Environmental reservoirs of multidrug-resistant pseudomonads in a geographical location in Kenya with high community-acquired infections

Polly Mubassu; Abednego Musyoki; Erick Odoyo; Collins Kigen; Lillian Musila

doi:10.12688/f1000research.147914.1

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Research Article

Environmental reservoirs of multidrug-resistant pseudomonads in a geographical location in Kenya with high community-acquired infections

[version 1; peer review: 2 approved with reservations]

Polly Mubassu ¹, Abednego Musyoki¹, Erick Odoyo^2,3, Collins Kigen^2,3, Lillian Musila^2,3

Polly Mubassu ¹, Abednego Musyoki¹, [...] Erick Odoyo^2,3, Collins Kigen^2,3, Lillian Musila^2,3

PUBLISHED 13 May 2024

Author details Author details

¹ Kenyatta University, Nairobi, Kenya
² Kenya Medical Research Institute, Nairobi, Kenya
³ Walter Reed Army Institute of Research - Africa, Kericho, Kenya

Polly Mubassu
Roles: Conceptualization, Formal Analysis, Investigation, Methodology, Visualization, Writing – Original Draft Preparation, Writing – Review & Editing

Abednego Musyoki
Roles: Conceptualization, Formal Analysis, Supervision, Validation, Visualization, Writing – Review & Editing

Erick Odoyo
Roles: Formal Analysis, Methodology, Project Administration, Supervision, Writing – Review & Editing

Collins Kigen
Roles: Data Curation, Investigation, Validation, Visualization, Writing – Review & Editing

Lillian Musila
Roles: Conceptualization, Formal Analysis, Funding Acquisition, Methodology, Supervision, Visualization, Writing – Original Draft Preparation, Writing – Review & Editing

OPEN PEER REVIEW

REVIEWER STATUS

This article is included in the Antimicrobial Resistance collection.

Abstract

Background

Pseudomonads are gram negative bacteria and readily form biofilms in the environment, allowing long-term colonization and persistence in sinks, water systems. They pose a risk of life-threatening opportunistic infections in immune-compromised individuals. MDR strains, make treatment increasingly difficult. Environmentally persistent MDR strains are typically problematic within healthcare facilities, however, data on MDR pseudomonad reservoirs in settings with community-acquired infections to inform preventive interventions, in resource-constrained settings is scarce. Here, we determined reservoirs and antibiotic susceptibility of Pseudomonas species in water sources in Kisumu County, Kenya with reported high levels of community acquired pseudomonad infections.

Methods

We adopted a cross-sectional design, randomly collecting 297 samples from tap heads, sinks, tanks, vendor and household storage containers in six selected sub-locations and one hospital (KCRH). Standard microbiological procedures were used for identification and AST of the isolates.

Results

We isolated Pseudomonads from 14.1% of the samples collected, predominantly from the community 10.4%. Seven different pseudomonads were identified, with Pseudomonas aeruginosa predominating 6.7% overall, in the community samples 5.7%, and among isolates from water tanks 21.4%. Pseudomonad isolates were 62% non-susceptible to piperacillin, 57% to tigecycline, 24% meropenem, 21% cefepime, 19% levofloxacin and 14% colistin. Carbapenem resistance was mainly detected in P. aeruginosa 80% (8/10) from Milimani sub-location 75% (6/8). 45% of the isolates recovered were MDR, mainly community-associated carbapenem-resistant P. aeruginosa (CRPA) 42%, strains susceptible to colistin. The MDR pseudomonads exhibited high multiple antibiotic resistance indices, ranging from 0.43 to 1.

Conclusion

This study reveals a higher prevalence of MDR pseudomonads, including CRPA strains in community water sources. These potential conduits of drug resistance present a critical public health threat, especially among immunocompromised. Regular cleaning of water storage facilities, water treatment and implementation of antimicrobial stewardship programs, are required to prevent a rise in AMR and eliminate the environmental reservoirs that put the vulnerable populations at risk.

Keywords

Pseudomonads, multidrug resistance, environmental reservoirs, carbapenem-resistant Pseudomonas aeruginosa

Corresponding authors: Polly Mubassu, Lillian Musila

Competing interests: No competing interests were disclosed.

Grant information: the Armed Forces Health Surveillance Division (AFHSD), Global Emerging Infections Surveillance (GEIS) Branch [PROMIS ID 17_KY_1.3.1].
The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Copyright: © 2024 Mubassu P et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

How to cite: Mubassu P, Musyoki A, Odoyo E et al. Environmental reservoirs of multidrug-resistant pseudomonads in a geographical location in Kenya with high community-acquired infections [version 1; peer review: 2 approved with reservations]. F1000Research 2024, 13:474 (https://doi.org/10.12688/f1000research.147914.1) First published: 13 May 2024, 13:474 (https://doi.org/10.12688/f1000research.147914.1) Latest published: 13 May 2024, 13:474 (https://doi.org/10.12688/f1000research.147914.1)

1. Background

Pseudomonads are gram-negative bacteria, ubiquitous in water soil, and decaying vegetation and frequently isolated from healthy persons’ skin, throat and stool. They comprise several clinically relevant species, including P. maltophilia, P. fluorescens, P. cepacia, P. stutzeri, P. putrefaciens, and P. putida,¹^,² with P. aeruginosa as the most common among these opportunistic pathogens. Pseudomonads form biofilms that confer protection from environmental stresses, including antibiotics and detergents, allowing long-term colonization and persistence in sinks, municipal drinking water systems, hot tubs, and swimming pools.³^,⁴

Pseudomonads pose a substantial risk of acute and chronic life-threatening multidrug-resistant (MDR) infections such as ventilator-associated pneumonia, community-acquired pneumonia, bloodstream infection, urinary tract infections, and skin and soft tissue infections among elderly individuals and those with cystic fibrosis, cancer, HIV, and diabetes.⁵^–⁹ Outbreaks of P. aeruginosa infections have been associated with tap water,¹⁰ bottled water,¹¹ hand-washing basin water,¹² surface cleaning equipment,¹³ therapy equipment such as catheters, humidifiers,¹⁴ sinks,¹⁵ and swimming pools.⁸

Treatment of infections caused by Pseudomonas species is increasingly difficult due to the rapid emergence of multidrug resistance, even during therapy courses.¹⁶ The resistance occurs mainly through reduced outer membrane permeability, expression of efflux pumps that transport antibiotics extracellularly, biofilm formation, and the production of beta-lactamases, and occasionally plasmid-borne enzymes. Of these enzymes, carbapenemases pose a public health concern because they inactivate carbapenems, which are among the antibiotics of last resort for infections caused MDR Gram-negative bacteria (GNB).¹⁷^,¹⁸

MDR P. aeruginosa clinical strains that are carbapenem-resistant (CR) are increasingly reported in Kenya¹⁹^–²¹ The available treatment options for CR-GNB include colistin and tigecycline, with colistin rarely used due to high toxicity and low efficacy concerns. Increased resistance to both drugs is growing with the emergence of resistant strains. Newer options for infections caused by CR-GNB include combinations of beta-lactam-beta-lactamase inhibitors (BL-BLI) such as meropenem-vaborbactam, ceftazidime-avibactam, imipenem-sulbactam, and ceftolozane-tazobactam²²; however, these drugs face challenges due to insufficient high-quality clinical data, delayed approval for susceptibility testing methods, antibacterial spectra complexity, and acquisition costs.²³ Therefore, preserving the clinical value of carbapenems through local, global and national mitigation strategies remains critical.

