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Asian Journal of Biotechnology and Genetic Engineering
3(2): 11-19, 2020; Article no.AJBGE.57707
Molecular and Antibiotic Susceptibility Profiling of
Bacteria Isolated from Pre-sterilized Food Samples
Used as Substrates for Outdoor Air Quality
Assessment
T. Sampson
1*
, G. Amaechi
1
and L. O. Amadi
1
1
Department of Microbiology, Rivers State University, P.M.B. 5080, Port Harcourt, Rivers State,
Nigeria.
Authors’ contributions
This work was carried out in collaboration among all authors. Author TS designed the study, wrote the
protocol and the first draft of the manuscript. Authors GA and LOA managed the analyses of the
study. Author AG also performed the statistical analysis and managed the literature searches. All
authors read and approved the final manuscript.
Article Information
Editor(s):
(1)
Dr. Prabakaran Nagarajan, The Ohio State University, USA.
Reviewers:
(1) Shiv Kumar Gupta, Sanskar College of Pharmacy and Research, India.
(2)
Sanjeev Jakati, Lenora Institute of Dental Sciences, India.
(3)
Abhijeet A. Gawai, Dr. Rajendra Gode Ayurved College Hospital & Research Centre, India.
Complete Peer review History:
http://www.sdiarticle4.com/review-history/57707
Received 22 March 2020
Accepted 28 May 2020
Published 04 June 2020
ABSTRACT
A large proportion of human population spend significant part of their life in the outdoor environment
due to activities relating to occupation and other lifestyle related events. This work was carried out
fundamentally, to identify the bacterial community influencing the quality of outdoor air, vis-à-vis
their antibiotic susceptibility pattern. The research was conducted at the River State University, Port
Harcourt, Nigeria, using pre-sterilized food (yam, pawpaw, and meat) as air sampling substrates, by
exposing the samples to air and studied during the wet and dry seasons. The bacterial species
were identified using a culture-dependent molecular technique, and the result recorded Escherichia
coli (CP040927), Klebsiella pneumoniae (MN177202), Shigella flexneri (EU009189), Salmonella
typhi. (CP003278), Bacillus subtilis (EF194103) and Staphylococcus aureus (CP042650) as the
predominant bacterial species. E. coli was however the most predominant species with a frequency
of 34.3% and 26.7% for the dry and wet season, respectively. It was also observed from the study
Original Research Article
Sampson et al.; AJBGE, 3(2): 11-19, 2020; Article no.AJBGE.57707
12
that the bacterial groups were higher during the wet season (35 isolates) than in the dry season (30
isolates). There was a statistical difference (p < 0.05) between the various substrates and seasons
sampled. The antibiotic susceptibility pattern of the bacterial isolates showed that 100% of the
isolates were resistant to Ceftazidime, Augmentin, Cefuroxime, Ceftriaxone and Cloxacillin, while
Erythromycin, Ofloxacin, Ciprofloxacin and Meropenem were active against all the isolates (100%).
Results from this study would be useful to public health professionals for deciphering the health risk
associated with outdoor air quality.
Keywords: Antibiotic susceptibility; molecular; outdoor air quality; pre-sterilized food sample; profiling;
sequencing.
1. INTRODUCTION
Air quality play a significant role in the wellbeing
of individuals inhabiting a particular environment.
The air quality of an environment is influenced
basically by physical, chemical and biological
factors. Microorganisms found in the air
environment are versatile and known for various
health issues relating to both upper and lower
respiratory tract infections, amongst others
associated with airborne microbial population.
The effect of airborne bacteria on human health
may include allergic asthma and seasonal
allergies, and other forms of diseases [1,2].
These diseases can be transmitted as
aerosolized droplets [3,4], causing various
disease syndromes in human when inhaled [5],
depending on the immunological and
physiological status of the host. This implies that
exposure to airborne microorganisms can affect
health negatively [6] and generally depends on
the particle size [7]. This has therefore, made the
outdoor air environment a current and important
area of research.
