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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

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Frontiers in Cellular and Infection Microbiology
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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 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.
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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 vefold 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
rst 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 ve 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 classies 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
identied 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
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ward is separated from NBU by two oors. 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). Identication (ID) and antimicrobial susceptibility
testing (AST) was done via VITEK-2 (bioMerieux SA, Marcy-
lE
toile, France) using GN83 and P580 cards and imipenem E-
test strips (Liolchem, 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
CRYOBANKmedium (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. Identication and AST
were conrmed 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 ow 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
ow 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). Condence 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 identied 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 ve-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 rst 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 blactamase (ESBL) type
bla
CTX-M-15
. For 42/51 sequenced CRO, a bla
NDM
-type
carbapenemase gene was identied. 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
OXA23
carbapenemase was
detected; one of those additionally harbored bla
OXA66
,two
others bla
OXA69
and one bla
OXA365
. Other detected
carbapenemases include bla
OXA232
and bla
OXA181
(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 conrmed by
sequence analysis. Results revealed 20 clusters of closely related
isolates, including ve 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 identied bacteria grouped by sample type. Admissionand dischargerefer 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 anking 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 ve-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,
ve 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
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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 ndings, 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 rst 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 signicant
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 reecting 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 signicantly associated with MDRO infections
(Haller et al., 2015). Such basic hygiene problems (possibly
originating from medical staff or mothers, or visitors) are
reected by the high rate of MDRO/CRO detections from
environmental samples (MDRO: n=18/164; CRO: n=3/164) and
are difcult 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 reected 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).
Conict of interest
The authors declare that the research was conducted in the
absence of any commercial or nancial relationships that could
be construed as a potential conict of interest.
Publishers note
All claims expressed in this article are solely those of the
authors and do not necessarily represent those of their afliated
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reviewers. Any product that may be evaluated in this article, or
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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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... Beta-lactamases were the most common AMR genes identified, with a predominance of AmpH, penicillin binding protein (PBP), TEM and CTX-M gene types, conferring resistance to ampicillin and 3 rd generation cephalosporins, which, along with Gentamicin, are WHO recommended first and second line antibiotics for neonatal sepsis. The low prevalence of carbapenem resistance genes in our isolates contrasts with higher levels reported from Kenya (14%) 52 , Ghana (15.6%) 53 , and Thailand (64%) 54 , likely reflecting the limited availability of carbapenem antibiotics in our setting and thus reduced selective pressure. However, nearly ubiquitous presence of blaMbl in A. baumannii is of concern due to risk of inter-species transfer due to mobile genetic elements 55 . ...
... The high maternal MDR-GNB carriage prevalence (76%) is consistent with some other African studies 24 , although is markedly higher than a similar neonatal-maternal dyad study in Kenya (15%) 52 , and contrasts with lower prevalence observed in Europe (France, 12.8%;) 24 and the Middle East (Lebanon, 19.1%). As maternal samples were obtained within 72 h of NNU admission following delivery at different health facilities, we cannot speculate on the source of maternal carriage which may reflect widespread community prevalence or health facility related acquisition during labour. ...