Although Pseudomonas spp. are significant clinical pathogens,²¹^,²⁴^–²⁶ information on the occurrence of MDR isolates in water sources and moist environments in community and hospital settings which could serve as reservoirs for human infections in Kenya is scarce.²⁷ In this study, we aimed to identify reservoirs and antibiotic susceptibility of Pseudomonas spp in community and hospital environments in Kisumu County where community-associated infections have been reported at the county referral hospital.

2. Methods

2.1 Study approval and consent

Approval to conduct this study was obtained from the Kenyatta University’s Graduate School, Kenya Medical Research Institute-Scientific Ethics Review Unit (KEMRI/SERU/CCR/0190/4117 dated February 15^th 2021) and the National Commission for Science, Technology and Innovation (NACOSTI/P/20/4221). Verbal consent was obtained and it was approved by KEMRI/SERU to collect samples from households, water distribution points owners and Kisumu County Referral Hospital management.

2.2 Study area and design

We conducted this study in the Kisumu County Referral Hospital (KCRH) and six sub-locations within Kisumu County (Figure 1), with the sites chosen based on data from an ongoing study by Musila et al., on antimicrobial resistance in military and civilian populations in Kenya (SSC 2767 WRAIR 2089), where it was observed that the majority of Pseudomonas aeruginosa infections were community-acquired (unpublished data).

Figure 1. Study map showing sampled sub-locations and Hospital in Kisumu County Kenya.

We adopted a cross-sectional study design with a random sampling strategy to obtain 297 (100 water and 197 swab) samples from KCRH and six sub-locations; Milimani, Nyalenda A, Nyalenda B, Manyatta, Manyatta B, and Kaloleni within two (2) weeks in April 2021. Seven households, two public schools and two communal water distribution points from each sub-location were randomly selected and 77 water and 172 swab samples from taps, shower heads, tanks (>1000 litres external), water storage containers (20 liters) and sinks were collected. In KCRH, a total of 48 samples were collected from taps, sinks and shower heads in the male general, surgical, pediatric and maternity wards, and from water reservoir tanks.

2.3 Sample collection

We collected water samples in clean and sterile screw-capped 250 mL Gosselin^TM polypropylene bottles containing 0.1 N of 30mg sodium thiosulphate (Thermofisher scientific Catalogue No: 15103917) by disinfecting the tap using 70% ethanol (plastic taps) or flaming (metal taps), and allowing the water to run for a few minutes before sampling. Swab samples of tap outlets, sink basins, shower heads, and interior of tanks and containers were collected using an environmental sampling kit (Puritan ESK, Guilford, ME, USA) as described by Schiavano and others.⁸ All samples were transported in a cool box (4-6°C) to the KCRH -based USAMRD-A laboratory in Kisumu for processing within 2 hours.

2.4 Bacterial isolation, identification and antimicrobial susceptibility testing

We processed the study samples following standard procedures outlined by the UNI EN ISO 16266:2008 standard on the detection and enumeration of P. aeruginosa method by membrane filtration.²⁸ Briefly, 100 mL of water was filtered through 0.45 μm, 47mm diameter cellulose ester membrane (MF-Millipore, Merck, KGaA, Darmstadt, Germany) to concentrate the bacteria, and the membranes were placed directly onto CHROMagar^TM Pseudomonas media (Becton Dickinson, France) and aerobically incubated at 37°C for 18 hrs. Blue or green pyocyanin-producing colonies were considered presumptive P. aeruginosa and fluorescent non-pyocyanin-producing colonies as other pseudomonads. The colonies were sub-cultured on Mueller Hinton Agar (MHA) Nutriselect^® Plus (Merck KGaA, Darmstadt, Germany) and screened by Gram staining and oxidase testing. All the oxidase-positive isolates were identified on the VITEK 2^® automated platform (bioMèrieux, Marcy I’Etolie, France) using the GN-ID card, and the O-Acetylase antigen-based PCR²⁹ was used to distinguish P. aeruginosa from other pseudomonads.

The VITEK 2 AST-XN05 card was used for antimicrobial susceptibility testing (AST) and interpreted based on the clinical laboratory standards institute guidelines of 2022.³⁰ P. aeruginosa ATCC 27853 and E. coli ATCC 25922 were used as positive and negative controls, respectively. The antibiotics panel included ticarcillin/clavulanic acid (8/2-128/2 μg/ml), piperacillin (4-128 μg/ml), ceftriaxone (0.25-64 μg/ml), cefepime (0.12-32 μg/ml), meropenem (0.25-16 μg/ml), levofloxacin (0.12-8 μg/ml), tigecycline (0.5-8 μg/ml) and chloramphenicol (4-64 μg/ml) on (AST-XN05, 26247, bioMèrieux, Marcy IÉtolie, France). For the colistin AST, the standard Cation adjusted Muller Hinton broth (CAMHB) method was used as described in the CLSI guidelines, with a known mcr-1 positive E. coli and ATCC 27853 as positive and negative control organisms, respectively.

3. Data analysis

We captured, compiled and analyzed the study data using MS Excel spreadsheet (Microsoft office 2019)³¹ bar graphs were generated on the same software. This study defined MDR pseudomonads as isolates resistant to 3 or more classes of antibiotics,²⁸ and we calculated the multiple antibiotic resistance indexes (MARI) as described by Davis and Brown³²: a/b where ‘a’ was the number of antibiotics to which an isolate exhibited resistance against those it was exposed to ‘b’, for susceptibility.

4. Results

4.1 Distribution of study samples

The highest proportion of samples were collected from the community (83.8%, n=249), drawn mainly from water storage containers (33%, n=98) and taps (24%, n=72) distributed across the different sub- locations and KCRH hospital in Kisumu county (Table 1).