Bacterial species form part of the many types of
biogenic aerosol particles, and they are known to
be ubiquitous in the atmosphere [8]. They can
exist in aerosolized forms as pathogenic and/or
non-pathogenic dead or live microorganisms [9].
Due to their size, bacteria have a long
atmospheric residence time (of the order of
several days) and can be transported by wind
over long distances. Bacteria enter the
atmosphere as aerosol particles from practically
all surfaces, including soil, water, and plant
surfaces [10]. Once in the air, they are carried
upwards by air currents and may remain in the
atmosphere for many days before being removed
by precipitation or direct deposition onto
surfaces. Meteorological parameters like wind
direction, wind speed, temperature, and relative
humidity determine the suspension,
transportation, and deposition of airborne
microbes [11]. A sound knowledge of the
concentration and distribution patterns of
airborne bacteria on a global scale is needed in
order to assess their importance in relation to the
climate and health effects of atmospheric
aerosol, including cloud formation and
development, microbial biodiversity, and
atmospheric chemistry.
The characteristics of atmosphere as a habitat
include extreme temperature variations, light, low
moisture content and organic matter. All these
characteristics make the atmosphere unsuitable
for growth of microorganisms.
Soil is one of the major sources of
microorganisms found in air, and are usually
transmitted following environmental perturbations
associated with wind and influenced as well by
gravitational forces. When wind blows it
dislodges the microorganisms from the soil and
liberates them into the air and these
microorganisms may remain suspended in the air
for a long time. Another way of transferring
microorganisms to the air is by manmade actions
like plugging and digging. Organisms can also be
released in the form of water droplets or aerosols
which are produced by wind or tidal actions.
Microorganisms from plant and animal surfaces
are also transferred by air currents through
human activities like coughing, sneezing,
laughing and even talking.
Above the land surface in a natural environment,
airborne dust consists of up to about 25% of
biological particles [10]. In urban and
agriculturally-dominated areas, the percentage is
usually higher [8]. Airborne biological particles as
a whole are also denoted as bio-aerosols.
Airborne microorganisms have impacts not only
on human health, but also on climate and
microbial biogeography. For example, the plant
pathogen Pseudomonas syringae and related
phylloplane bacteria have strong ice nucleation
ability at 33°C warmer (−5°C) than the
homogeneous freezing temperature of cloud
droplets composed of pure water [12].
Sampson et al.; AJBGE, 3(2): 11-19, 2020; Article no.AJBGE.57707
13
Bacteria have evolved diverse and remarkable
ways to avoid antimicrobials in several cases,
resulting in resistance due to a minor structural
alteration in the target so that it is no longer
bound by the drug, yet still functions. For
example, streptomycin normally binds to a part of
prokaryotic 30S ribosomal subunit that is critical
for protein synthesis. A slight alteration in the
structure of ribosome result in a distortion, so
that streptomycin is no longer able to bind but the
ribosome can still functionally translate mRNA.
Alteration in membrane permeability or its other
function may also confer antibiotic resistance.
There is paucity of information regarding the
abundance of microbial population resident in the
air environment. Also, there is a limited
understanding of the quantities and types of
bacteria found in the atmosphere [13]. This
scanty information may be due to methods used
in the isolation and identification of
microorganisms associated with the air
environment. However, with recent advances in
high-throughput sequencing, the dynamics of
bacteria in the atmosphere can be better
understood [14], and thus provide a more
comprehensive data set for deciphering those
bacteria found in the atmosphere and the control
of their populations. Surveillance of antibiotic
resistance has recently been given much
attention by researchers as a major tool to
assess the health risk of drug-resistant airborne
microbes as well as bacteria from other
environmental sources [15,16].
The potential of sterile food sources serving as a
medium for bacterial growth in the outdoor air
environment, with the ultimate aim of applying
them as a novel technique in catching and
probing bacterial community lurking the outdoor
air environment has been evaluated and reported
by Sampson, et al. [17]. This was done with the
view of using these pre-sterilized food samples to
determine the outdoor air quality at heights
significantly above ground level. This paper
however looks at the bacterial determinants of an
outdoor air quality, using sequence-based
molecular technique and as well, evaluate the
antibiotic susceptibility pattern of the isolates to
conventional antibiotics.