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Background This detailed genomic study characterised multi-drug resistant-Gram negative bacilli (MDR-GNB) carriage in neonates < 2 kg and paired mothers at a low-resource African hospital. Methods This cross-sectional cohort study was conducted at the neonatal referral unit in The Gambia with weekly neonatal skin and peri-anal sampling and paired maternal recto-vaginal swabs. Prospective bacteriological culture used MacConkey agar with species identification by API20E and API20NE. All GNB isolates underwent whole genome sequencing on Illumina Miseq platform. Multi-Locus Sequence Typing and SNP-distance analysis identified strain type and relatedness. Results 135 swabs from 34 neonates and 21 paired mothers, yielded 137 GNB isolates, of which 112 are high quality de novo assemblies. Neonatal MDR-GNB carriage prevalence is 41% (14/34) at admission with 85% (11/13) new acquisition by 7d. Multiple MDR and ESBL-GNB species are carried at different timepoints, most frequently K. pneumoniae and E. coli, with heterogeneous strain diversity and no evidence of clonality. 111 distinct antibiotic resistance genes are mostly beta lactamases (Bla-AMPH, Bla-PBP, CTX-M-15, Bla-TEM-105). 76% (16/21) and 62% (13/21) of mothers have recto-vaginal carriage of ≥1 MDR-GNB and ESBL-GNB respectively, mostly MDR-E. coli (76%, 16/21) and MDR-K. pneumoniae (24%, 5/21). Of 21 newborn-mother dyads, only one have genetically identical isolates (E. coli ST131 and K. pneumoniae ST3476). Conclusions Gambian hospitalised neonates exhibit high MDR and ESBL-GNB carriage prevalence with acquisition between birth and 7d with limited evidence supporting mother to neonate transmission. Genomic studies in similar settings are required to further understand transmission and inform targeted surveillance and infection prevention policies.
... Among CRO, the most prevalent were K. pneumoniae and E. coli harboring blaNDM-1, blaNDM-5 and blaNDM-7, but blaOXA-181 and blaOXA-232 were also identified. Furthermore, a 3% (n = 3/164) CRO rate was reported in the hospital environment [82]. A surveillance report published in 2023 evaluated 119 stool samples and rectal swabs collected from 42 infants in 2018-2019. ...
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Antimicrobial resistance (AMR) is a worldwide healthcare problem. Multidrug resistant organisms (MDRO) have the ability to spread quickly owing to their resistance mechanisms. Although colonized individuals are crucial MDRO dispensers, colonizing microbes have the potential to turn pathogenic under certain conditions, leading to symptomatic infections in carriers. Carbapenemase producing Enterobacterales (CPE) are among the most important MDRO involved in infections and colonizations, associating with multiple resistance mechanisms and virulence factors, causing infections with severe outcomes. All research papers identified in the most comprehensive online databases which contained information related to the topic of this article were analyzed, and relevant data was extracted and included. The first information on CPE could be traced back to the mid-2000s, but pertinent data for many African countries was established in the past 5-8 years. Information is presented chronologically for each country. Although no clear conclusions could be drawn for some countries, it was observed that CPE colonizations are present in most African countries and carbapenem-resistance levels are rising. The most common CPE involved are Klebsiella pneumoniae and Escherichia coli, and the most prevalent carbapenemases are NDM-type and OXA-48-type enzymes. Prophylactic measures, such as screening, are required to combat this phenomenon.
... Although β-lactams are the most commonly used antibiotics in community and hospital settings in Djibouti, and often inappropriately so, carbapenems are beginning to be prescribed as a treatment of last resort for life-threatening infections caused by multidrug-resistant bacteria. Other studies first carried out in East Africa reported the presence of the bla NDM gene in Gram-negative bacteria, including one strain of A. baumannii in Kenya in 2013 [31,32], three bla NDM genes in Ethiopia in 2017 [31], and in surrounding countries like Yemen in which the bla NDM gene has also been reported in 2014 [33]. The emergence of these species exhibiting an MDR phenotype can be explained by the importation of resistant isolates from countries bordering Djibouti during travel or migratory flows. ...