Table 1. Sources and distribution of samples by a) sample source and b) sample location.

a. Sample source				b. Sampling location
Sources	Overall n (%)	Community n (%)	Hospital n (%)	Sub-location	n (%)
Taps	95 (32%)	72 (24%)	23 (8%)	Kaloleni	40 (13.5%
Sinks	38 (13%)	20 (7%	18 (6%)	Milimani	40 (13.5%)
Storage containers	98 (33%)	98 (33%)	0 (0%)	Manyatta A	38 (12.8%)
Tank	35 (12%)	28 (9%)	7 (2%)	Manyatta B	41 (13.8%)
Borehole	6 (2%)	6 (2%)	0 0%	Nyalenda A	41 (13.8%)
Water distribution outlets	8 (3%)	8 (3%)	0 0%	Nyalenda B	49 (16.5%)
Vendor Containers	17 (6%)	17 (6%)	0 0%	Hospital	48 (16.2%)
Total	297 (100%)	249 (84%)	48 (16%)	Total	297 (100%)

4.2 Prevalence and distribution of Pseudomonad isolates

In this study, we isolated pseudomonads from 14.1% (42/297) of the samples collected, predominantly from the community samples (10.4%, 31/297), and identified seven⁷ different species namely; P. aeruginosa, P. fluorescens, P. putida, P. fluorescens, P. oleovarans, P. mendocina and P. stutzeri. Pseudomonas aeruginosa was the most common species overall (6.7%, 20/297) and in the community samples (5.7%, 17/297). P. mendocina, P. alkaligens and P. putida were only detected in the community samples. P. fluorescens (2.0%, 6/297) was the main species in the hospital samples and P. oleovarans was exclusive to the hospital (Figure 2).

Figure 2. Prevalence and distribution of pseudomonad isolates in the hospital and community samples.

4.3 Distribution of Pseudomonads by sampling sources and locations

We found pseudomonads in all the study sampling sources, predominantly in taps and sinks (33.3%, 14/42). P. aeruginosa was the most common species in tanks (21.4%, 7/42) but was not isolated from vendor containers, household storage containers, or water distribution outlets, Figure 3A.

Figure 3. A – Distribution of pseudomonads by sampling sources. B – Distribution of pseudomonads by sub-locations.

Generally, the prevalence and distribution of Pseudomonas spp. varied in all the study sub-locations. The highest prevalence was observed in Milimani (35.7%, 15/42), KCRH (26.2%, 11/42), and Manyatta B (19%, 8/42). P. aeruginosa was predominant in Milimani (28.6%, 12/42), with a few isolates from KCRH and Manyatta but was not isolated in Nyalenda A, Nyalenda B, and Manyatta A (Figure 3B). The greatest diversity of Pseudomonas spp. was observed in taps, KCRH and in Kaloleni sub-location.

4.4 Reservoirs of Pseudomonads in community setting

Households accounted for 67.7% of the 31 pseudomonads isolated in the community environment, with the majority from taps (32.3%), sinks (22.6%), and tanks (19.4%). P. aeruginosa was the predominant species, recovered mostly from sinks (16.1%) and taps (12.9%) but absent in vendor containers, boreholes, and tank samples. Similarly, P. aeruginosa was the leading isolate (16.1%) in schools, within taps and boreholes (Figure 4).

Figure 4. Distribution of pseudomonads in community setting.

4.5 Distribution of pseudomonads in hospital setting

In the hospital environment, the majority of pseudomonads (36.4%, 4/11) were isolated from swab samples from the tank (27.3%, 3/11) and tap water (9.1%, 1/11). Tank swabs were the only source of P. aeruginosa in hospital samples, Figure 5.

Figure 5. Distribution of pseudomonads in hospital environment.

4.6 Pseudomonads antimicrobial susceptibility profiles

Pseudomonads isolates were 62% (26/42) non-susceptible to piperacillin, 57% (24/42) to tigecycline, 21% (9/42) to cefepime, 19% (8/42) to levofloxacin and 14% (6/42) to colistin (Table 2). Carbapenem resistance (non-susceptibility to meropenem) was 24% (10/42), mainly recorded in P. aeruginosa (80%, 8/10) from the Milimani sub-location (75%, 6/8). Six isolates (6/42 15%), were non-susceptibility to colistin and were mainly P. putida (50%, 3/6), with P. fluorescens (17%, 1/6) exhibiting resistance to both meropenem and colistin. A single isolate grew poorly during the VITEK 2 AST analysis and were indicated as a ‘terminated result’ (TRM) with 3 repeats.

Table 2. Pseudomonas AST profiles on VITEK 2 platform. Colistin results based on CAMHB micro dilution method.

