Evidence on Vector-Associated Dissemination of Multidrug-Resistant Salmonella in the Philippines Food Supply Chain: A One Health Scoping Review

Abstract

This scoping review evaluates the role of vector-associated dissemination in contaminating the Philippine food supply chain with antimicrobial-resistant (AMR) Salmonella, an emerging infectious disease threat, using a One Health perspective to map the mechanisms through which insects and rodents bridge environmental reservoirs to human food systems. This scoping review was conducted and reported in accordance with the PRISMA-ScR guidelines. From 1969 records identified through systematic database searches, 52 studies met the inclusion criteria. These comprised 21 primary Philippine studies, 28 non-Philippine studies (including ASEAN-based historical baseline reports), and 3 policy/gray literature studies, prioritized to reflect tropical ecological and agricultural settings. Results suggest that intensive swine and poultry farming may contribute to the emergence of multidrug resistance (MDR) linked to genes such as bla_TEM and qnr. Evidence suggests that Salmonella persists in environmental matrices, such as manure and irrigation water, and that synanthropic vectors, including Rattus rattus and various fly species, potentially serve as biological and mechanical bridges in transmission. Clinical data reveal an alarming trend toward invasive non-typhoidal salmonellosis (iNTS) showing reduced susceptibility to cephalosporins and fluoroquinolones. Despite these findings, major evidence gaps remain, particularly regarding the prevalence of vector-borne Salmonella in pre-harvest produce. Consequently, mitigation requires a One Health framework that integrates non-antibiotic interventions, pest management to disrupt transmission pathways, and rapid diagnostic tools, such as loop-mediated isothermal amplification (LAMP), to enhance market surveillance.

1. Introduction

Antimicrobial resistance (AMR) represents a critical global public health threat, complicating the treatment of common infections and imposing substantial economic burdens. The widespread misuse and overuse of antimicrobial agents in human medicine, animal agriculture, and environmental settings have accelerated the emergence and spread of resistant bacteria, compromising decades of progress in infectious disease control and food safety [1,2]. The evolution of Salmonella spp. exemplifies this crisis as a primary driver of foodborne illness that is increasingly associated with multidrug resistance (MDR), particularly in low- and middle-income countries (LMICs) such as the Philippines. The Philippine food supply chain, comprising small-scale farms, informal markets, and densely populated urban–rural interfaces, offers numerous opportunities for the introduction and amplification of pathogens such as Salmonella. Local research has documented extensive contamination in retail products sold in wet markets and slaughterhouses, where a high proportion of isolates exhibit MDR profiles and harbor critical resistance determinants, including extended-spectrum β-lactamases (ESBLs) [3,4].

Addressing this escalating prevalence within Philippine food systems requires a One Health framework to map the dynamics within the interconnected human, animal, and environmental sectors. Resistance emerges from the combined effects of selective pressures across animal husbandry, clinical settings, and environmental reservoirs, thereby allowing Salmonella to persist and circulate. Multiple studies have already documented the presence of these pathogens carrying clinically relevant resistance markers in swine and poultry, including bla and qnr genes and pESI plasmids, across slaughterhouses and retail markets [5,6].

Synanthropic vectors, including flies and rodents, may act as biological and mechanical bridges, transporting pathogens from manure and contaminated surfaces to animal feed, carcasses, and food-handling sites [7]. While genomic surveillance of human clinical isolates in the Philippines reveals a high prevalence of fluoroquinolone resistance [8,9], the specific contribution of vector-mediated dissemination remains underexplored. By extending pathogen reach beyond direct or animal-environmental contact, these vectors underscore the need to integrate insect and rodent management into food safety and AMR mitigation strategies, setting the stage for a One Health Approach to map the complex ecological carriers of Salmonella dissemination in the Philippine food system.

Considering these interlinked dynamics, this review synthesizes evidence on vector-associated contamination of the Philippine food supply chain by AMR-Salmonella. Specifically, this review aims to address four key research questions: (1) What are the mechanisms and impacts of vector-mediated AMR-Salmonella contamination? (2) What is the prevalence and persistence of Salmonella within animal-environmental reservoirs? (3) Which vector species and food system nodes are most susceptible to Salmonella dissemination? (4) What strategies and policies currently exist to control vector-mediated AMR Salmonella transmission? Overall, this review synthesizes existing evidence and proposes a One Health framework to mitigate vector-mediated transmission of AMR-Salmonella across animal, environmental, and human health systems.

2. Methods

2.1. Study Design

A systematic scoping review was conducted to map the extent, nature, and characteristics of evidence on AMR in Salmonella and its transmission vectors across the food chain within a One Health framework. The conduct and reporting of this review adhere to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews (PRISMA-ScR) guidelines. To ensure methodological transparency, minimize the risk of bias, and address limitations associated with non-prospective tracking, a comprehensive review protocol was formally registered in the Open Science Framework (OSF) registry under DOI: 10.17605/OSF.IO/FWRBN. This registered protocol outlines the predefined search terms, selection criteria, and data extraction plans.

2.2. Search Strategy

A comprehensive and systematic literature search was executed between December 2025 and May 2026 across six electronic databases: PubMed/MEDLINE, ScienceDirect, CABI/CAB Abstracts, Cochrane Library, Herdin Plus, and Philippine E-Journal. The search strategy used a combination of controlled vocabulary and free-text keywords (detailed in

Table 1. Keywords and search strategies.

Data Base	Category	Keywords
PubMed/MEDLINE	Livestock & Retail	(Salmonella* OR salmonellosis) AND (“antimicrobial resistance” OR “MDR” OR “antibiotic resistance”) AND (vector* OR insect* OR fly OR flies OR rodent* OR dissemination) AND (poultry OR swine OR cattle OR farm* OR abattoir* OR “livestock environment” OR produce OR “food contamination”) AND (“Philippines”)
ScienceDirect	Produce	Salmonella AND (“antimicrobial resistance”) AND (vector OR dissemination OR transfer) AND (“food safety”) AND (Philippines)
Herdin Plus	Synanthropic Vectors	Salmonella
CABI	Livestock & Retail	Salmonella AND “antimicrobial resistance” AND (vectors OR rodents OR flies OR wild bird OR poultry) AND “food safety” AND Philippines
Cochrane library	Produce	Salmonella* OR salmonellosis AND vector* OR insect* OR flies OR rodent* OR dissemination AND “Philippines”
E-Journal	Synanthropic Vectors	Vector transmission of Salmonella

Note: Boolean operators (AND, OR) were used to combine search terms. The asterisk symbol (*) denotes truncation to include all variations of the root word (e.g., Salmonella).

), meticulously adapted to each database’s syntax to maximize sensitivity and retrieve relevant peer-reviewed and gray literature. The search strategy, utilizing exact Boolean search strings, underwent preliminary pilot testing to calibrate keyword effectiveness and was subsequently refined to align with the scope of this review. The systematic search results were managed and deduplicated using Mendeley Reference Manager (v2.145.0).

To minimize selection bias, the screening process was conducted independently by six reviewers. Titles and abstracts were screened for relevance in the initial phase, followed by a systematic full-text review of all shortlisted articles. Following this independent screening, the six reviewers re-evaluated all collected references. They held consensus meetings to validate final selections, resolve discrepancies, and ensure strict adherence to the predefined inclusion and exclusion criteria.

2.3. Selection Criteria

Studies were included in this review if they met the following criteria: (1) focus on non-typhoidal Salmonella spp.; (2) reporting of phenotypic (e.g., AST, MIC) or genotypic (e.g., PCR, WGS) antimicrobial resistance (AMR) data; (3) examination of at least one One Health interface; and (4) publication as peer-reviewed research or official reports in English. Eligible study designs included primary observational research (e.g., cross-sectional or prevalence surveys), experimental field studies, and laboratory-based analyses focusing on Salmonella isolation, AMR profiles, and associated vectors. To uphold a rigorous standard of evidence and mitigate the risk of including records from predatory or non-validated sources, inclusion was restricted to studies indexed in major international medical databases or published in reputable, peer-reviewed regional journals. These criteria served as a quality assurance protocol to ensure that all synthesized evidence underwent expert editorial oversight.