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Introduction: The antimicrobial resistance (AMR) of bacteria is increasing rapidly against all classes of antibiotics, with the increasing detection of carbapenem-resistant isolates. However, while growing prevalence has been reported around the world, data on the prevalence of carbapenem resistance in developing countries are fairly limited. In this study, we investigated and determined the resistance rate to carbapenems among multidrug-resistant Gram-negative bacteria (MDR-GNB) isolated in Djibouti and characterized their resistance mechanisms. Results: Of the 256 isolates, 235 (91.8%) were identified as Gram-negative bacteria (GNB). Of these GNBs, 225 (95.7%) isolates exhibited a multidrug resistance phenotype, and 20 (8.5%) isolates were resistant to carbapenems, including 13 Escherichia coli, 4 Acinetobacter baumannii, 2 Klebsiella pneumoniae and 1 Proteus mirabilis. The most predominant GNB in this hospital setting were E. coli and K. pneumoniae species. Carbapenemase genes such as blaOXA-48 and blaNDM-5 were identified, respectively, in six and four E. coli isolates, whereas the carbapenemase blaNDM-1 was identified in three E. coli, two K. pneumoniae, one P. mirabilis and one A. baumannii. Moreover, three A. baumannii isolates co-hosted blaOXA-23 and blaNDM-1. Materials and Methods: A total of 256 clinical strains collected between 2019 and 2020 were identified using matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF). Antibiotic susceptibility testing was performed using disk diffusion and E-test methods. Real-time polymerase chain reaction (RT-PCR), standard PCR and sequencing were used to investigate genes encoding for extended-spectrum-β-lactamases, carbapenemases and colistin resistance genes. Conclusions: We report, for the first time, the presence of MDR-GNB clinical isolates and the emergence of carbapenem-resistant isolates in Djibouti. In addition to performing antimicrobial susceptibility testing, we recommend phenotypic and molecular screening to track the spread of carbapenemase genes among clinical GNB isolates.
... Multi-drug resistance (MDR) bacteria were alarmingly reported in the latest years as causing agents of both EOS and LOS [6][7][8][9]. Moreover, several outbreaks caused by MDR organisms in Neonatal Intensive Care Units (NICUs) recently occurred in different regions, including high-income countries (HICs) [10][11][12][13][14], and consistent colonization of both patients admitted to NICUs [15][16][17] and of pregnant women [18] is reported, threatening the outcomes of both EOS and LOS cases. ...
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Background: Infections by multi-drug-resistant (MDR) organisms are sharply increasing in newborns worldwide. In low and middle-income countries, a disproportionate amount of neonatal sepsis caused by MDR Gram negatives was recently reported. Newborns with infections by MDR organisms with limited treatment options may benefit from novel antimicrobials. Methods: We performed a literature search investigating the use in newborns, infants and children of novel antimicrobials for the treatment of MDR Gram negatives, namely ceftazidime/avibactam, ceftolozane/tazobactam, cefiderocol, meropenem/vaborbactam, imipenem/relebactam, and Gram positives with resistance of concern, namely ceftaroline and dalbavancin. PubMed, EMBASE, and Web of Science were searched. Results: A total of 50 records fulfilled the inclusion criteria. Most articles were case reports or case series, and ceftazidime/avibactam was the most studied agent. All studies showed favorable efficacy and safety profile in newborns and across different age cohorts. Conclusions: novel antibiotics may be considered in newborns for the treatment of MDR Gram negatives with limited treatment options and for Gram positives with resistance concerns. Further studies are needed to address their effectiveness and safety in newborns.
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Carbapenem-resistant bacteria (CRB) present a significant global public health concern. Sub-Saharan Africa has borne a heavy burden of CRB with a reported prevalence of up to 60% in some patient populations. es in Africa focus on clinical CRB isolates, with limited data on their spread in the natural environment. Therefore, the purpose of this study was to report the recovery of CRB from Nairobi River surface waters and nearby anthropogenic and zoonotic sources in Nairobi County, Kenya. A total of 336 CRB were recovered from 336 (250 mL) samples, with 230 of the samples (68.5%) producing one or more CRB isolates. CRB were recovered most commonly from untreated sewage influent (100% of 36 samples; 79 total isolates), treated effluent (93% of 118 samples; 116 total isolates), Nairobi River surface waters upstream (100% of 36 samples; 57 total isolates), downstream (100% of 36 samples; 45 total isolates), and way downstream from the wastewater treatment plant (73% of 11 samples; 19 total isolates), slaughterhouse effluent discharges 1.5%, (5/336), animal contact areas 0.9%, (3/336), a manhole sewer from the affluent neighborhood of Karen at 2.7%, (9/336) respectively. The CRB included Escherichia coli (158, 47%), Klebsiella pneumoniae (74, 22%), and Enterobacter spp (43, 13%). Aeromonas spp (29, 9%) Acinetobacter baumannii (12, 3.6%), Citrobacter freundii (7, 2.1%), Pseudomonas aeruginosa (5, 1.5%) and other species (8, 2.4%). CRB genotypes included blaNDM (246, 73.2%), blaKPC (40, 12%), blaVIM (51, 15.2%), blaOXA-48-like (65, 19.3%), blaIMP (15, 4.5%), and blaGES (7, 2.1%). Sixty-nine of the CRB isolates (20.5%) harbored multiple carbapenemase-encoding genes. Our results indicate that clinically important CRB are commonly present in Nairobi River surface water and from nearby wastewater and livestock sources. These pose an important public health threat that requires urgent intervention strategies and additional investigation.