2. MATERIALS AND METHODS
2.1 Study Area and Sampling Techniques
The air sampling was conducted at the River
State University, Harcourt, Nigeria as described
by Sampson et al. [17]. All microbiological
analyses were carried out at the Microbiology
Laboratory of the River State University,
Harcourt, Nigeria.
2.2 Study Period, Sampling Frequency
and Duration
The study was carried out between the months of
May 2018 to May 2019. The samples were
studied at daily intervals for five consecutive
days in two seasons (wet and dry).
2.3 Isolation of Pure Culture
To get a pure culture, an inoculum of the
colonies was taken and sub-cultured on fresh
agar plates using the streak plate method and
incubated for 24 hours as described by [16,17].
2.4 Molecular Identification
2.4.1 DNA extraction and quantification
Extraction of DNA from the pure isolates was
done using the boiling method. This was
achieved by centrifuging five milliliters of an
overnight broth culture of the bacterial isolates
grown in Luria Bertani (LB) media at a speed of
14000 rpm for 3 min. This was followed by re-
suspending the cells in a vial containing 500 µl
volume of normal saline and was subjected to a
heating process at a temperature of 95°C for a
period of 20 min, after which it was allowed to
cool on ice before later been spun for another
period of 3 min at same speed of 14000
revolutions per minute (rpm). The DNA
suspension was decanted to a micro-centrifuge
tube of 1.5 ml volume and stored at -20°C for
other downstream reactions.
The genomic DNA was quantified using a
spectrophotometer (Nanodrop 1000). The
software of the equipment was lunched by
double clicking on the Nanodrop icon. The
equipment was initialized with 2 µl of sterile
distilled water and blanked using normal saline.
Two microliter of the extracted DNA was loaded
onto the lower pedestal, the upper pedestal was
brought down to contact the extracted DNA on
the lower pedestal. The DNA concentration was
measured by clicking on the “measure” button,
and read via computer device attached to the
system.
2.4.2 16S rRNA amplification
The amplification of the gene was done using
Polymerase Chain Reaction (PCR) method. The
Sampson et al.; AJBGE, 3(2): 11-19, 2020; Article no.AJBGE.57707
14
16s rRNA region of the rRNA gene of the isolates
were amplified using the 27F: 5'-
AGAGTTTGATCMTGGCTCAG-3' and 1492R: 5'-
CGGTTACCTTGTTACGACTT-3’ primers on an
ABI 9700 Applied Biosystems thermal cycler at a
final volume of 40 microliters for 35 cycles. The
PCR mix included: The X2 Dream taq Master mix
supplied by Inqaba, South Africa (taq
polymerase, DNTPs, MgCl), the primers at a
concentration of 0.5 µM and the extracted DNA
as template. The gene amplification was done
using a set of conditions that involved a first step
of denaturing the DNA at a temperature of 95°C
for a duration of 5 minutes, followed by another
cycle of DNA denaturing at same temperature,
albeit for 30 seconds. The next was a 35 cycle
series of annealing at 52°C and extension at
72°C, for 30 seconds each, except for the final
extension that was maintained for a period of 5
minutes. The final PCR product was
electrophoresed at 130V for 30 minutes using
1% agarose gel concentration, and the DNA
bands were visualized with the aid of a blue light
trans-illuminator.
2.4.3 Sequencing
Sequencing analysis was performed at Inqaba
Biotechnical Pty Ltd, South Africa. This was done
using a BigDye Terminator kit on a 3510 ABI
sequencer maintained at a final volume of 10 µl.
The components included 0.25 µl Big Dye®
terminator v1.1/v3.1, 2.25 ul of 5 x Big Dye
sequencing buffer, 10 µM, Primer PCR primer,
and 2-10 ng PCR template per 100 bp. The
sequencing conditions involved 32 cycles of
96°C for 10s, 55°C for 5s and 60°C for 4 min.