The exclusion process was conducted in two distinct stages to maintain the rigor and reproducibility of the evidence synthesis. During the initial title and abstract screening, records were excluded based on predefined thematic, temporal, and geographical parameters. Records were removed due to an irrelevant research focus, incongruity in the target pathogen, inapplicable publication type (e.g., book chapters, meeting proceedings, or secondary reviews), or a lack of geographic/temporal relevance. A temporal cutoff was established to include studies from January 1996 through June 2026, a window selected to capture the emergence and global dissemination of significant mobile genetic elements, such as Salmonella Genomic Island 1 (SGI1). Finally, reports were excluded if the full text was unavailable or if they were derived from non-indexed sources; however, studies lacking a Digital Object Identifier (DOI) were retained, provided they were published in reputable, peer-reviewed, and indexed academic journals.

During the subsequent full-text screening, strict objective criteria were applied to the reports assessed to ensure comparability of data. Studies were excluded for deviating from the defined regional baseline (1996–2009), a historical window that provides a foundational reference frame for the Philippine landscape by representing a critical phase of rapid transition in ASEAN smallholder livestock and traditional market systems.

To ensure scientific analogy, regional proxy data were included only if they originated from ecological settings comparable to the Philippine climate and agricultural systems. These parameters were explicitly defined as: (1) inclusion within Köppen tropical climate classifications (i.e., Af, Am, As, Aw); (2) documented presence of common synanthropic vector species (e.g., Rattus rattus, Musca domestica); and (3) analogous food systems characterized by high-density smallholder livestock production and traditional wet market distribution.

Records were further excluded due to insufficient data granularity, specifically when studies failed to link Salmonella isolates to specific reservoirs or lacked essential serovar identification, rendering them unsuitable for transmission pathway mapping. The absence of standardized AMR reporting metrics necessitated the exclusion of studies that relied solely on qualitative descriptions, and studies lacking peer-reviewed validation or explicit numerical reporting were excluded for incompatibility with methodological parameters. These parameters served as objective eligibility markers rather than subjective quality assessments, ensuring that the synthesized phenotypic and genotypic AMR data were standardized and interpretable. Finally, in instances of data redundancy, only the most comprehensive record from overlapping datasets was retained to prevent statistical bias.

2.4. Data Extraction and Synthesis

Data extraction was conducted systematically using a standardized charting form that captured key study characteristics, including publication year, geographical location, study design, sample size, specific Salmonella serovars, detected AMR patterns, and methodological approaches used for resistance detection (e.g., phenotypic MIC data, PCR, or WGS). Synthesized data were mapped to the four research objectives: (1) the role of vector-mediated transmission in food chain contamination by antimicrobial-resistant (AMR) Salmonella; (2) evidence across One Health interfaces (human, animal, and environmental); (3) identification of implicated vector species and contamination points; and (4) existing One Health interventions and research gaps. Following the JBI Manual for Evidence Synthesis, data were charted to identify sub-themes across interfaces, intervention types, and outcome measures. Descriptive statistics were utilized to summarize the longitudinal characteristics of the included studies. Subsequently, a narrative synthesis was employed to identify patterns, resistance trends, and thematic associations across literature. Findings were analyzed as a single dataset; Philippine-specific data were prioritized, while regional proxy data were integrated to provide a broader ecological context, ensuring that evidence was assessed for its relevance to tropical agricultural systems. This synthesis strategy provides a comprehensive overview of the current evidence base while transparently identifying key areas where primary research remains insufficient.

3. Results

3.1. Results: Sources and Environmental Persistence

3.1.1. Search Results

The systematic literature search identified a comprehensive body of evidence to establish contemporary and historical baseline metrics for AMR-Salmonella in the Philippines and analogous ASEAN ecological settings. The search, capturing primary research and official reports detailing data collection periods from January 1996 through June 2026, yielded a total of 1969 records across six major databases (PubMed/MEDLINE, ScienceDirect, CABI, Cochrane Library, HERDIN Plus, and E-Journal/PEJ), supplemented by three records from gray literature. Following the removal of 509 duplicate records, 1463 unique records were screened by title and abstract.

During the screening phase, 1463 records were reviewed; 1250 were excluded based on the established exclusion criteria: irrelevant research focus (n = 522), incongruity in the target pathogen (n = 317), inapplicable publication type (n = 265), and lack of geographic or temporal relevance (n = 146). This resulted in a total of 213 reports sought for retrieval. Of these, 28 were excluded due to the unavailability of full-text versions or the absence of a Digital Object Identifier (DOI). The remaining 185 reports underwent a rigorous full-text eligibility assessment. Of these, 136 were excluded due to deviations from the defined regional baseline (n = 98), insufficient data granularity (n = 19), lack of standardized AMR reporting metrics (n = 7), incompatibility with methodological parameters (n = 9), and duplicate reporting of shared datasets (n = 3). All excluded records were processed through a single-pathway hierarchy to ensure no overlapping exclusions occurred. Ultimately, 52 studies met the inclusion criteria for this scoping review, comprising 21 primary local research studies, 28 studies establishing the historical ASEAN baseline (1996–2009), and 3 policy/gray literature documents. These studies are synthesized in the Appendix A 

Table A1. Summary of individual sources of evidence included in the scoping review.

