, TS, and VK.
Data analysis WGS and Figure design: TS and DV.
Writing of the manuscript DV, TS, VK, MM, and CS, II.
All authors contributed to the article and approved the
submitted version.
Funding
The authors have no competing interests to disclose.
Funding for this study was provided by DLR (Deutsches
Zentrum für Luft- und Raumfahrt) in cooperation with
German Federal Ministry of Education and Research (BMBF;
grant number 01KA1772) and partially by the LOEWE Center
DRUID (Novel Drug Targets against Poverty-Related and
Neglected Tropical Infectious Diseases). Findings and
conclusions of this study do not necessarily represent views of
the University.
Acknowledgments
We thank all laboratory and clinical staff at KNH and UHF
involved in the study, in particular G. Revathi (Aga Khan
University Hospital) and B. Maugo, M. Alacoque, S. Kinara
and C. Onsinyo (all KNH).
Conflict of interest
The authors declare that the research was conducted in the
absence of any commercial or financial relationships that could
be construed as a potential conflict of interest.
Publisher’s note
All claims expressed in this article are solely those of the
authors and do not necessarily represent those of their affiliated
Villinger et al. 10.3389/fcimb.2022.892126
Frontiers in Cellular and Infection Microbiology frontiersin.org07
organizations, or those of the publisher, the editors and the
reviewers. Any product that may be evaluated in this article, or
claim that may be made by its manufacturer, is not guaranteed
or endorsed by the publisher.
Supplementary material
The Supplementary Material for this article can be found
online at: https://www.frontiersin.org/articles/10.3389/
fcimb.2022.892126/full#supplementary-material
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