2.5 Antibiotics Susceptibility Test
Antibiotics Sensitivity Test was performed
according to NCCLS [18]. A set of antibiotics
discs (multi-disc) was dispensed onto the surface
of the agar plate inoculated with the isolates, using
the Kirby Bauer disc diffusion method. With the
aid of a sterile forceps, the respective antibiotic
discs were placed onto the agar and slightly
pressed down to ensure its contact with the agar.
Within 30 minutes of applying the discs, the
plates were inverted and incubated at 37°C for
18 hrs. After overnight incubation, the test plate
was examined. Using a ruler on the underside of
the plate, the diameter of each zone of inhibition
was measured in mm. The measurement
included the diameter of the disc and
susceptibility or resistance of the isolates was
reported by referring to Zone Diameter
Interpretative Standards and equivalent Minimum
Inhibitory Concentration Breakpoints of the NCCLS
[18] and the organisms were reported as either
susceptible, intermediate, or resistant to the agents
that were tested.
3. RESULTS AND DISCUSSION
3.1 Molecular Characterization of
Bacterial Isolates
The identification and characterization bacterial
isolates is fundamental in understanding the
ecology and environmental health concerns of a
habitat, as the resident micro flora of a place
influences to a large extent the quality of such
environment. Different microbiological
approaches have been used by researchers to
probe the microbiological parameters of an
environment (aquatic, terrestrial, air and other
environments). The use of a high-throughput
approach undeniably ensures the reliability of a
method. This research therefore explored the
use of a culture-dependent molecular technique
in accessing the bacterial diversity of an outdoor
air environment.
As stated in the methodology, pre-sterilized food
samples (yam, meat and paw paw) were
exposed to an outdoor air environment and left to
be contaminated by microflora, after which the
bacterial isolates were subjected to a sequence
based molecular characterization. It follows that
the obtained 16s rRNA sequence from the
isolates produced an exact match during the
mega blast search for highly similar sequences
from the NCBI non-redundant nucleotide (nr/nt)
database. The 16S rRNA of the isolate Klebsiella
spp showed a percentage similarity to other
species at 100%. The evolutionary distances
computed using the Jukes-Cantor method were
in agreement with the phylogenetic placement of
the 16S rRNA of the isolate MN177202 within the
Klebsiella spp and revealed a close relatedness
to E. coli, Shigella spp., Salmonella spp., Bacillus
spp. and Staphylococcus aureus as shown in
Fig. 1.
Culture-based probing of atmospheric samples
identify far fewer taxonomic groups of bacteria,
and presents the Gram-positive spore-forming
bacteria as the most commonly cultured airborne
bacterial taxa [19]. This research is however
opposed to this as most of the isolates were
found to be relatively rare members of the
airborne bacterial communities and highly
dominated by Gram negative bacteria. This
Sampson et al.; AJBGE, 3(2): 11-19, 2020; Article no.AJBGE.57707
15
observed difference is attributable to the method
adopted in this study which involved the use of a
novel method of air quality assessment alongside
molecular characterization of the isolates. We
have stated in our previous publication [17] that
the bacteriological quality of air is determined by
the type of substrate used to capture the
bacterial population lurking the air environment.
The identification of these isolates in an outdoor
air environment may be due to human activities
and other environmental sources. The presence
of these organisms therefore makes the air
unsafe as they are associated with different
disease forms like pneumonia, diarrhea,
tuberculosis, typhoid fever, pertussis, etc.
3.2 Seasonal Prevalence of Bacteria in
the Air Environment Studied
The study on the effect of seasonal changes on
the occurrence of bacterial population in the
outdoor environment revealed that the bacterial
genera were isolated mostly during the wet
season than dry season. The result as presented
in Table 1 shows that the wet season sampling
had a total of 35 isolates while 30 was recorded
during the dry season sampling. Also seasonal
variation influenced the occurrence of the
individual isolates in the various food samples
used. It follows that, E. coli constituted 34.3%
and 26.6% of the total bacteria isolated during
the wet and dry season, respectively. This shows
that the frequency of occurrence of E. coli was
higher during the wet season than in the dry
season. Similar pattern was observed for both
Bacillus and Klebsiella species, while
Staphylococcus, Salmonella and Shigella
species had higher frequencies during the dry
season (Table 1, Fig. 2). This difference in the
frequency of occurrence of the individual isolates
with respect to season (dry and wet) is
attributable to their metabolic and physiological
variations. It follows that while some organisms
can adapt to some environmental conditions,
others may be negatively affected by such
environmental conditions of temperature,
desiccation, and other atmospheric and
meteorological factors.