Author/Publish Year/Country	Methods	Samples (N) Prevalence %	Serovar	AMR	ARGs	Plasmid
Nagpala et al. (2025) Philippines [3]	XLD agar isolation, NovaSeq 6000 genomic sequencing (WGS), AMRFinderPlus screening, and VITEK 2 AST	N: 95 isolates (from 253 cuts) Prevalence: 73.68% resistant to ≥1 class; 45.26% MDR	Infantis (51.58%), Brancaster (9.47%), Anatum (7.37%), London (7.37%), Uganda (6.32%), Derby (4.21%), monophasic 1,4,[5],12:i: (2.11%), Breda (2.11%), Albany (2.11%), Kentucky (2.11%)	First detection of a highly virulent pESI-like megaplasmid clone and rare Salmonella Isangi in Philippine poultry.	tet(A), tet(B), tet(M), sul1, sul2, sul3, dfrA12, dfrA14, aac(3)-IId, aac(3)-IV, aac(6′)-Iaa, aac(6′)-Iy, ant(3″)-IIa, aph(3′)-Ia, aph(4)-Ia, aph(6)-Id, aadA2, aadA22, cmlA1, floR, fosA3, fosA4, fosA7	Plasmids: IncFIB(K)_1_Kpn3, ColRNAI, IncFIA(HI1)_1_HI1, IncHI1B(R27)_1_R27, IncHI1A_1, IncX1_1, IncX1_3, IncN_1, Col(BS512)_1, IncFII(S)_1 Genes: blaCTX-M-65, blaTEM-1, blaTEM-176, qnrS1. Mutation: gyrA (D87Y, S83F, S83Y).
Madayag et al. (2024) Philippines [4]	culture isolation, boiling temperature lysis, singleplex PCR for blaCTX-M groups (I, II, IV) confirmed via Sanger sequencing, and VITEK 2 automated AST panels [67]	N: 89 Salmonella isolates randomly selected from chicken meat across 5 Metro Manila cities Prevalence: 24.72% carrying blaCTX-M (n = 22); 11.24% carrying blaTEM (n = 10)	Salmonella enterica isolates	First local report of simultaneous blaCTX-M group II and IV coexistence; 95.5% of positive strains exhibited multidrug resistance (MDR).	NR	Coexistence of blaCTX-M groups II and IV; blaSHV was absent
Pavon et al. (2026) Philippines [5]	Check & Trace microarray platform serotyping, multiplex virulence/AMR PCR, and automated VITEK 2 phenotypic AST	N: 110 S. enterica swine meat isolates Prevalence: 90% successfully typed (n = 99/110); 14.81% Multidrug Resistant (MDR) rate	Rissen (23.64%), Anatum (11.82%), Derby (11.82%), monophasic Typhimurium 1,4,[5],12:i:- (10.91%), Uganda (9.09%), London (5.45%), Weltevreden (4.55%), Schwarzengrund (3.64%), Enteritidis (2.73%), Lexington (2.73%), Typhimurium (1.82%), Newport (0.91%), and Soerenga (0.91%)	First detection of Salmonella serovar Soerenga in the Philippines and Asia, with high prevalence of SPI 1–5 virulence genes.	NR	Genes: blaTEM detected in 44.55% of isolates. Plasmids: Plasmid-borne virulence factors spvC and spvR were completely absent (0%) across all swine isolates.
Calayag et al. (2017) Philippines [6]	Conventional culture extraction, invA gene confirmation PCR, multiplex PCR serogrouping, and VITEK 2 compact automated AST	N: 240 swine across 8 Metro Manila abattoirs Prevalence: 44.0% in accredited abattoirs; 46.7% in locally registered abattoirs	Predominantly Serogroup O:3,10 (E1)	Resistance profiles in various Philippine abattoir systems; Phenotypic resistance tested: 67.8% Ampicillin, 80.3% Trimethoprim/ Sulfamethoxazole	NR	NR
Sukontason et al. (2007) Thailand [7]	Field collection using insect sweep nets from 5 fresh-food markets in urban Chiang Mai, Thailand, followed by individual saline washing and standard microbiological inoculation/culturing (PEA, MacConkey, SS agar, Selenite-F broth, TCBS, and alkaline peptone water)	N: 60 adult flies total (130 Musca domestica and 130 Chrysomya megacephala) Prevalence: Chrysomya megacephala: 87.7% (114/130 flies positive for bacteria); Musca domestica: 66.2% (86/130 flies positive for bacteria)	NR	C. megacephala was significantly more likely to carry bacterial species than M. domestica, though sex was not a significant factor within species.	NR	NR
Azanza (2006) Philippines [8]	Epidemiological review of health department outbreak records	N: 60 outbreaks, 3313 morbidities, 25 mortalities Prevalence: Salmonella caused 30% of total cases (985 morbidities)	S. Typhi, S. Enteritidis, S. Typhimurium.	Meat dishes, specifically spaghetti, were the top food vehicles. Workplaces and schools were the main risk settings.	NR	NR
Azanza et al. (2019) Philippines [9]	Epidemiological review of health department outbreak records	N: 209 outbreaks involving 13,591 total cases Prevalence: 2.46% (335 cases) for Salmonella spp., 0.82% (112 cases) for S. Enteritidis	Salmonella spp., S. Enteritidis	Meat dishes, specifically spaghetti, were the top food vehicles. Workplaces and schools were the main risk settings.	NR	NR
Sia (2020) Philippines [10]	Sven Gard slide agglutination, White-Kauffmann-LeMinor classification, and AST via Vitek 2, Kirby-Bauer disk diffusion, and gradient diffusion (CLSI criteria)	N: 2387 clinical human isolates collected over 15 years (2004–2018) Prevalence: Typhoidal: 79.39% (n = 1895); Non-Typhoidal (NTS): 20.61% (n = 464, including 212 invasive NTS isolates)	S. Typhi (79.39%), S. Enteritidis (7.62%), S. Typhimurium (3.64%), and S. Weltevreden (1.00%)	Typhoidal cases peaked in males aged 6–17 years; MDR rates were low, S. Typhi resistance remained < 5%, but NTS showed high cephalosporin resistance (33.07%).	NR	NR
Bangtrakulnonth (2006) Thailand [11]	Comparative enrichment (RV+MSRV vs. DIASALM) and Kirby-Bauer disk diffusion	N: 50 meat samples Prevalence: RV+MSRV method (64–92%); DIASALM method (12–88%)	S. Anatum, S. Rissen, S. Stanley, S. Virchow	The RV+MSRV protocol yielded superior recovery over DIASALM. 50–60% resistant to Tetracycline, Streptomycin, and Ampicillin. 60% MDR rate across all meats.	NR	NR
Angkititrakul et al. (2005) Thailand [12]	Culture, serotyping, disk diffusion	N: 50 meat samples Prevalence: RV+MSRV method (64–92%); DIASALM method (12–88%)	S. Anatum, S. Rissen, S. Stanley, S. Virchow	No difference in AMR rates between sources.	Pork: Tet 88.5%, Str 100%, Sulfa 100% Chicken: Tet 100%, Str 100%, Sulfa 100% Human: Tet 92.6%, Str 100%, Sulfa 100%	Disk diffusion (NCCLS)
Develos et al. (2024) Philippines [15]	Enzyme-linked immunosorbent assay (ELISA) screening, sample homogenization, tissue centrifugation, and Mann–Whitney U testing	N: 146 total pork samples (74 muscle meat, 72 liver) Prevalence: 100% positive for residues	NA (Chemical residue analysis)	100% of samples contained residues; concentrations were significantly higher in the liver than in the muscle, but all stayed below safety limits.	NR	NR
Elumba et al. (2018) Philippines [16]	Nutrient broth swab enrichment, Salmonella-Shigella (SS) agar selective isolation, biochemical validation, and CLSI disk diffusion AST	N: 50 retail chicken pieces (25 drumsticks, 25 wings) in Bukidnon Prevalence: 18% overall (n = 9/50); Drumsticks: 4% (1/25); Wings: 32% (8/25)	Salmonella spp.	Retail poultry sensitivity in Valencia City, Bukidnon	NR	NR
Mora et al. (2024) Philippines [18]	Culture isolation, multiplex PCR, Illumina Whole Genome Sequencing (WGS), and VITEK 2 Compact AST	N: 105 isolates Prevalence: 65% resistant to ≥1 drug; 37% MDR; 57% ESBL producers	Infantis (26.7%), Anatum (19.1%), Rissen (18.1%), London (13.3%), Hvittingfoss (3.8%), Derby (2.9%), monophasic 1,4,[5],12:i:- (2.9%), Newport (2.9%), Uganda (2.9%)	Salmonella Infantis was linked to poultry, while Anatum and London were linked to swine; genomic clusters spanned markets and abattoirs.	tet(A), tet(B), tet(D), tet(M), tet(W), sul1, sul2, sul3, dfrA1, dfrA12, dfrA14, aadA1, aadA2, aph(6)-Id, aph(3′)-Ib, aac(3)-IVa, aac(3)-IId, aac(3)-IIe, aph(4)-Ia, cmlA1, floR	Plasmids: ColE1, Col4401, IncFIA, IncFIB, IncFII, IncHI1A, IncHI1B(R27), IncQ1, IncQ2, IncI1-Alpha, IncR, IncX1, IncX3, IncX4, p0111. Genes: blaCTX-M-65, blaTEM-1, blaTEM-150, blaTEM-176, qnrS1, qnrB2.
Calayag et al. (2021) Philippines [19]	Selective culture isolation, invA PCR identification, flagellar antigen profiling, monoplex PCR for resistance genes, and Vitek 2 automated AST	N: 178 S. enterica isolates from hog tonsils and jejunum tissue samples Prevalence: Initial environmental positivity rate not det. 13.5% (n = 24) of the analyzed isolates were multidrug-resistant (MDR)	Classified by serogroups: O:3,10 (38.8%), O:7 (30.3%), O:4 (21.3%), O:8 (1.7%), O:9 (1.7%), and Unidentified (6.2%). Group O:9 isolates were presumptive S. Enteritidis	High non-susceptibility was found for ampicillin (71.9%) and trimethoprim/ (70.8%). Ciprofloxacin non-susceptibility was 15.7%. High co-carriage of β-lactam and fluoroquinolone resistance factors was noted.	blaTEM (61.2%), blaCTX-M (5.1%, CTX-M-1 and CTX-M-2 variants), qnrA (12.9%), qnrB (39.3%), qnrS (61.2%)	qnrA, qnrB, and qnrS plasmid-mediated quinolone resistance genes. Co-carriage of blaTEM along with one to three of these qnr subtypes was found in 45.5% of total isolates.
Pavon et al. (2022) Philippines [20]	invA confirmatory PCR followed by multiplex/singleplex PCR assays optimized via temperature gradients	N: 799 Salmonella isolates from wet markets & abattoirs Prevalence: High frequency of SPI virulence markers across all 799 validated isolates	587 serogrouped: O:3 (n = 250), O:4 (n = 133), O:6,7 (n = 99), O:8 (n = 93), O:9 (n = 12)	Detection rates: mgtC (98.62%), pipB (97.37%), avrA (88.24%), hilA (71.21%), spi4R (65.71%), sseC (64.71%). 29.16% carried all 6 SPI genes.	NR	Plasmid-borne virulence traits spvC and spvR were detected in exactly 1 isolate (0.13%) from a pig sample.
Ng & Rivera (2014) Philippines [21]	Multiplex PCR (targeting invA gene), Culture methods	N: 320 (Raw and processed market meats) Prevalence: 30.64% (n = 98)	S. enterica serogroups: E1 (78.57%), C1 (29.59%), C2 (20.41%), B (17.35%), D (6.1%)	MDR Salmonella in tonsil/jejunum of slaughtered pigs.	NR	spvC gene
Labrador et al. (2025) Philippines [22]	Pooled sampling per market stall followed by molecular PCR assay detection	N: 54 commercial broiler chicken pieces (27 breast, 27 thigh samples tested in triplicate) Prevalence: 0% (0/54)	ND	No Salmonella spp. contamination was found across the commercial broiler samples evaluated.	NR	NR