Isolates	S/ID	S/Loc	TIM	PIP	CRO	FEF	MEM	LVX	TGC	CHL	CST
P. aeruginosa	H5	KCRH	TRM	TRM	NG	S (<=1)	S (<=0.25)	S (<0.12)	R (0.5)	TRM	S≤1μg/l
	H6	KCRH	R (>=128)	S (8)	NG	S (2)	S (<=0.25)	S (0.25)	S (2)	NG	S≤1μg/l
	H7	KCRH	R (>=128)	R (>=128)	NG	R (8)	R (>=16)	R (2)	R (>=8)	NG	NG
	C4	KLN	R (>=128)	R (64)	NG	S (<=1)	R (8)	S (0.25)	R (<0.5)	NG	NG
	C7	MLN	R (>=128)	R <=4)	NG	S (>1)	S (<=0.25)	S (0.5)	R (2)	NG	S≤1μg/l
	C8	MLN	R (>=128)	R (16)	NG	S (<=1)	S (<=0.25)	S (<=0.5)	R (4)	NG	S≤1μg/l
	C9	MLN	S (64)	S (16)	NG	S (2)	S (<=0.25)	S (0.5)	R (2)	NG	S≤1μg/l
	C10	MLN	S (64)	S (16)	NG	S (2)	S (<=0.25)	S (0.25)	R (2)	NG	S≤1μg/l
	C11	MLN	S (64)	S (16)	NG	S (2)	S (<=0.25)	S (0.25)	R (2)	NG	S≤1μg/l
	C12	MLN	R (>=128)	R (32)	NG	S (2)	I (4)	S (1)	R (>=8)	NG	S≤1μg/l
	C13	MLN	R (>=128)	R (16)	NG	S (2)	I (4)	S (1)	R (>=8)	NG	S≤1μg/l
	C15	MLN	S (64)	R (>=128)	NG	R (8)	R (8)	R (2)	R (>=8)	NG	S≤1μg/l
	C16	MLN	S (64)	R (16)	NG	S (<=1)	R (>=16)	S (0.25	R (2)	NG	S≤1μg/l
	C17	MLN	S (64)	R (16)	NG	S (<=1)	I (4)	S (<=0.12)	R (2)	NG	S≤1μg/l
	C18	MLN	S (64)	R (16)	NG	S (<=1)	TRM	S (<=0.12)	R (2)	NG	S≤1μg/l
	C19	MLN	S (<=8)	R(32)	NG	R (>=64)	R (8)	R (>=8)	R (<=0.5)	NG	S≤1μg/l
	C23	MLN	R (>=128)	R (>=128)	NG	R (16)	S (0.5)	R (2)	R (>=8)	NG	S≤1μg/l
	C25	MNYB	R (>=128)	S (32)	NG	S (2)	S (0.5)	S (0.5)	R (>=8)	NG	S≤1μg/l
	C26	MNYB	R (>=128)	R (>=128)	NG	S (4)	S (0.5)	S (1)	R (4)	NG	S≤1μg/l
	C31	MLN	R (>=128)	R (>=128)	NG	R (16)	S (1)	R (2)	R (>=8)	NG	R≤4μg/l
P. fluorescens	H1	KCRH	TRM	I (64)	R (>=64)	R (>=64)	S (<=0.25)	S (0.5)	S (<=0.5)	S (<=2)	S≤1μg/l
	H2	KCRH	TRM	R (>=128)	I (32)	R (>=64)	S (<=25)	R (>=8)	S (1)	I (16)	S≤1μg/l
	H4	KCRH	TRM	R (>=128)	R (>=64)	R (32)	R (>=16)	S (0.5)	S (<=0.5)	I (16)	R≤4μg/l
	H8	KCRH	TRM	R (>=128)	R (>=64)	S (4)	R (>=16)	I (4)	I (4)	R (>64)	S≤1μg/l
	H9	KCRH	TRM	R (>=128)	S (4)	S (<=1)	S (<=0.25)	S (2)	S (2)	S (<=2)	S≤1μg/l
	H11	KCRH	TRM	R (>=128)	I (32)	R (>=64)	S (<=25)	R (>=8)	S (1)	I (16)	S≤1μg/l
P. putida	C3	KLN	S (<=8)	S (<=4)	S (<=1)	S (<=1)	S (<=0.25)	S (1)	S (<=0.5)	I (16)	R≥2μg/l
	C5	MLN	R (>=128)	I (32)	I (32)	S (2)	S (4)	S (1)	R (>=8)	R (>64)	S≤1μg/l
	C6	MLN	R (>=128)	S (16)	I (32)	S (2)	S (4)	S (1)	R (>=8)	R (>64)	S≤1μg/l
	C14	MLN	TRM	I (64)	I (16)	S (2)	S (<=0.25)	S (1)	S (<=0.5)	S (<=2)	R≥4μg/l
	C22	MNYB	TRM	S (16)	I (32)	S (2)	S (4)	S (1)	S (2)	R (>64)	R≥4μg/l
	C24	MNYB	R (>=128)	I (64)	I (32)	S (2)	S (4)	S (0.5)	S (2)	R (=64)	S≤1μg/l
P. alcaligens	C27	MBYB	R (>=128)	R (>=128)	S (<=1)	S (4)	S (0.5)	S (1)	R (4)	S (<=2)	S≤1μg/l
	C28	NYAA	S (<=8)	S (<=4)	S (<=1)	S (<=1)	S (<=0.25)	S (1)	S (<=0.5)	I (16)	S≤1μg/l
	C29	NYAB	S (<=8)	S (<=4)	S (<=1)	S (<=1)	S (<=0.25)	S (0.5)	S (<=0.5)	I (16)	S≤1μg/l
	C30	NYAA	S (<=8)	S (<=4)	S (<=1)	S (<=1)	S (<=0.25)	S (4)	S (<=0.5)	I (16)	S≤1μg/l
P. oleovarans	H10	KCRH	S (<=8)	R (>=128)	S (8)	S (4)	S (<=0.25)	S (1)	S (<=0.5)	R (32)	S≤1μg/l
P. mendocina	C20	MNYA	S (<=8)	S (<=4)	S (<=1)	S (<=1)	S (<=0.25)	S (1)	S (<=0.5)	I (16)	R≥4μg/l
P. mendocina	CI	KLN	S (<=8)	S (<=4)	S (<=1)	S (<=1)	S (<=0.25)	S (1)	S (<=0.5)	I (16)	S≤1μg/l
P. stutzeri	C2	KLH	S (<=8)	S (<=4)	S (<=1)	S (<=1)	S (<=0.25)	S (1)	S (<=0.5)	I (16)	S≤1μg/l

4.7 Pseudomonad Multidrug-resistant phenotypes

In this study, 45% (19/42) of the isolates were MDR, predominated by carbapenem-resistant P. aeruginosa (CRPA) (42%, 8/19) and carbapenem-susceptible P. putida (26%, 5/19) mainly from the community samples (Table 3). All MDR CRPA remained susceptible to colistin and were isolated from the Milimani sub-location (80%, 8/10). P. oleovarans, P. alcaligens, P. mendocina, and P. stutzeri were non-MDR, whereas MDR P. putida were carbapenem-susceptible. MDR-pseudomonads exhibited high multiple antibiotic resistance indices (MARI), ranging from 0.43 to 1.

Table 3. Pseudomonads multidrug-resistant phenotypes.

Isolate	ID	Phenotype	# resistant ABS classes	MARI	MDR n (%)
Carbapenem-resistant Pseudomonads
P. aeruginosa (8)	C4	TIM-PIP/MEM/TGC	3	0.57	1 (5.3)
	C13, C12,	TIM-PIP/MEM/TGC	3	0.57	2 (10.5)
	C16, C17	PIP/MEM/TGC	3	0.43	2 (10.5)
	H7	TIM-PIP/FEP/MEM/LVX/TGC	5	0.86	1 (5.3)
	C19, C15	PIP/FEP/MEM/LVX/TGC	5	0.71	2 (10.5)
P. fluorescens (2)	H4	PIP/CRO-FEP/MEM/CHL/COL	5	0.86	1 (5.3)
P. fluorescens (2)	H8,	PIP/CRO-FEP/MEM/LVX/TGC/CHL	6	1.00	1 (5.3)
Carbapenem-susceptible Pseudomonads
P. aeruginosa (2)	C23	TIM-PIP/FEF/LVX/TGC	4	0.71	1 (5.3)
P. aeruginosa (2)	C31	TIM-PIP/FEP/LVX/TGC/COL	5	0.86	1 (5.3)
P. fluorescens (2)	H2	PIP/CRO-FEF/LVX	3	0.57	1 (5.3)
P. fluorescens (2)	H11	PIP/CRO-FEF/LVX/CHL	4	0.71	1 (5.3)
P. putida (5)	C5, C24	TIM-PIP/CRO/CHL	3	0.57	2 (10.5)
	C22	CRO/CHL/CST	3	0.43	1 (5.3)
	C14	PIP/CRO/CST	3	0.43	1 (5.3)
	C6	TIM/CRO/TCG/CHL	4	0.44	1 (5.3)