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Importance In low- and middle-income countries (LMICs), neonatal bacterial infections are mainly caused by Enterobacterales species and Staphylococcus aureus , which are also the leading causes of mortality directly attributable to antimicrobial resistance. As bacterial colonization often precedes infection, better knowledge of colonization is crucial to prevent antibiotic-resistant neonatal sepsis. Objective To synthesize current evidence on the prevalence of and factors associated with colonization with third-generation cephalosporin–resistant Enterobacterales (3GCRE), carbapenem-resistant Enterobacterales (CRE), and methicillin-resistant S aureus (MRSA) during the first 3 months of life in LMICs. Data Sources PubMed, Scopus, Web of Science, and the World Health Organization Global Index Medicus were searched for articles published from January 1, 2000, through July 29, 2024. Study Selection Included studies were conducted in LMICs and reported prevalence rates or factors associated with colonization with 3GCRE, CRE, or MRSA in neonates and infants up to 3 months of age. Outbreak reports were excluded. Data Extraction and Synthesis Data extraction and risk-of-bias assessment using a Joanna Briggs Institute tool were performed by 2 independent reviewers. Pooled prevalence for each pathogen was computed using a random-effects model. Reporting followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guideline. Main Outcomes and Measures Prevalence of and factors associated with 3GCRE, CRE, and MRSA colonization. Results Of the 3147 articles identified in the search, 67 studies (51 for 3GCRE and CRE and 16 for MRSA) including 17 152 individuals were eligible. The pooled prevalence of 3GCRE colonization was 30.2% (95% CI, 21.4%-40.7%; τ ² = 1.48; I ² = 95.1%), varying from 18.2% (95% CI, 10.8%-29.1%) in nonhospitalized individuals to 48.2% (95% CI, 36.4%-60.2%) in hospitalized individuals. The prevalence of CRE colonization was 2.6% (95% CI, 0.7%-8.8%; τ ² = 7.79; I ² = 95.6%), while it was 2.7% (95% CI, 1.0%-6.7%; τ ² = 2.58; I ² = 93.5%) for MRSA. Increased risk of colonization with 3GCRE was associated with hospital birth (odds ratio [OR], 1.87; 95% CI, 1.33-2.64), neonatal antibiotic use (OR, 2.96; 95% CI, 1.43-6.11), and prolonged rupture of membranes (OR, 3.86; 95% CI, 2.19-6.84). Conclusions and Relevance In this systematic review and meta-analysis of antibiotic-resistant pathogen carriage in individuals aged 0 to 3 months, the pooled prevalence was substantial despite a limited exposure period. Although high heterogeneity between studies limited extrapolation of results, the findings highlight the need for further investigation to identify transmission routes and to design targeted and effective preventive measures.