Nuñal et al. (2023) Philippines [23]	BAM-Bacteriological Analytical Manual (Chapter 5) extraction, pre-enrichment (Lactose Broth), selective enrichment (RV and TT broths), plating (HE, XLD, BS agars), and biochemical validation tests (TSI, LIA)	N: 36 sample batches tracked across 5 value-chain nodes (Farms, Consolidators, Wholesalers, Wet Markets, Restaurants) Prevalence: 0% absolute detection for Salmonella spp. (n = 0/36 batches negative across all channels)	ND	No Salmonella was detected, but E. coli and Vibrio parahaemolyticus contamination increased from farm to retail due to poor handling practices.	ND	ND
Chuanchuen et al. (2008) Thailand [24]	Susceptibility testing and MIC evaluations, efflux system inhibition using CCCP, and cyclohexane tolerance testing	N: 257 Salmonella enterica isolates (125 poultry, 132 swine) Prevalence: ND	44 distinct serotypes including S. Albany, S. Altona, S. Agona, S. Amsterdam, S. Anatum, S. Bovismorbificans, S. Bareilly, S. Blockley, S. Corvallis, S. Enteritidis, S. Infantis, and S. Paratyphi B/B2, among others	42% of the isolates exhibited multidrug resistance (MDR); identified proton-dependent AcrAB-TolC efflux pump activity contributing to resistance.	NR	NR
Lapuz et al. (2012) Philippines [25]	Culture (HI broth, HTT, DHL agar), Serotyping, PFGE analysis	N: 380 (280 high rodent; 100 low rodent) Prevalence: 6.05% (n = 23); High Rodent: 7.14% S. Enteritidis, (n = 20), 1.07%; S. Infantis (n = 3); Low Rodent: 0%	S. Enteritidis, S. Infantis	Rodent density is a predictor of Salmonella in layer hens.	NR	NR
Umali et al. (2012) Japan [26]	Culture (BHI, HTT, DHL agar), Serotyping (O & H antigens), PFGE analysis	N: 128 (Captive wild roof rats) Prevalence: 41.2% of cages positive for S. Infantis; 3.92% of cages positive for S. Enteritidis	S. Infantis, S. Enteritidis	Fecal shedding patterns in wild Rattus rattus populations.	NR	NR
Vital et al. (2017) Philippines [27]	Selective broth enrichment, culture plating (XLD, BSA, HEA), invA simplex PCR, disk diffusion AST, and multiplex resistance screening	N: 410 fresh produce samples (lettuce, tomato, sprouts, etc.) Prevalence: 5.85% overall Salmonella prevalence (n = 24 isolates out of 410 surveyed). Serovars: Salmonella spp.	Salmonella spp.	Fresh produce as a vehicle for MDR Salmonella transmission.	tet(A) (75% of tetracycline-resistant isolates), tet(B) (9%), catI (67% of chloramphenicol-resistant isolates), catIII (33%)	qnrA, qnrB, qnrS (Screened via multiplex PCR from quinolone-resistant isolates)
DENR Administrative Order (2021) Philippines [28]	Review and policy update under the Philippine Clean Water Act of 2004 (RA 9275)	N: National statutory policy parameter updates Prevalence: Class AA/SA require ≤ 20 MPN/100 mL Fecal Coliform	Not applicable (targets broad bacterial indicators including fecal coliforms).	Sets explicit Fecal Coliform general effluent limits: Class A (100 MPN/100 mL), Class B/SB (200), Class C/SC (400), Class D/SD (800). Discharges strictly banned in AA/SA zones.	NR	NR
Garcia et al. (2015) Philippines [29]	Culture/Biochemical isolation, PCR screening	N: 165 (Retail meat cuts: 55 chicken, 55 pork, 55 beef from Metro Manila markets) Prevalence: 19.39% (n = 32)	S. enterica (Dominant serogroups: B, C1, C2, E1)	Fecal contamination and survival in irrigation systems.	blaTEM (44.55%)	qnr variants
Van et al. (2007) Vietnam [30]	Disk diffusion; PCR for Class 1 integrons; RFLP; Plasmid profiling; Conjugation (Mating)	N: 180 samples (91 isolates) Prevalence: 60.8% (Meat) and 18.0% (Shellfish)	Multiple types including S. Havana and S. Anatum	Resistance to at least one antibiotic; some were MDR.	dhfrXII, orfF, aadA2, aadA1, aadA5, aacA4, dfrA1, dhfrA17, blaPSE1, catB3	Class 1 integrons; Large plasmids (>95 kb)
Ribas et al. (2016) Thailand [31]	Trapping, molecular identification, and ISO 6579:2002 culture/serotyping	N: 110 Prevalence: 54 (49.10%)	S. Typhimurium, S. Weltevreden, S. 4,[5],12:i:-	Rodents are a potential reservoir; S. 4,[5],12:i:- reported in rodents for the first time.	NR	NR
Choo et al. (2011) Malaysia [32]	Culture isolation, biochemical identification, slide agglutination test, and serotyping	N: 60 flies (20 pooled samples per location) Prevalence: 13.3% (8 positive pools)	S. Hadar, S. Muenster, S. Indiana, S. Newington	Houseflies carried Salmonella (13.3%) and may serve as mechanical vectors for pathogen transmission in livestock and food environments.	NR	NR
Ly et al. (2010) Vietnam [33]	Capture, morphological ID, BPW/Hajna Tetrathionate enrichment, selective agar (BGA, MLCB), biochemical tests, and serotyping	N: 494 Prevalence: 38 (7.7%)	14 types, including S. Typhimurium, S. Panama, S. Newport, S. Derby, S. Bareilly, S. Lexington, S. Anatum	Flies act as an epidemiological link. Resistance to at least one antibiotic; some show multidrug resistance.	NR	NR
Nazni et al. (2005) Malaysia [34]	Baiting with 10% sugar solution; Peptone water isolation; Nutrient/Blood agar culture	N: Various (food courts, dumping grounds, processing areas, poultry farms) Prevalence: ND	Various genera isolated (Bacillus, Staphylococcus, Streptococcus, etc.)	Fly feces, vomitus, and external surfaces harbor bacteria.	NR	NR
Chuanchuen and Padungtod (2009) Thailand [38]	MIC via 2-fold agar dilution; PCR and Real-Time PCR; DNA Sequencing	N: 184 resistant isolates Prevalence: 100%	34 serotypes including Stanley, Typhimurium, Enteritidis, Rissen, Bsilla, Weltevreden, Anatum, Corvallis, Kedougou, Albany, and Amsterdam	Sulfamethoxazole, streptomycin	blaTEM, blaPSE-1, cmlA, catA, catB, aadB, tetA, tetB, dfrA12, dfrA1, dfrA10	Class 1 integrons; Salmonella Genomic Island 1 (SGI1) variants A and F
Thong (2004) Malaysia [39]	Disk diffusion and XbaI-PFGE molecular subtyping	N: 23 isolates (17 human, 4 env, 2 food) Prevalence: ND	S. Tshiongwe	Pulsotypes X4/X4a confirmed local cross-contamination. Tetracycline; streptomycin	NR	NR
Chuanchuen et al. (2007) Thailand [40]	ISO 6579, slide agglutination, agar dilution, and PCR/sequencing	N: 122 S. enterica isolates Prevalence: 100%	24 serotypes including S. Weltevreden, S. Anatum, and S. Stanley	High antibiotic resistance and multidrug resistance were observed.	qacEΔ1 was found in 27% of isolates; qacE was absent. intI1 was present in 70% of qacEΔ1-positive strains	Class 1 integrons carrying qacEΔ1 linked upstream of the 3′ conserved segment
Manguiat & Fang (2013) Philippines [43]	Culture (Selective media enrichment), Biochemical validation	N: 110 (Street-vended food samples in Laguna) Prevalence: 0% (n = 0)	None Detected	High microbial load in street-vended meat in Laguna.	ND	ND
Santos et al. (2020) Philippines [44]	ISO 6579 culture technique modified using selective broth/agar lines, boiling template DNA extraction across three processing protocols (TEPs I–III), invA gene validation PCR, and multi-step molecular serotyping PCR assays	N: 720 meat samples collected from 9 Metro Manila wet markets Prevalence: 57.64% overall contamination rate (n = 415/720); Raw Meat: 85.77% (n = 235/274); Processed Meat: 40.36% (n = 180/446)	Predominantly Serogroup O:3. Putative serovar clones: S. Anatum (most common in pork and beef), S. Saintpaul (beef), and S. Kentucky (most common in poultry)	Uncovered frequent simultaneous multi-serovar contamination within single retail samples.	NR	NR
Pornruangwong (2008) Thailand [45]	Disk diffusion (10 antimicrobials) and PFGE (XbaI enzyme)	N: 138 Salmonella isolates (108 human cases, 30 swine sources) Prevalence: Not Det	Monophasic S. 4,[5],12:i:- (108), S. Typhimurium (30)	100% resistance to Nalidixic acid. Common resistance to ampicillin, tetracycline, and sulfamethoxazole-trimethoprim.	NR	NR
Lagrada et al. (2022) Philippines [46]	Illumina WGS, in silico MLST, Pathogenwatch resistance profiling, and Vitek 2 AST	N: 213 confirmed high-quality Salmonella genomes (148 S. Typhi, 65 NTS) collected during 2013–2014. Prevalence: S. Typhi isolates were largely pan-susceptible. Among NTS isolates, 75.4% showed resistance to at least one antimicrobial class, but only five isolates were multidrug-resistant (MDR).	S. Typhi (n = 148), S. Enteritidis (n = 21), and monophasic variant of S. Typhimurium 1,4,[5],12:i:- (n = 16)	High ciprofloxacin insusceptibility.	blaTEM-1, blaCTX-M-15, blaCMY-2, blaDHA-1, catA2, cmlA1, floR, qnrA6, qnrS1, qnrB4, oqxA, oqxB, QRDR mutations (gyrA, parC)	qnrA6, qnrS1, and qnrB4 and plasmid-mediated quinolone resistance indi. ESBL plasmids harboring genes like blaCTX-M-15 and blaCMY-2 were successfully confirmed in five multi-resistant NTS genomes.
Boonmar et al. (1998) Thailand [47]	Disk diffusion (9 antimicrobial disks)	N: 1715 Salmonella strains (1308 human, 407 frozen chicken) Prevalence: ND	S. Enteritidis (600), S. Derby (290), S. Weltevreden (257), S. Anatum (235), S. Typhimurium (211), S. 1,4,5,12:i:- (122)	High resistance to kanamycin, amikacin, and ceftriaxone. High susceptibility to ofloxacin.	NR	NR
Padungtod and Kaneene (2006) Thailand [48]	Culture (BPW, RV, XLT4), biochemical/serological typing, microbroth dilution	N: 1326 livestock, 508 humans Prevalence: Chickens (3–57%), Pigs (6–37%), Cows (0–3%), Humans (7–36%)	S. Anatum, S. Emek, S. Rissen, S. Stanley, S. Weltevreden	Tetracycline, nalidixic acid	NR	NR
Nagpala et al. (2025) Philippines [50]	Illumina and Oxford Nanopore hybrid sequencing; NCBI PGAP annotation	N: 1 isolate (SCD6R1a) Prevalence: 100% (Case report)	S. Infantis	Large mega-plasmid	aadA1, qacEΔ1. sul1, tet (A), blaCTX-M-65, floR, aph(4)-Ia, aac(3)—IVa	pESI-like mega-plasmid (308 kb); Small mobilization plasmid pSCD6R1a_5.4k
Hendriksen et al. (2008) Thailand and Denmark [51]	Disk diffusion (10 antimicrobials) and PFGE (XbaI enzyme)	N: 112 Prevalence: NR	S. Rissen	Nalidixic acid, ampicillin, tetracycline	tetA, tetB, sul1, sul2, sul3, gyrA, blaCTX-M-14	PCR, Sensititre® MIC