5. Discussion

Pseudomonas aeruginosa is a well-studied opportunistic Pseudomonad with a predilection to cause infections in vulnerable populations such as immunocompromised individuals. The global rise in MDR P. aeruginosa, particularly the carbapenem-resistant strains, pose a critical public health challenge due to limited treatment options. In our study setting in Kisumu county, Kenya, P. aeruginosa and other pseudomonads were previously isolated from patients who acquired them in the hospital and in the communities, prompting the need to identify their environmental reservoirs and antibiotic susceptibility patterns to inform the design of targeted infection prevention and control (IPC) interventions both in the community and hospital environments. This study identified pseudomonads in the water sources from the community (schools, households, water distribution points) and the KCRH hospital within Kisumu county at a rate of 14% (42/297). In these water sources P. aeruginosa was the most prevalent species (6.7%), being isolated from tanks (19%, 7/36), borehole (17%, 1/6), sinks (16%, 6/37) and taps (6%, 6/98). A study by Opperman³³ reported Pseudomonas in stagnant water, which presents a conducive environment for its proliferation through formation and dissemination of biofilms.³⁴ In the current study, we did not recover P. aeruginosa from water storage containers both in homes and from water vendors, probably due to the shorter static period of water in these containers, considering that these containers were used for ferrying water as opposed to holding it for long periods. Colonization at the point of use, including tap heads, plays a critical role in P. aeruginosa infections as opposed to the water distribution system.³⁵ These data suggest that community interventions should be focused on long- term storage receptacles and piping systems that terminate in tap heads.

In the community setting, the occurrence of P. aeruginosa varied among the sampled sub-locations, with 65% (13/20) of the isolates derived from Milimani sub-location, mainly in households (69%, 9/13) and school (31%,4/13). This observation could be attributable to the high coverage of old water plumbing systems, probably made of materials that allow for accumulation of biofilms.³⁵ Sink/tap contamination may also be another factor,²⁷ considering that Milimani had the highest water distribution coverage with more than 85% (6/7) of sampled households having multiple plumping fixtures (taps and sinks) as well as consistent flow of piped water. This suggests that regular cleaning and removal of biofilms from old plumbing systems such as those found in Milimani sub-location could reduce the risks of P. aeruginosa infections.

An interesting observation was that the same species of pseudomonads were isolated at different sampling points within the same household in three of the houses in Milimani, highlighting the possibility of cross-contamination at the household level as opposed to water distribution system contamination. We isolated no pseudomonad from Nyalenda A and B sub-locations, where up to 10 households used single stand-alone taps commonly located in an open space with no associated sinks or drains. We had a similar observation from households using short-term water holding and ferrying 20-litre-containers. These findings suggest the role of sinks and drains in pseudomonads transmission in communities.

In this study, we isolated P. fluorescence, P. oleovarans, P. alcaligenes, P. mendocina, P. putida and P. stutzeri in water sources at a prevalence of 7.4% (22/297). Even though not as common as P. aeruginosa, these pseudomonads were previously isolated from clinical specimens in KCRH and elsewhere, with P. stutzeri reported in wound and blood,³⁶ P. putida in neonatal bacteremia and sepsis,³⁷ P. fluorescens in respiratory infections,³⁸ P. alcaligenes in bloodstream infections,¹⁹ and P. mendocina in infective endocarditis and central nervous system infections among others.²⁰ These findings highlight the increasing clinical importance of non-P. aeruginosa pseudomonads and the need to track their environmental reservoirs. This study found these species in taps and sinks reflecting their largely environmental origin and these sources as key transmission points in the community and hospitals.

Pseudomonas species are well known for their intrinsic resistance to a wide range of antimicrobials, mainly due to the synergies between their low outer membrane permeability, possession of multidrug efflux pumps and inbuilt antimicrobial inactivation.³⁹ In the current study, antibiotic non-susceptibility among the pseudomonads ranged from 19.5% for levofloxacin and colistin and 62% for piperacillin. Carbapenem- resistant-P. aeruginosa (CRPA) isolates, based on meropenem non-susceptibility, constituted 40% of all pseudomonads, which was consistent with 31%⁴⁰ and 40%⁴¹ observed in clinical isolates (unpublished data), but lower than a recent study where CRPA were 100% non-susceptible from community and hospital acquired infections in a Kenyan referral hospital.⁴² The variation in these findings may be attributable to differences in the selection of study isolates, among other factors, but may suggest increased over-reliance on or misuse of carbapenem in Kisumu County, Kenya.

The prevalence of MDR pseudomonads was 45% in our study, a higher occurrence than 31% recently documented in Kenyan hospitals.⁴⁰ In the current study, the highest proportion of the MDR isolates was P. aeruginosa, mainly from the community (23%, 10/24), higher than the 13.4 % reported from environmental isolates in Ghana.⁴³ Our study found only one MDR CRPA in the hospital environment (2.3%, 1/42), which corroborates the 0.3% reported by Odoyo and others from environmental samples in Kenyan hospitals,⁴⁴ highlighting the lower risk of MDR Pseudomonas infections from hospital environment reservoirs than community reservoirs. Other MDR pseudomonads, specifically P. fluorescens, were isolated from the hospital environment at a 9.5% (4/42) rate. Previous studies suggest that P. fluorescens MDR phenotypes are naturally abundant or may result from human environmental activities.⁴⁵ MDR pseudomonads in the natural environment may carry mobile resistance genes which could be a reservoir for non-MDR but more pathogenic pseudomonads that, when the selection pressure from the overuse of carbapenems is applied, could drive MDR infections. All pseudomonad isolates had a MARI greater than 0.43, suggesting a high selective pressure in the current study environments, probably due to widespread antibiotic use and abuse, as reported in a previous study on the use and disposal of antibiotics in households in Kisumu, Kenya.⁴⁶ To prevent dissemination of MDR-pseudomonads, protecting water systems from contamination, thus incorporating the principle of one-health where environmental health translates directly to human health remains a top priority.

6. Conclusion

This study reveals a high prevalence of MDR pseudomonads, including CRPA strains in community tanks, taps, sinks, and other water sources, presenting a critical public health threat, especially among immunocompromised persons and acting as potential conduits or reservoirs of drug resistance. Interventions, such as regular cleaning of water storage facilities, water treatment, maintenance of water piping systems, and strict implementation of antimicrobial stewardship programs, are urgently required to prevent increased resistance due to drug overuse and to eliminate environmental factors that place the vulnerable populations at risk.