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Antimicrobial resistance (AMR) is a worldwide healthcare problem. Multidrug-resistant organisms (MDROs) can spread quickly owing to their resistance mechanisms. Although colonized individuals are crucial for MDRO dissemination, colonizing microbes can lead to symptomatic infections in carriers. Carbapenemase-producing Enterobacterales (CPE) are among the most important MDROs involved in colonizations and infections with severe outcomes. This review aimed to track down the first reports of CPE in Africa, describe their dissemination throughout African countries and summarize the current status of CRE and CPE data, highlighting current knowledge and limitations of reported data. Two database queries were undertaken using Medical Subject Headings (MeSH), employing relevant keywords to identify articles that had as their topics beta-lactamases, carbapenemases and carbapenem resistance pertaining to Africa or African regions and countries. The first information on CPE could be traced back to the mid-2000s, but data for many African countries were established after 2015–2018. Information is presented chronologically for each country. Although no clear conclusions could be drawn for some countries, it was observed that CPE infections and colonizations are present in most African countries and that carbapenem-resistance levels are rising. The most common CPE involved are Klebsiella pneumoniae and Escherichia coli, and the most prevalent carbapenemases are NDM-type and OXA-48-type enzymes. Prophylactic measures, such as screening, are required to combat this phenomenon.
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Background In resource-constrained settings, limited antibiotic options make treating carbapenem-resistant bacterial infections difficult for healthcare providers. This study aimed to assess carbapenemase expression in Gram-negative bacteria isolated from clinical samples in Jimma, Ethiopia. Methods A cross-sectional study was conducted to assess carbapenemase expression in Gram-negative bacteria isolated from patients attending Jimma Medical Center. Totally, 846 Gram-negative bacteria were isolated and identified using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). Phenotypic antibiotic resistance patterns were determined using the Kirby-Bauer disk diffusion method and Etest strips. Extended-spectrum β-lactamase phenotype was determined using MAST disks, and carbapenemases were characterized using multiplex polymerase chain reactions (PCR). Results Among the isolates, 19% (157/846) showed phenotypic resistance to carbapenem antibiotics. PCR analysis revealed that at least one carbapenemase gene was detected in 69% (107/155) of these strains. The most frequently detected acquired genes were blaNDM in 35% (37/107), blaVIM in 24% (26/107), and blaKPC42 in 13% (14/107) of the isolates. Coexistence of two or more acquired genes was observed in 31% (33/107) of the isolates. The most common coexisting acquired genes were blaNDM + blaOXA-23, detected in 24% (8/33) of these isolates. No carbapenemase-encoding genes could be detected in 31% (48/155) of carbapenem-resistant isolates, with P. aeruginosa accounting for 85% (41/48) thereof. Conclusion This study revealed high and incremental rates of carbapenem-resistant bacteria in clinical samples with various carbapenemase-encoding genes. This imposes a severe challenge to effective patient care in the context of already limited treatment options against Gram-negative bacterial infections in resource-constrained settings.
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Background Since the beginning of the war in Ukraine in February 2022, Ukrainians have been seeking shelter in other European countries. Aim We aimed to investigate the prevalence and the molecular epidemiology of multidrug-resistant Gram-negative (MDRGN) bacteria and meticillin-resistant Staphylococcus aureus (MRSA) in Ukrainian patients at admittance to the University Hospital Frankfurt, Germany. Methods We performed screening and observational analysis of all patients from March until June 2022. Genomes of MDRGN isolates were analysed for antimicrobial resistance, virulence genes and phylogenetic relatedness. Results We included 103 patients (median age: 39 ± 23.7 years), 57 of whom were female (55.3%; 95% confidence interval (CI): 45.2–5.1). Patients were most frequently admitted to the Department of Paediatrics (29/103; 28.2%; 95% CI: 19.7–37.9). We found 34 MDRGN isolates in 17 of 103 patients (16.5%; 95% CI: 9.9–25.1). Ten patients carried 21 carbapenem-resistant (CR) bacteria, five of them more than one CR isolate. Four of six patients with war-related injuries carried eight CR isolates. In six of 10 patients, CR isolates caused infections. Genomic characterisation revealed that the CR isolates harboured at least one carbapenemase gene, bla NDM-1 being the most frequent (n = 10). Core genome and plasmid analysis revealed no epidemiological connection between most of these isolates. Hypervirulence marker genes were found in five of six Klebsiella pneumoniae CR isolates. No MRSA was found. Conclusion Hospitals should consider infection control strategies to cover the elevated prevalence of MDRGN bacteria in Ukrainian patients with war-related injuries and/or hospital pre-treatment and to prevent the spread of hypervirulent CR isolates.