Note: ND–Not Determined, NR–Not Reported.

and detailed in the PRISMA flow diagram (see Figure 1). The completed PRISMA-ScR checklist is provided in Supplementary Materials Table S1.

3.1.2. Livestock and Poultry Systems as Drivers of AMR Selection

Salmonellosis is a major cause of foodborne illness in the Philippines, primarily due to non-typhoidal Salmonella enterica serovars found in contaminated animal products (e.g., livestock and poultry). Two extensive studies evaluating the Philippine foodborne disease outbreaks (FBDOs) for the periods 1995–2004 and 2005–2018 identified Salmonella spp. as the most prevalent biological agent [8,9]. In the earlier report, meat-based and processed food products—particularly spaghetti meat sauce—were identified as the leading vehicle for local outbreaks, accounting for eighty (80) morbidities per outbreak. Most of these cases occurred within households, potentially implicating the use of low-cost, inferior-quality meat alongside unhygienic food preparation and handling. Moreover, Salmonella spp. was identified as a primary cause of foodborne infections, accounting for 30% of recorded morbidity cases during the aforementioned period, followed by Vibrio spp. and various intoxications [8]. In the subsequent report (2005–2018), Salmonella spp. remained the most prevalent cause of FBDOs (2.46%), alongside chemical toxins such as staphylococcal enterotoxins (1.24%), paralytic shellfish poisoning (PSP) (1.14%), and carbamates (0.96%) [9]. Furthermore, among 69 local Salmonella serotypes identified from 2004 to 2018, S. Typhi, S. Enteritidis, and S. Typhimurium were major causes of enteric fever, salmonellosis, and non-typhoidal Salmonella (NTS) infections [10].

The prevalence of Salmonella in livestock further contributes to this risk. Studies indicate that between 44% and 46.7% of pigs from slaughterhouses may carry the pathogen [6]. Historical data from Thailand (2006)—a comparable tropical setting—showed that registered commercial meat, even after strict processing, harbored a wider variety of Salmonella types than non-registered retail meat, with high resistance rates to tetracycline (60%), streptomycin (50%), and ampicillin (50%) in the bacteria they recovered [11]. This mirrors regional findings, in which high baseline resistance to tetracycline (88–100%) was documented in S. Rissen and S. Anatum isolates shared across pork, poultry, and human clinical samples [12].

The escalation of AMR in these systems is driven by routine antibiotic use—including tetracyclines (e.g., oxytetracycline), fluoroquinolones (e.g., enrofloxacin), and macrolides (e.g., tylosin)—for both therapeutic purposes and growth promotion [13,14,15]. This selective pressure is compounded by the use of antimicrobial growth promoters (AMGPs) in poultry feed [16]. The spread of AMR is further facilitated by limited policy implementation regarding the use and distribution of veterinary medicinal products (VMPs) to farmers, the accessibility and cost-effectiveness of VMPs in local retail outlets, and inadequate awareness of antibiotic misuse [17,18].

Genetically, this resistance is linked to antimicrobial resistance genes (ARGs), such as qnr and bla, which are frequently identified in local swine and chicken meat [18,19]. Specifically, bla subtypes (TEM, SHV, and CTX-M) encode β-lactamases that degrade the β-lactam ring, rendering extended-spectrum cephalosporins (ESCs) ineffective. A high prevalence of bla_TEM (44.55%) has been observed among swine isolates from Metro Manila, corroborating phenotypic ampicillin resistance [5,20]. These enzymes are often associated with plasmid-mediated quinolone resistance (PMQR) markers, which serve as common carriers of ARGs [19]. In swine, 67.8% of isolates are multidrug-resistant, with 93.4% of strains resistant to nitrofurantoin—an agent historically restricted in Philippine veterinary medicine [6].

As pork is a staple livestock product in the country, Salmonella infections—fostered by these agricultural practices—may significantly impact public health by hindering the supply of quality hogs. S. enterica isolates from slaughterhouses in Metro Manila have shown broad resistance, including to amikacin, cefazolin, and cefuroxime, with amikacin and gentamicin exhibiting broader resistance than streptomycin and kanamycin [21]. Additionally, isolates from swine samples in Metro Manila wet markets exhibited high resistance to ampicillin (39.81%) and trimethoprim/sulfamethoxazole (36.11%) [5]. Similarly, poultry products (e.g., chicken meat and eggs) may serve as high-risk vehicles for zoonotic infections [3,22]. This vulnerability may also extend to the aquatic food system; local market monitoring of fresh bivalves (i.e., oysters and mussels) established that baseline contamination frequently exceeds consumer safety thresholds, with Salmonella persistently detected across simulated farm-to-market transport channels [23]. S. Infantis, a predominant Salmonella serovar, has been linked to the emergence of ARGs and virulence genes [3], with horizontal gene transfer (HGT) further accelerating this spread; notably, the first pESI-like megaplasmid in Philippine Salmonella isolates was recently documented in broiler meat [3].