7. Study limitations

The limited sampling duration and distribution and techniques may have limited the detection of pseudomonads due to temporal, diurnal and culture requirement variations. Genomic characterization of the study isolates would further identify strain types and inform of the transmission patterns of isolates based on their relatedness between the environmental sources, as well as AMR mechanisms.

Authors contributions

Conceptualization: L.M., A.M., P.M. Funding acquisition: L.M. Investigation- P.M., AM., and E.O. Data analysis P. M, A. M, and C.K. Writing-original draft preparation: P. M and L.M. Writing-review and editing: P.M., L.M., A.M. All authors read and approved the final manuscript.

Disclaimer

The views here in are solely private opinions and assertions of the authors.

Ethics and consent

Approval to conduct this study was obtained from the Kenyatta University’s Graduate School, Kenya Medical Research institute – Scientific Ethics Review Unit (KEMRI/SERU/CCR/0190/4117 dated February 15^th 2021) and the National Commission for Science, Technology and Innovation (NACOSTI/P/20/4221). Permission to collect samples from Kisumu County Hospital was sought from the hospital management. Verbal consent was obtained and it was approved by KEMRI/SERU to collect samples from households, water distribution points owners and Kisumu County Referral Hospital management

Data availability

Underlying data

Figshare: Study samples & isolates (dataset) DOI 10.6084/m9.figshare.25284709

https://figshare.com/s/37d537fd7cb2f0519913.⁴⁷

This project contains the following underlying data

Study samples (297) and isolates (dataset in excel format)

Data are available under the terms of Creative Commons Attribution 4.0 international license (CC BY 4.0)

Supplementary material

No supplementary material is available for this paper.

Acknowledgement

The authors appreciate Paul Kimani, Angela Muraya for assistance with lab procedures and Alfred Odindo, Catherine Wawira, Martin Odindo and Paul Ojore for assistance with sample collection at KCRH.

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Comments on this article Comments (0)

Version 1

VERSION 1 PUBLISHED 13 May 2024

Author details Author details

¹ Kenyatta University, Nairobi, Kenya
² Kenya Medical Research Institute, Nairobi, Kenya
³ Walter Reed Army Institute of Research - Africa, Kericho, Kenya

Polly Mubassu
Roles: Conceptualization, Formal Analysis, Investigation, Methodology, Visualization, Writing – Original Draft Preparation, Writing – Review & Editing

Abednego Musyoki
Roles: Conceptualization, Formal Analysis, Supervision, Validation, Visualization, Writing – Review & Editing

Erick Odoyo
Roles: Formal Analysis, Methodology, Project Administration, Supervision, Writing – Review & Editing

Collins Kigen
Roles: Data Curation, Investigation, Validation, Visualization, Writing – Review & Editing

Lillian Musila
Roles: Conceptualization, Formal Analysis, Funding Acquisition, Methodology, Supervision, Visualization, Writing – Original Draft Preparation, Writing – Review & Editing

Competing interests

No competing interests were disclosed.

Grant information

the Armed Forces Health Surveillance Division (AFHSD), Global Emerging Infections Surveillance (GEIS) Branch [PROMIS ID 17_KY_1.3.1].
The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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Published: 13 May 2024, 13:474

https://doi.org/10.12688/f1000research.147914.1

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Mubassu P, Musyoki A, Odoyo E et al. Environmental reservoirs of multidrug-resistant pseudomonads in a geographical location in Kenya with high community-acquired infections [version 1; peer review: 2 approved with reservations]. F1000Research 2024, 13:474 (https://doi.org/10.12688/f1000research.147914.1)

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Reviewer Report 15 Jul 2024

Balram Ji Omar, Department of Microbiology, All India Institute of Medical Sciences, Rishikesh, Uttarkhand, India

Approved with Reservations

https://doi.org/10.5256/f1000research.162161.r285314

In the submitted manuscript authors describe resistance profile of Pseudomonas aeruginosa from various water sources from Kisumu County, Kenya emphasizing Multidrug resistance of various other pseudomonads also . The study is relevant for a better understanding of the worldwide dissemination ... Continue reading

The abstract seems ok to me

Background

The second sentence from the 4th paragraph must be supported by a reference. The sentence "these drugs face. acquisition costs" is not clear and must be rephrased. In the first sentence of the last paragraph, substitute "clinical" by "opportunistic".

Methods

2.2. information corresponding to unpublished data must be further presented. In the second paragraph, the specific number of samples per collection site (i.e. taps, shower heads, etc) must be mentioned
Clarify if any biofilm formation experiments were done in these isolated pseudomonads

Results

Add The data of other bacteria isolated during the culture of these samples or clarify that only pseudomonads were only isolated bacteria.

Is the work clearly and accurately presented and does it cite the current literature?

Yes
Is the study design appropriate and is the work technically sound?

Yes
Are sufficient details of methods and analysis provided to allow replication by others?

Partly
If applicable, is the statistical analysis and its interpretation appropriate?

I cannot comment. A qualified statistician is required.
Are all the source data underlying the results available to ensure full reproducibility?

Partly
Are the conclusions drawn adequately supported by the results?

Partly

Competing Interests: No competing interests were disclosed.

Reviewer Expertise: Bacteriology , Anaerobic Bacteriology ,Virology ,MDR ,Candidemia , Neonatal malaria , Phytochemicals

I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard, however I have significant reservations, as outlined above.

CITE

Report a concern

Author Response 28 Mar 2025

Polly Mubassu, Kenyatta University, Nairobi, Kenya

28 Mar 2025

Author Response
Your review to this article is highly appreciated. Please see our response is in bold;

Background
- The sentence "these drugs face. acquisition costs" is not clear and must
... Continue reading
Your review to this article is highly appreciated. Please see our response is in bold;

Background

The sentence "these drugs face. acquisition costs" is not clear and must be rephrased. The sentence has been rephrased to these drugs have challenges, due to insufficient high-quality clinical data, delayed approval for susceptibility testing methods, antibacterial spectra complexity, and are costly and will be added to the reviewed article.

In the first sentence of the last paragraph, substitute "clinical" by "opportunistic". Done, and will be reflected on the reviewed article.

Methods

2.2. information corresponding to unpublished data must be further presented. Noted: The data has since been updated on fig share, DOI - 10.6084/m9.figshare.26054509, and will be linked to the reviewed article.

In the second paragraph, the specific number of samples per collection site (i.e. taps, shower heads, etc) must be mentioned Noted; The specific number of samples are captured on table 1 by sampling sites/spots and location.

Clarify if any biofilm formation experiments were done in these isolated pseudomonads-No biofilm experiments were done in this study.