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Background Widespread increases in facility delivery have not substantially reduced neonatal mortality in sub-Saharan Africa and South Asia over the past 2 decades. This may be due to poor quality care available in widely used primary care clinics. In this study, we examine the association between hospital delivery and neonatal mortality. Methods and findings We used an ecological study design to assess cross-sectional associations between the share of hospital delivery and neonatal mortality across country regions. Data were from the Demographic and Health Surveys from 2009 to 2018, covering 682,239 births across all regions. We assess the association between the share of facility births in a region that occurred in hospitals (versus lower-level clinics) and early (0 to 7 days) neonatal mortality per 1,000 births, controlling for potential confounders including the share of facility births, small at birth, maternal age, maternal education, urbanicity, antenatal care visits, income, region, and survey year. We examined changes in this association in different contexts of country income, global region, and urbanicity using interaction models. Across the 1,143 regions from 37 countries in sub-Saharan Africa and South Asia, 42%, 29%, and 28% of births took place in a hospital, clinic, and at home, respectively. A 10-percentage point higher share of facility deliveries occurring in hospitals was associated with 1.2 per 1,000 fewer deaths (p-value < 0.01; 95% CI: 0.82 to 1.60), relative to mean mortality of 22. Associations were strongest in South Asian countries, middle-income countries, and urban regions. The study’s limitations include the inability to control for all confounding factors given the ecological and cross-sectional design and potential misclassification of facility levels in our data. Conclusions Regions with more hospital deliveries than clinic deliveries have reduced neonatal mortality. Increasing delivery in hospitals while improving quality across the health system may help to reduce high neonatal mortality.
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Background Sick newborns admitted to neonatal units in low-resource settings are at an increased risk of developing hospital-acquired infections due to poor clinical care practices. Clusters of infection, due to the same species, with a consistent antibiotic resistance profile, and in the same ward over a short period of time might be indicative of an outbreak. We used whole-genome sequencing (WGS) to define the transmission pathways and characterise two distinct outbreaks of neonatal bacteraemia in a west African neonatal unit. Methods We studied two outbreaks of Burkholderia cepacia and multidrug-resistant extended spectrum β-lactamase (ESBL)-producing Klebsiella pneumoniae in a neonatal unit that provides non-intensive care on the neonatal ward in the Edward Francis Small Teaching Hospital, Banjul, The Gambia. We used WGS to validate and expand findings from the outbreak investigation. We retrospectively sequenced all clinical isolates associated with each outbreak, including isolates obtained from swabs of ward surfaces, environmental fluid cultures, intravenous fluids, and antibiotics administered to newborns. We also sequenced historical B cepacia isolates associated with neonatal sepsis in the same ward. Results Between March 1 and Dec 31, 2016, 321 blood cultures were done, of which 178 (55%) were positive with a clinically significant isolate. 49 episodes of neonatal B cepacia bacteraemia and 45 episodes of bacteraemia due to ESBL-producing K pneumoniae were reported. WGS revealed the suspected K pneumoniae outbreak to be contemporaneous outbreaks of K pneumoniae (ST39) and previously unreported Klebsiella quasipneumoniae subspecies similipneumoniae (ST1535). Genomic analysis showed near-identical strain clusters for each of the three outbreak pathogens, consistent with transmission within the neonatal ward from extrinsically contaminated in-use intravenous fluids and antibiotics. Time-dated phylogeny, including retrospective analysis of archived bacterial strains, suggest B cepacia has been endemic in the neonatal ward over several years, with the Klebsiella species a more recent introduction. Interpretation Our study highlights the emerging threat of previously unreported strains of multidrug-resistant Klebsiella species in this neonatal unit. Genome-based surveillance studies can improve identification of circulating pathogen strains, characterisation of antimicrobial resistance, and help understand probable infection acquisition routes during outbreaks in newborn units in low-resource settings. Our data provide evidence for the need to regularly monitor endemic transmission of bacteria within the hospital setting, identify the introduction of resistant strains from the community, and improve clinical practices to reduce or prevent the spread of infection and resistance. Funding Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Fajara, The Gambia.