Fig. 1. Phylogeny of the bacterial isolates
Sampson et al.; AJBGE, 3(2): 11-19, 2020; Article no.AJBGE.57707
16
Table 1. Seasonal pattern of bacterial colonization of pre-sterilized food samples in air
Isolate
Frequency (Number) of isolates
Wet season Dry season
Yam Paw Meat Total (%) Yam Paw Meat Total (%)
E. coli 4 3 5 12 (34.3) 2 2 4 8 (26.6)
Salmonella sp. - - 2 2 (5.7) - - 4 4 (13.3)
Staphylococcus aureus 1 3 1 5 (14.3) 2 2 1 5 (16.7)
Bacillus sp. 3 1 - 4 (11.4) 2 1 - 3 (10)
Klebsiella pneumoniae 2 2 4 8 (22.9) 1 2 2 5 (16.7)
Shigella sp.
-
2
2
4 (11.4)
-
1
4
5 (16.7)
Total 10 11 14 35 (100) 7 8 15 30 (100)
Fig. 2. Occurrence of the bacterial isolates in the wet and dry season
Fig. 3. Antibacterial activity of the various antibiotics tested against the isolates
Keys: CAZ – Ceftazidime; CRX – Cefuroxime; GEN – Gentamicin; CTR – Ceftriaxone; ERY – Erythromycin;
CXC – Cloxacin; OFL – Ofloxacin; AUG – Augumentin; CXM – Cefixime; NIT – Nitrfurantion; CPR – Ciprofloxacin
Other factors observed that influenced the
seasonal variation of these bacterial populations
in the outdoor environment was the nature of the
substrate. From Table 1 it is deducible that all the
food samples used as substrate, except for meat,
had higher number of isolates during the wet
34.3
25.7
14.3
11.4
22.9
11.4
26.7
13.3
16.7
10
16.7 16.7
0
5
10
15
20
25
30
35
40
Percentage Prevalence
Isolates
WET SEASON
DRY SEASON
0
20
40
60
80
100
120
PERCENTAGE
ANTIBIOTICS
% Resistance
% Susceptibility
Sampson et al.; AJBGE, 3(2): 11-19, 2020; Article no.AJBGE.57707
17
season than the dry season. This shows that
weather-related conditions affect the nature of
the substrates which in turn influences the
proliferation of bacteria in the outdoor air
environment.
The features of the atmosphere such as extreme
temperature variations, light, low moisture
content and organic matter influence its habitat
potentials and to this extent determine the type of
flora and fauna that inhabits this environment;
since only well adapted species can survive in
this milieu [20].
The findings from this study show that
transmission or spread of diseases is influenced
by weather as well as other environmental
factors. Climate conditions like temperature,
winds and relative humidity in any territory, either
all year round or at isolated moments (days or
weeks) are the main factors affecting the spread,
duration and infectiousness of droplets
containing pathogens. For instance, influenza
virus, is spread easily in northern countries (north
hemisphere), because of climate conditions
which favors the pathogenicity/virulence of the
virus but on the other hand, lots of bacterial
infections cannot spread outdoor most of the
year, keeping it in a latent stage [21].
3.3 Susceptibility Pattern of Isolates to
Various Antibiotics
The result of the antibiotic susceptibility assay
(Fig. 3) showed that all the isolates (100%) were
susceptible to Ceftazidime, Augumentin
Cefuroxime, Ceftriaxon and Cloxacillin. It also
followed that Erythromycin, Ofloxacin,
Ciprofloxacin and Meropenem were inhibitory to
all (100% of) the isolates tested.