Finally, pathogen persistence may be sustained by overall farm hygiene. A fundamental regional baseline established in 2008 confirms that Salmonella may survive in the environment for extended periods, remaining persistent in swine and poultry facilities despite adequate cleaning and disinfection protocols being performed [24]. Poultry flocks may become contaminated through shared environments, with eggs exposed to manure or via Salmonella migrating from the cloaca to reproductive organs [25]. Furthermore, synanthropic vectors such as roof rats (Rattus rattus) may facilitate pathogen dissemination [25,26], with their fecal droppings acting as an overlooked source of contamination in litter and feed.

3.1.3. Environmental Persistence Through Reservoirs and Genetic Exchange Hotspots

The environment may serve as a dynamic bridge that connects animal, food, and human systems through microbial persistence and genetic exchange. Environmental matrices, including water, organic waste, and constructed surfaces, may harbor Salmonella even in the absence of direct animal contact, allowing resistant traits to circulate across ecological boundaries [7,27]. Mechanical vectors, particularly flies, may intensify this linkage by translocating pathogens between waste and food environments. While studies on direct environmental recovery in the Philippines remain limited, the prevalence of MDR-Salmonella (e.g., S. Infantis) in chicken meat sold in Metro Manila wet markets confirms that these retail environments may act as reservoirs where antimicrobial-resistant bacteria are preserved and reintroduced into the food system [3,4].

Environmental water sources may also contribute to pathogen survival and dissemination. In the Philippines, the Department of Environment and Natural Resources (DENR) regulates water quality through the Water Quality Guidelines and General Effluent Standards, which utilize microbial indicators for monitoring [28]. However, agricultural studies in the Philippines reveal that irrigation water frequently surpasses acceptable microbial thresholds and may contain Salmonella spp., particularly in areas exposed to livestock activities and urban runoff [29]. Significantly, investigations of irrigation canals and runoff in urban and peri-urban farming areas—such as Metro Manila and Laguna—show that fecal contamination and Salmonella may be harbored in these systems [29], emphasizing that water sources may act not only as transitional carriers of these microorganisms but as stable biological habitats [7]. This extended persistence enables contaminated irrigation water to continuously seed soils, crops, and farm surfaces, thereby increasing the likelihood of entry into agricultural production systems.

Additionally, tropical conditions, particularly high humidity and temperature, may enable Salmonella to outlast common fecal indicators such as E. coli and somatic coliphages [29]. Studies in comparable tropical settings, such as Vietnam, observed that high temperatures may facilitate active Salmonella replication on unprocessed carcasses before and during selling [30]. Such research highlights that retail raw food samples in developing countries may consistently yield higher Salmonella loads than in developed nations, illustrating the impact of ambient temperature on rapid microbial growth.

Furthermore, the use of organic waste and manure on poultry farms may contribute to microbial persistence and the development of AMR. Manure, animal effluents, spilled feed, and decomposing organic debris are nutrient-rich biological inputs that may support dense microbial communities, including Salmonella [25]. These environments harbor diverse bacterial populations and sublethal antibiotic residues, creating favorable conditions for horizontal gene transfer (HGT). Within these reservoirs, resistance determinants such as bla_TEM and qnr can be exchanged between environmental bacteria and food-associated Salmonella populations [14]. Recent swine supply chain surveillance in Metro Manila detected a high proportion of bla_TEM among Salmonella enterica isolates from both abattoir and wet-market swine meat samples [5]. The co-detection of Salmonella in agricultural water and soil suggests that organic inputs create a genetic mixing zone, where waste management practices may fuel the evolution and spread of resistance.

In addition, this environmental pressure may be exacerbated by poor farm cleanliness and inadequate disinfectants. A regional baseline study in Thailand found that swine Salmonella strains often exhibit higher resistance levels than those found in poultry, with 42% of these strains resistant to multiple drugs [24]. Furthermore, persistent AMR is often linked to compromised agricultural infrastructure, such as broken flooring, fractured walls, and blocked drainage, which may create ideal moisture-retaining microhabitats where organic matter accumulates. However, there is a scarcity of studies directly assessing how infrastructure failures serve as reservoirs for vectors and AMR microorganisms in the Philippines; aging infrastructure paired with heavy seasonal flooding may transform these sites into stable ecological pockets where moisture, structural waste, and vectors converge. This environment may serve as a reservoir for the amplification of MDR-Salmonella, driven by the mixing of agricultural runoff and the environmental exchange of resistance genes within localized farm pathways [3].

3.2. Results: Synanthropic Vectors and the Dynamics of Cross-Sectoral Dissemination

3.2.1. Pathogen Carriage in Rodent and Arthropod Vector Species

As established in Section 3.1.3, the environmental interface may function as a stable biological niche for Salmonella enterica. However, the transfer of pathogens from stagnant reservoirs, such as contaminated manure and irrigation water, into the human food chain is primarily driven by synanthropic vectors. These organisms may exploit compromised infrastructure and moisture-retaining microhabitats previously described, serving as a link between environmental persistence and active animal or human exposure.

Rodents, particularly the roof rat (Rattus rattus), may be significant contributors to the persistence of Salmonella on Philippine poultry farms, exploiting gaps in walls and blocked drainage systems for nesting. A local study demonstrated that naturally infected rodents exhibit prolonged fecal shedding, potentially facilitating the continuous deposition of Salmonella [26]. Such shedding likely contributes to contamination of feed, water sources, litter, housing surfaces, and equipment. At the farm level, higher rodent population densities have been associated with significantly increased Salmonella prevalence (measured via internal organ isolation) in layer hens, indicating a possible density-dependent relationship between rodent infestation and poultry infection [25]. While specific Philippine-based studies that directly trap and isolate Salmonella from rodents on poultry or swine farms remain limited, regional evidence from similar tropical agricultural settings, such as Thailand, demonstrates that naturally infected rodents exhibit sustained intestinal colonization and prolonged fecal shedding [31].

While rodents provide persistence, insects such as house flies (Musca domestica) may act as secondary vectors, amplifying pathogen spread, as described in Section 3.1.3. Research in Malaysia and Vietnam has confirmed that these insects may harbor Salmonella in environments ranging from poultry farms to wet markets [32,33]. These arthropods may facilitate the translocation of MDR strains from organic waste directly to retail surfaces [32,34]. However, a notable surveillance gap remains in the Philippines: no studies have yet documented direct carriage rates of AMR-Salmonella in synanthropic flies or rodents within Philippine livestock production facilities. Furthermore, while darkling beetles (Alphitobius diaperinus) are globally recognized as significant reservoirs of Salmonella in poultry litter, no localized studies of these beetles have been identified in the Philippines or the broader Southeast Asian context; current literature on beetle-mediated transmission remains restricted to investigations conducted outside the region.

3.2.2. Mechanical and Biological Mechanisms of Vector Dissemination

The physiological and behavioral traits of synanthropic vectors may fundamentally drive the translocation of AMR-Salmonella across the human–animal–environment interface. Vector-borne mobility may transport resistant bacteria into the food supply chain through mechanical and biological pathways. This dissemination may occur mainly through two mechanisms: mechanical external transport and biological internal carriage, which are particularly relevant to agricultural settings such as in the Philippines.

Mechanical transmission may be a primary route of contamination, occurring through the passive transport of microorganisms on external surfaces, including legs, wings, and mouthparts, after contact with waste or animal feces [29]. Research in Southeast Asian settings supports this, with studies in Malaysia demonstrating that house flies (Musca domestica) frequently carry pathogenic bacteria on their body surfaces, potentially facilitating rapid contamination [32,34]. In tropical open-market environments, the high mobility of these vectors may lead to direct cross-contamination of exposed food. This process may be further accelerated by flies’ regurgitation behavior, which transfers bacteria from previously contaminated substrates without requiring host colonization [33,34]. Consequently, these vectors may serve as mechanical transition vehicles that connect contaminated poultry litter and organic waste to otherwise “clean” environmental and retail surfaces [33].

In contrast, biological dissemination involves internal carriage, potentially providing a more persistent reservoir than mechanical transport. In flies, the crop and gut may serve as microbial niches where pathogens such as Salmonella can survive digestion and be deposited onto food during feeding or excretion [35]. These internal environments may also facilitate horizontal gene transfer (HGT), contributing to the maintenance and spread of ARGs within the vector population [32]. Other arthropods, such as the lesser mealworm (Alphitobius diaperinus), and vertebrate pests, such as rodents, may further contribute to biological persistence by harboring the pathogen internally [33]. Because these vectors can withstand standard cleaning and disinfection procedures, they may enable Salmonella to persist across successive poultry flock cycles and resist environmental stressors [29].