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Background: Multi-drug resistant organisms are an increasingly important cause of neonatal sepsis. Aim: This study aimed to review neonatal sepsis caused by multi-drug resistant Enterobacteriaceae (MDRE) in neonates in Johannesburg, South Africa. Methods: This was a cross sectional retrospective review of MDRE in neonates admitted to a tertiary neonatal unit between 1 January 2013 and 31 December 2015. Results: There were 465 infections in 291 neonates. 68.6% were very low birth weight (< 1500 g). The median age of infection was 14.0 days. Risk factors for MDRE included prematurity (p = 0.01), lower birth weight (p = 0.04), maternal HIV infection (p = 0.02) and oxygen on day 28 (p < 0.001). The most common isolate was Klebsiella pneumoniae (66.2%). Total MDRE isolates increased from 0.39 per 1000 neonatal admissions in 2013 to 1.4 per 1000 neonatal admissions in 2015 (p < 0.001). There was an increase in carbapenem-resistant Enterobacteriaceae (CRE) from 2.6% in 2013 to 8.9% in 2015 (p = 0.06). Most of the CRE were New Delhi metallo-β lactamase- (NDM) producers. The all-cause mortality rate was 33.3%. Birth weight (p = 0.003), necrotising enterocolitis (p < 0.001) and mechanical ventilation (p = 0.007) were significantly associated with mortality. Serratia marcescens was isolated in 55.2% of neonates that died. Conclusions: There was a significant increase in MDRE in neonatal sepsis during the study period, with the emergence of CRE. This confirms the urgent need to intensify antimicrobial stewardship efforts and address infection control and prevention in neonatal units in LMICs. Overuse of broad- spectrum antibiotics should be prevented.
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Background: Aetiological data for neonatal infections are essential to inform policies and programme strategies, but such data are scarce from sub-Saharan Africa. We therefore completed a systematic review and meta-analysis of available data from the African continent since 1980, with a focus on regional differences in aetiology and antimicrobial resistance (AMR) in the past decade (2008-18). Methods: We included data for microbiologically confirmed invasive bacterial infection including meningitis and AMR among neonates in sub-Saharan Africa and assessed the quality of scientific reporting according to Strengthening the Reporting of Observational Studies in Epidemiology for Newborn Infection (STROBE-NI) checklist. We calculated pooled proportions for reported bacterial isolates and AMR. Findings: We included 151 studies comprising data from 84 534 neonates from 26 countries, almost all of which were hospital-based. Of the 82 studies published between 2008 and 2018, insufficient details were reported regarding most STROBE-NI items. Regarding culture positive bacteraemia or sepsis, Staphylococcus aureus, Klebsiella spp, and Escherichia coli accounted for 25% (95% CI 21-29), 21% (16-27), and 10% (8-10) respectively. For meningitis, the predominant identified causes were group B streptococcus 25% (16-33), Streptococcus pneumoniae 17% (9-6), and S aureus 12% (3-25). Resistance to WHO recommended β-lactams was reported in 614 (68%) of 904 cases and resistance to aminoglycosides in 317 (27%) of 1176 cases. Interpretation: Hospital-acquired neonatal infections and AMR are a major burden in Africa. More population-based neonatal infection studies and improved routine surveillance are needed to improve clinical care, plan health systems approaches, and address AMR. Future studies should be reported according to standardised reporting guidelines, such as STROBE-NI, to aid comparability and reduce research waste. Funding: Uduak Okomo was supported by a Medical Research Council PhD Studentship.