The goal of susceptibility testing is to predict the
likely outcome of treating a patient’s infection
with a particular antimicrobial agent [22]. This
research has shown the susceptibility pattern of
bacteria isolated from the outdoor air
environment. From the report, it was observed
that while some antibacterial agents were potent
against all the isolates, some showed no
inhibitory activity on all the isolates. This implies
that in the event of any infection involving these
bacterial organisms isolated in this study,
Ceftazidime, Augumentin Cefuroxime, Ceftriaxon
and Cloxacillin may not have any therapeutic
value. This is attributable to the fact that these
isolates may have developed some form of
resistance to these drugs. Also, the susceptibility
of all the isolates to Erythromycin, Ofloxacin,
Ciprofloxacin and Meropenem is indicative of
lack of prior exposure to these agents. From the
foregoing analysis, it can be inferred that while
some of the isolates may be from human
sources, others may be of an environmental
origin. This is in agreement with the fact that the
susceptibility pattern of an isolate to various
antibiotics is dependent on the source of the
bacterial contaminant, as organisms without prior
exposure may show low level resistance
compared to pathogens of human origin with
prior exposure [23].
A study by Hakam et al. [24] on antimicrobial
efficacy of some herbs on resistant strains of
Pseudomonas species isolated from West
African Mud Creeper (Tympanotonus fuscatus),
showed that some of the Pseudomonas species
were found to be resistant to some conventional
antibiotics previously used against the organisms
but were susceptible to methanol extracts of
ginger, garlic, bitter cola seed, bitter cola bark,
turmeric. This finding by Hakam et al. [24] further
buttresses the fact that resistance to an
antimicrobial agent may be linked to prior
exposure to the antimicrobial agent.
4. CONCLUSION
The molecular profiling of the bacterial population
of an outdoor air environment has shown that the
region of the air environment sampled was
composed of some bacterial species such as
Escherichia coli (CP040927), Klebsiella
pneumoniae (MN177202), Shigella flexneri
(EU009189), Salmonella typhi. (CP003278),
Bacillus subtilis (EF194103) and Staphylococcus
aureus (CP042650) known to cause various
degrees of ailment in man, ranging from
respiratory related illness to gastroenteritis. Their
growth and survival in the atmosphere is
however influenced by both substrate type and
availability as well as other environmental
dynamics associated with seasonal variation.
From the study it was observed that while some
organisms were predominant during the wet
season, others were predominant during the dry
season. This variation is therefore attributable to
the physiological and metabolic dynamism as
well as functional variation that exist among the
organisms. Also, the contribution of the nature of
the substrate in the growth and survival of
bacteria in the air environment was discovered in
this study. It was observed that number of
isolates from the different food samples used as
Sampson et al.; AJBGE, 3(2): 11-19, 2020; Article no.AJBGE.57707
18
substrate for the air quality determination varied
with respect to season. This may be as result of
the impact of climate on the water activity of the
substrate, which had a concomitant effect on the
proliferation of the organisms. This observation
therefore implies that the transmission of disease
causing agents is influenced by various factors
including particulate matter in the air, climatic
factors and the physiological aspect of the
organism.
From the study on the susceptibility of the
isolates to conventional antibiotics, it was
observed that some of the antibacterial drugs
were inhibitory to all the bacterial isolates, while
all the isolates were resistant to some of the
drugs tested. This implies that a community of
bacteria in the environment presents similar
pattern of susceptibility to drugs depending on
exposure/contact status. The presence of drug
resistant strains or species in the air environment
is of a great public health concern. These drug
resistant populations are attributable to
anthropogenic sources with prior exposure to
these antibacterial drugs, and thus human
activities in the environment relating to biogenic
waste generation and disposal should be
regulated. Also, Metagenomic evaluation of air
quality using sterile food substrates is
recommended.
COMPETING INTERESTS
Authors have declared that no competing
interests exist.
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© 2020 Sampson et al.; This is an Open Access article distributed under the terms of the Creative Commons Attribution
License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any
medium, provided the original work is properly cited.
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