Furthermore, vector-mediated transmission is a multifaceted process in which fly physiology, foraging behavior, and the farm environment collectively influence the dissemination of AMR and pathogen loads throughout the production chain [7]. Although biological transfer may occur more slowly than immediate mechanical contact, its ability to sustain chronic infection cycles, particularly in humid, tropical agricultural systems, makes it a significant long-term biosecurity risk [36]. Ultimately, these pathways suggest that synanthropic vectors act not merely as passive indicators of contamination, but as active ecological agents that may sustain and amplify multidrug-resistant Salmonella.

3.2.3. Vulnerabilities Within the Philippine Food Supply Chain

The safety of the Philippine food supply chain may be compromised at several vital stages of the food production system across both the fresh produce and livestock sectors. As established by multiple studies, the occurrence of AMR in Salmonella, potentially driven by the transmission of resistance genes, may be considered a primary cause of foodborne diseases, especially in the Philippines [3,5,27]. While historical data (between 1996 and 2009) from regional neighbors—such as Thailand, Vietnam, and Malaysia—have long established baseline trends for Salmonella resistance, local surveillance corroborates these patterns, suggesting similar escalations in MDR strains [30,37,38,39]. The prudent use of antibiotics and disinfectants such as benzalkonium chloride (BKC) and chlorhexidine (CHX) in animal production, as documented during this period, created selective pressure that facilitated the emergence of resistant strains, as these agents are considered cheap and accessible to the public [24,40].

During the primary production stage, highly polluted irrigation water in urban centers such as Metro Manila may introduce fecal pathogens. A study reported the prevalence of Salmonella on fresh produce in the Philippines, with antimicrobial resistance observed in supermarkets, especially in open-air markets (e.g., Divisoria, Baguio, and Pateros) [27]. Consequently, crops such as carrots, peppers, and mung bean sprouts were found to be infected with resistant strains of Salmonella because they are close to the soil, increasing their exposure to potential contaminants. As discussed in Section 3.1.3, Salmonella may transfer from water to soil and eventually enter the food chain through “internalization,” where the bacteria attach to plant surfaces or penetrate roots and stomata [29]. This internalization poses a safety challenge, as these bacteria may not be eradicated by simply washing the crops, exposing consumers who eat these vegetables raw to risk. Additionally, when contaminated crops are processed into animal feed, they may serve as a secondary vehicle for pathogen transmission. Research indicates that animal-based raw materials, such as rendered waste and fish meal, may carry a 3.9-fold higher risk of Salmonella detection than plant-based components, further bridging the gap between environmental reservoirs and livestock [41].

In food processing and packaging environments, non-typhoidal Salmonella (NTS), specifically S. Typhimurium and S. Enteritidis, is a growing concern due to the concentration of fresh and processed food products and their broad transmission along the production-to-consumption continuum [18]. These bacteria can readily colonize processing infrastructure, such as cutting utensils, chopping boards, and knives, potentially facilitating widespread cross-contamination [39]. At the same time, recent research underscores that conventional cleaning and disinfection protocols often fail to eliminate these persistent pathogens, necessitating advanced interventions such as bacteriophage-driven biocontrol to mitigate Salmonella colonization in broiler facilities [3]. Optimized multi-phage lytic cocktails targeting S. Enteritidis and S. Typhimurium demonstrate extensive synergistic effects, capable of inhibiting up to 94% of nascent biofilm formation on surface matrices and providing strong prophylactic protection in vivo [42]. Local operational conditions may further intensify the challenge. Equipment in “clean zones,” particularly coolers, may be a high-risk site where pathogens enter a growth phase and form resilient biofilms. In the Philippine context, high environmental humidity provides the necessary moisture for these biofilms to persist on surfaces even after heat treatments, compromising subsequent feed batches and resulting in high Salmonella prevalence in finished products despite modern, improved mill designs [41].

Finally, the pathogen may further disseminate during transport and distribution. In the livestock sector, transportation stress may cause animals to shed Salmonella at higher rates, potentially contaminating carcasses and transport vehicles. Without adequate cold storage during transport, microbial loads may rapidly escalate even before reaching the street-vending industry. This contamination may persist as products move through public markets and bus terminals, where prolonged exposure to ambient temperatures facilitates further pathogen growth. Studies of street-vended foods in Laguna, Philippines, have demonstrated significantly poorer microbial quality compared to regional counterparts [43]. This disparity is attributed to inadequate sanitation, cross-contamination from handling accessories, and a lack of temperature-controlled infrastructure [44]. Ultimately, effective biosafety strategies must aim to address these critical points, from polluted irrigation and contaminated feed to persistent surface contamination and a fragmented cold chain, to ensure food security.

3.2.4. Human Health Outcomes and the Evidence of Farm-to-Patient Transmission

Human clinical health is the paramount public health outcome of Salmonella transmission via agricultural and vector-borne pathways. Longitudinal data from the Philippine Antimicrobial Resistance Surveillance Program (ARSP) reveal a concerning escalation in the resistance profiles of clinical Non-Typhoidal Salmonella (NTS) over the last two decades. Between 2004 and 2009, resistance was primarily concentrated in first-line drugs like ampicillin (which peaked at 63.3% in 2004) and sulfamethoxazole-trimethoprim [10]. This aligns with the 2003–2006 regional baseline from Thailand, where similar resistance trends, often exceeding 70–92% for first-line agents, were documented across various regional poultry and swine production systems [45].

However, the Philippine landscape appears to have diverged. Long-term surveillance (2004–2018) shows third-generation cephalosporin resistance (ceftriaxone) at 33.07% [10], while localized phenotypic insusceptibility to ciprofloxacin reaches 55.4% in a multi-center genomic and phenotypic tracking study conducted between 2013 and 2014 [46]. This represents a significant escalation compared to the early-2000s regional baselines, where quinolone and cephalosporin resistance in humans and food systems generally remained below 1%—despite early, localized pediatric clinical spikes. In contrast, a 2004 Vietnam retail study documented an evolutionary footprint of quinolone selection pressure, including the region’s earliest documented emergence of mobile genomic islands (SGI1-F) [30,37,47,48]. While these historical elements are genetically distinct from the plasmids currently circulating, this historical footprint may mirror the broader, multi-sectoral resistance trends now threatening clinical outcomes in the Philippines.

The 2013–2014 period marked a critical transition toward invasive lineages, with S. Enteritidis and S. Typhimurium constituting 60.9% and 13.0% of all recovered invasive NTS (iNTS) clinical isolates, respectively [3]. The 97.8% recovery rate of iNTS from blood samples suggests that these pathogens have evolved from agents of localized gastroenteritis into drivers of systemic bloodstream infections, including life-threatening meningoencephalitis [10].

Consequently, NTS in the Philippines may now represent a systemic threat that increasingly bypasses standard clinical protocols. The widespread identification of the pESI-like megaplasmid—carrying critical resistance genes such as bla_CTX-M-15 and qnr variants—across human, poultry, and swine sectors suggests that traditional human-to-human containment strategies are no longer sufficient, as agricultural livestock and the environment may serve as the primary vehicles for the dissemination of resistance [3,49]. Recent characterization of MDR S. Infantis strains from raw chicken in Metro Manila revealed a closed, circular pESI plasmid (308,757 bp) that concurrently harbors bla_CTX-M-65, tet(A), and sul1 resistance genes [50]. Furthermore, 57% of retail and abattoir isolates in Metro Manila are extended-spectrum β-lactamase (ESBL) producers, with the emerging S. Infantis serovar showing high carriage of the IncFIB(K) plasmid family [18].

These molecular findings, primarily derived from Whole-Genome Sequencing (WGS), confirm that modern human isolates share high genetic similarity with those found in retail meat [5]. Specifically, the distribution of Sequence Types ST34 and ST11 across both sectors supports a high degree of genetic relatedness, strongly implying a shared reservoir and supporting the likelihood of transmission along the food supply chain [5]. While foundational regional baselines (2002–2008) first used pulsed-field gel electrophoresis (PFGE) to elucidate epidemiological links, these studies provide the historical framework for understanding modern genomic transmission. For instance, landmark research from this period identified that specific monophasic variants of S. Typhimurium—S. 4,5,12:i:-—were associated with both septicemic infections in humans and contaminated swine products in Thailand [45]. This was further reinforced by evidence of identical MDR S. Rissen clones circulating in both clinical patients and retail pork [51], as well as research in Malaysia linking S. Weltevreden from agricultural produce to human cases [39].