Results

Add The data of other bacteria isolated during the culture of these samples or clarify that only pseudomonads were only isolated bacteria. - We used chrome agar pseudomonas which is selective for Pseudomonas, the species of interest in this study, we did not further identify the resultant non-Pseudomonas species.
Your review to this article is highly appreciated. Please see our response is in bold;

Background

The sentence "these drugs face. acquisition costs" is not clear and must be rephrased. The sentence has been rephrased to these drugs have challenges, due to insufficient high-quality clinical data, delayed approval for susceptibility testing methods, antibacterial spectra complexity, and are costly and will be added to the reviewed article.

In the first sentence of the last paragraph, substitute "clinical" by "opportunistic". Done, and will be reflected on the reviewed article.

Methods

2.2. information corresponding to unpublished data must be further presented. Noted: The data has since been updated on fig share, DOI - 10.6084/m9.figshare.26054509, and will be linked to the reviewed article.

In the second paragraph, the specific number of samples per collection site (i.e. taps, shower heads, etc) must be mentioned Noted; The specific number of samples are captured on table 1 by sampling sites/spots and location.

Clarify if any biofilm formation experiments were done in these isolated pseudomonads-No biofilm experiments were done in this study.

Results

Add The data of other bacteria isolated during the culture of these samples or clarify that only pseudomonads were only isolated bacteria. - We used chrome agar pseudomonas which is selective for Pseudomonas, the species of interest in this study, we did not further identify the resultant non-Pseudomonas species.
Competing Interests: No competing interests to disclose. Close
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COMMENTS ON THIS REPORT

Author Response 28 Mar 2025

Polly Mubassu, Kenyatta University, Nairobi, Kenya

28 Mar 2025

Author Response
Your review to this article is highly appreciated. Please see our response is in bold;

Background
- The sentence "these drugs face. acquisition costs" is not clear and must
... Continue reading
Your review to this article is highly appreciated. Please see our response is in bold;

Background

The sentence "these drugs face. acquisition costs" is not clear and must be rephrased. The sentence has been rephrased to these drugs have challenges, due to insufficient high-quality clinical data, delayed approval for susceptibility testing methods, antibacterial spectra complexity, and are costly and will be added to the reviewed article.

In the first sentence of the last paragraph, substitute "clinical" by "opportunistic". Done, and will be reflected on the reviewed article.

Methods

2.2. information corresponding to unpublished data must be further presented. Noted: The data has since been updated on fig share, DOI - 10.6084/m9.figshare.26054509, and will be linked to the reviewed article.

In the second paragraph, the specific number of samples per collection site (i.e. taps, shower heads, etc) must be mentioned Noted; The specific number of samples are captured on table 1 by sampling sites/spots and location.

Clarify if any biofilm formation experiments were done in these isolated pseudomonads-No biofilm experiments were done in this study.

Results

Add The data of other bacteria isolated during the culture of these samples or clarify that only pseudomonads were only isolated bacteria. - We used chrome agar pseudomonas which is selective for Pseudomonas, the species of interest in this study, we did not further identify the resultant non-Pseudomonas species.
Your review to this article is highly appreciated. Please see our response is in bold;

Background

The sentence "these drugs face. acquisition costs" is not clear and must be rephrased. The sentence has been rephrased to these drugs have challenges, due to insufficient high-quality clinical data, delayed approval for susceptibility testing methods, antibacterial spectra complexity, and are costly and will be added to the reviewed article.

In the first sentence of the last paragraph, substitute "clinical" by "opportunistic". Done, and will be reflected on the reviewed article.

Methods

2.2. information corresponding to unpublished data must be further presented. Noted: The data has since been updated on fig share, DOI - 10.6084/m9.figshare.26054509, and will be linked to the reviewed article.

In the second paragraph, the specific number of samples per collection site (i.e. taps, shower heads, etc) must be mentioned Noted; The specific number of samples are captured on table 1 by sampling sites/spots and location.

Clarify if any biofilm formation experiments were done in these isolated pseudomonads-No biofilm experiments were done in this study.

Results

Add The data of other bacteria isolated during the culture of these samples or clarify that only pseudomonads were only isolated bacteria. - We used chrome agar pseudomonas which is selective for Pseudomonas, the species of interest in this study, we did not further identify the resultant non-Pseudomonas species.
Competing Interests: No competing interests to disclose. Close
Report a concern

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Reviewer Report 08 Jun 2024

Manuela Oliveira, Faculty of Veterinary Medicine, University of Lisbon, AL4AnimalS , cE3c, Lisbon, Portugal

Approved with Reservations

https://doi.org/10.5256/f1000research.162161.r280048

The authors aimed to describe the resistance profile of Pseudomonas aeruginosa from water sources from Kisumu County, Kenya. The study is relevant for a better understanding of the worldwide dissemination of AMR.
Comments:

- Abstract
The abstract must be reviewed. The meaning of MDR and AST must be included. The sentence "in settings with community-acquired.... scarce" is not clear and must be rephrased. What do the authors mean by reservoirs? Pseudomonads is not in italics. The % values must follow the results to which they correspond to (as in the results section). The sentence "42% strains susceptible to colistin" is not clear and must be rephrased.

- Background
Pseudomonads is not in italics. Remove "therapy equipment such as". The second sentence from the 4th paragraph must be supported by a reference. The sentence "these drugs face... acquisition costs" is not clear and must be rephrased. In the first sentence of the last paragraph, substitute "clinical" by "opportunistic".

Methods
- 2.2. The information corresponding to unpublished data must be further presented. In the second paragraph, the specific number of samples per collection site (i.e. taps, shower heads, etc) must be mentioned (in the text or as a table).
- 2.4, second paragraph. The format of reference 30 must be corrected in the reference list. A table with the susceptibility limits considered should be included. As it is the first time E. coli is mentioned, the genus must be in full. Were the intrintrinsic resistance considered in the analysis of the resistance profiles? A reference regarding the E. coli mcr-1 positive isolate must be included.
- 3. The definition of the MAR Index is not clear and must be better explained. The authors must perform the statistical analysis of the results, to determine the differences between the distribution of bacterial species and sample locations, between resistance profiles and bacterial species, between resistance profiles and sample locations. The results obtained in the statistical analysis must also be presented in the Results section and discussed in the Discussion section.

Results
- In the first paragraph there is an "and" that should not be in italics. In Table 1, the description of the sample sources must be similar to the one presented in the Material and Methods - and the same comment applied to the legend of Figure 3. The titles 4.4. and 4.5. are not necessary and should be eliminated.

Discussion
- Pseudomonad is not in italics. There is a repetition of the results in some parts of the discussion (example: the first 4 lines following Tabel 3, the first two lines in the following paragraph). The information corresponding to unpublished data must be further presented.

Study limitations
- Explain what were the "temporal, diurnal and culture requirements variations". Although the genomic characterization of the study isolates would allow to access transmission patterns, the resistance profiles could also be used for a preliminary evaluation. The authors could include this analysis in their manuscript.

Is the work clearly and accurately presented and does it cite the current literature?

Yes
Is the study design appropriate and is the work technically sound?

Partly
Are sufficient details of methods and analysis provided to allow replication by others?

Yes
If applicable, is the statistical analysis and its interpretation appropriate?

No
Are all the source data underlying the results available to ensure full reproducibility?

Yes
Are the conclusions drawn adequately supported by the results?

Partly

Competing Interests: No competing interests were disclosed.

Reviewer Expertise: Bacteriology, antimicrobial resistance

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Version 1 13 May 24	read	read

Manuela Oliveira, University of Lisbon, AL4AnimalS , cE3c, Lisbon, Portugal
Balram Ji Omar, All India Institute of Medical Sciences, Rishikesh, India

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15 Jul 2024 | for Version 1

Balram Ji Omar, Department of Microbiology, All India Institute of Medical Sciences, Rishikesh, Uttarkhand, India

5 Views Cite this report Responses(1)

Approved With Reservations

The abstract seems ok to me

Background

The second sentence from the 4th paragraph must be supported by a reference. The sentence "these drugs face. acquisition costs" is not clear and must be rephrased. In the first sentence of the last paragraph, substitute "clinical" by "opportunistic".

Methods

2.2. information corresponding to unpublished data must be further presented. In the second paragraph, the specific number of samples per collection site (i.e. taps, shower heads, etc) must be mentioned
Clarify if any biofilm formation experiments were done in these isolated pseudomonads

Results

Add The data of other bacteria isolated during the culture of these samples or clarify that only pseudomonads were only isolated bacteria.

Is the work clearly and accurately presented and does it cite the current literature?

Yes
Is the study design appropriate and is the work technically sound?

Yes
Are sufficient details of methods and analysis provided to allow replication by others?

Partly
If applicable, is the statistical analysis and its interpretation appropriate?

I cannot comment. A qualified statistician is required.
Are all the source data underlying the results available to ensure full reproducibility?

Partly
Are the conclusions drawn adequately supported by the results?

Partly

Competing Interests

No competing interests were disclosed.

Reviewer Expertise

Bacteriology , Anaerobic Bacteriology ,Virology ,MDR ,Candidemia , Neonatal malaria , Phytochemicals

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Responses (1)

Author Response

28 Mar 2025

Polly Mubassu, Kenyatta University, Nairobi, Kenya

Your review to this article is highly appreciated. Please see our response is in bold;

Background

The sentence "these drugs face. acquisition costs" is not clear and must be rephrased. The sentence has been rephrased to these drugs have challenges, due to insufficient high-quality clinical data, delayed approval for susceptibility testing methods, antibacterial spectra complexity, and are costly and will be added to the reviewed article.
In the first sentence of the last paragraph, substitute "clinical" by "opportunistic". Done, and will be reflected on the reviewed article.

Methods

2.2. information corresponding to unpublished data must be further presented. Noted: The data has since been updated on fig share, DOI - 10.6084/m9.figshare.26054509, and will be linked to the reviewed article.
In the second paragraph, the specific number of samples per collection site (i.e. taps, shower heads, etc) must be mentioned Noted; The specific number of samples are captured on table 1 by sampling sites/spots and location.
Clarify if any biofilm formation experiments were done in these isolated pseudomonads-No biofilm experiments were done in this study.

Results

Add The data of other bacteria isolated during the culture of these samples or clarify that only pseudomonads were only isolated bacteria. - We used chrome agar pseudomonas which is selective for Pseudomonas, the species of interest in this study, we did not further identify the resultant non-Pseudomonas species.

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Competing Interests

No competing interests to disclose.

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Reviewer Report

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08 Jun 2024 | for Version 1

Manuela Oliveira, Faculty of Veterinary Medicine, University of Lisbon, AL4AnimalS , cE3c, Lisbon, Portugal

16 Views Cite this report Responses(0)

Approved With Reservations

Is the work clearly and accurately presented and does it cite the current literature?

Yes
Is the study design appropriate and is the work technically sound?

Partly
Are sufficient details of methods and analysis provided to allow replication by others?

Yes
If applicable, is the statistical analysis and its interpretation appropriate?

No
Are all the source data underlying the results available to ensure full reproducibility?

Yes
Are the conclusions drawn adequately supported by the results?

Partly

Competing Interests

No competing interests were disclosed.

Reviewer Expertise

Bacteriology, antimicrobial resistance

Respond to this report

Responses (0)

Alongside their report, reviewers assign a status to the article:

Approved - the paper is scientifically sound in its current form and only minor, if any, improvements are suggested

Approved with reservations - A number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.

Not approved - fundamental flaws in the paper seriously undermine the findings and conclusions

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Environmental reservoirs of multidrug-resistant pseudomonads in a geographical location in Kenya with high community-acquired infections

Abstract

Background

Methods

Results

Conclusion

Keywords

1. Background

2. Methods

2.1 Study approval and consent

2.2 Study area and design

Figure 1. Study map showing sampled sub-locations and Hospital in Kisumu County Kenya.

2.3 Sample collection

2.4 Bacterial isolation, identification and antimicrobial susceptibility testing

3. Data analysis

4. Results

4.1 Distribution of study samples

Table 1. Sources and distribution of samples by a) sample source and b) sample location.

4.2 Prevalence and distribution of Pseudomonad isolates

Figure 2. Prevalence and distribution of pseudomonad isolates in the hospital and community samples.

4.3 Distribution of Pseudomonads by sampling sources and locations

Figure 3. A – Distribution of pseudomonads by sampling sources. B – Distribution of pseudomonads by sub-locations.

4.4 Reservoirs of Pseudomonads in community setting

Figure 4. Distribution of pseudomonads in community setting.

4.5 Distribution of pseudomonads in hospital setting

Figure 5. Distribution of pseudomonads in hospital environment.

4.6 Pseudomonads antimicrobial susceptibility profiles

Table 2. Pseudomonas AST profiles on VITEK 2 platform. Colistin results based on CAMHB micro dilution method.

4.7 Pseudomonad Multidrug-resistant phenotypes

Table 3. Pseudomonads multidrug-resistant phenotypes.

5. Discussion

6. Conclusion

7. Study limitations

Authors contributions

Disclaimer

Ethics and consent

Data availability

Underlying data

Supplementary material

Acknowledgement

References

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