Ultimately, our modern Whole-Genome Sequencing (WGS) data definitively map how these localized food production systems may act as critical pathways within the broader ecological resistance cycle, building directly upon these early established regional benchmarks.

4. Discussion

4.1. The One Health Synthesis and the Interconnectedness of Resistance Drivers

The One Health approach to AMR-Salmonella highlights the interconnected roles of human, animal, and environmental interfaces in addressing the increasing pressure of antimicrobial resistance within Philippine agriculture and public health. Figure 2 presents the synthesis of evidence across these interfaces, revealing AMR-Salmonella is not merely a series of accidental contaminations, but a persistent, recurring process driven by systemic agricultural and ecological pressures.

The foundational driver of this process is the continuous selective environment maintained within the animal interface, stemming from intensive agricultural practices. The routine administration of antibiotics, including for subtherapeutic purposes and growth promotion, may reduce the effectiveness of clinically important antimicrobial agents by creating a biological filter that favors resistant genotypes [15,16]. This selective pressure reshapes the farm’s microbial community, potentially facilitating the shedding of resistant Salmonella strains that carry multidrug resistance (MDR) determinants, such as bla_TEM and qnr genes, which are optimized for survival against common antimicrobial classes [3,5,21]. The emergence of these resistance markers in Philippine swine and poultry aligns with broader regional trends, suggesting that current production standards have fostered the development of robust, multidrug-resistant lineages that are now entrenched in the local food system [5,6].

Once introduced into the environment, selective pressure is sustained by residual antimicrobial compounds in manure, soils, and wastewater runoff. These nutrient-rich environments may serve as hotspots where Salmonella transitions from primary selection in the host to genomic amplification in the environment through accelerated Horizontal Gene Transfer (HGT) [34]. The recurring detection of Salmonella in agricultural water and soil suggests that organic inputs create a genetic reservoir in which waste management practices, rather than antibiotic use alone, fuel the evolution and spread of resistance [31]. Environmental persistence is further intensified by compromised farm infrastructure, such as fractured flooring and blocked drainage, which produce moisture-retaining microhabitats that shield Salmonella from environmental stressors. These conditions create an ecological niche in which organic waste and inadequate sanitation amplify AMR-Salmonella at the animal–environment interface, a finding consistent with studies on pathogen persistence in tropical agricultural environments [3,7,29,52].

Synanthropic vectors may serve as a primary route of contamination, transforming AMR-Salmonella from a localized environmental hazard into a widely distributed threat. Local evidence suggests a density-dependent association between rodent infestation and flock contamination, with these pests operating as mobile reservoirs rather than superficial mechanical passengers [25,26]. By harboring MDR strains in their internal organs, these vectors shield pathogens from ultraviolet radiation, disinfectants, and climatic extremes, effectively circumventing standard biosecurity barriers [38,39]. Rodents and flies can carry pathogens from confined reservoirs such as manure pits and litter into sensitive spaces, including feed storage and processing areas. Through these movements, vectors facilitate the translocation of resistant strains from rural reservoirs to critical nodes such as slaughterhouses and urban markets [25,26,33,34]. The lack of quantitative data on the contribution of synanthropic vectors to the AMR burden in Philippine food systems is a critical finding of this scoping review, underscoring the urgent need for integrated vector surveillance.

The vulnerability of the Philippine food supply chain illustrates a One Health intersection in which the health of the environment, agricultural animals, and humans is linked. The pre-harvest use of contaminated irrigation water, often polluted by livestock runoff, facilitates the internalization of Salmonella into fresh produce. This process cannot be remediated by simple surface washing [27,29]. During harvest and processing, high-risk operational environments such as abattoirs may act as points of amplification, where inadequate cold-chain infrastructure and persistent biofilms on processing equipment promote cross-contamination [18,41]. Furthermore, the post-harvest phase, characterized by transport stress and prolonged exposure to ambient temperatures in public markets, may lead to microbial quality challenges that surpass those observed in regional counterparts [48,49]. Collectively, this flow of pathogens from agricultural ecosystems into the domestic setting suggests that human clinical risk is often the downstream outcome of a continuous, multi-sectoral process.

These points of failure within the food supply chain highlight how pathogens bypass current control measures. Consequently, the interconnectedness of these resistance drivers suggests that the burden of MDR-Salmonella in the Philippines is not limited to any single stage but is influenced by a combination of environmental and agricultural biosecurity challenges [10,53]. The identification of high-risk plasmids—such as pESI-like megaplasmids—across human, poultry, and swine sectors indicates that containment strategies focusing on a single sector are often insufficient [3,50]. Genomic evidence showing relatedness between retail meat isolates and clinical human samples suggests that localized food production systems may act as critical pathways within the broader ecological resistance cycle [5]. This synthesis establishes that unmanaged environmental reservoirs and their associated vectors contribute to the spillover of highly adapted resistant pathogens into the human interface, positioning the public as the potential endpoint of this transmission.

4.2. Current Surveillance and Control Gaps

In the Philippines, surveillance systems for Salmonella remain fragmented despite its longstanding recognition as a major foodborne pathogen across human, animal, and environmental sectors. Human clinical monitoring is conducted independently of agricultural and environmental systems, preventing a comprehensive understanding of transmission along the agri-food spectrum. This fragmentation may be a consequence of the persistent lack of centralized leadership and coordination among the key government agencies in health, agriculture, science and technology, and the environment, as well as partner agencies in areas such as animal health and ecological management. Current programs primarily prioritize laboratory-confirmed human cases and targeted testing of food-producing livestock. However, environmental surveillance remains predominantly reactive, as routine sampling of water systems, agricultural infrastructure, and food-processing environments is performed inconsistently. Furthermore, the monitoring of biological vectors is often limited to outbreak investigations, preventing the generation of longitudinal data needed to track the persistence, evolution, and dissemination across interconnected interfaces. Consequently, the lack of continuous environmental datasets inhibits the identification of stable genomic reservoirs and recurring contamination pathways, limiting the ability to implement preventative interventions before clinical spillover occurs [1,49]. The inconsistencies in the country’s AMR monitoring and surveillance system stem from several factors, including a shortage of human resources, limited funding, weak management, and an overall lack of public awareness of AMR. From a One Health perspective, this lack of integration facilitates a downstream, case-driven response that overlooks upstream environmental drivers of transmission, leading to missed opportunities for early intervention and perpetuating a reactive cycle that impedes effective Salmonella control [46].

The Philippine National Action Plan (PNAP), organized by the Inter-Agency Committee on Antimicrobial Resistance (ICAMR), is a multisectoral initiative focused on establishing localized policies to combat AMR. By leveraging the One Health framework, it highlights the complex interplay between human health, veterinary health, food, trade, and environmental sectors. Notable efforts include the establishment of the National Poultry Salmonella Prevention and Control Surveillance Program in 2017 and the continuation of monitoring of non-typhoidal Salmonella (NTS), carried over from the previous PNAP into the current development [53]. However, despite Salmonella being a key sentinel pathogen [53], a stable rate of ciprofloxacin resistance contributed to a reduction in clinical monitoring targets for NTS from 25% to 10% in the current PNAP 2024–2028 [54]. This reduction occurs even though AMR-Salmonella continues to challenge data systems due to the lack of robust environmental monitoring.

Despite these national initiatives, a critical gap remains in characterizing the environmental interface as both a reservoir and a transmission pathway. This deficiency is evident when evaluating Salmonella alongside analogous diseases like Leptospirosis [46,55]. In the Philippines, Leptospira transmission is driven by inadequate sanitation and proximity to open sewage—factors that also drive Salmonella persistence. Although exposure routes differ, both pathogens exploit identical structural vulnerabilities. Critically, because Philippine Local Government Units (LGUs) already have experience managing zoonotic waterborne diseases through drainage and sanitation control, these existing protocols offer a feasible blueprint for mitigating environmental Salmonella. By failing to address the transmission of AMR-Salmonella through environmental vectors, current protocols represent a strategic oversight. This surveillance disconnect necessitates a transition from reactive monitoring to the integrated, multi-modal framework proposed in the following section.

4.3. A Proposed One Health Framework for Intervention

This study proposes a multi-modal One Health intervention framework designed to disrupt the dissemination of AMR-Salmonella across animal, environmental, and human interfaces (see Figure 3). The following interventions are conceptual recommendations synthesized from the broader One Health literature, rather than evidence-based outcomes derived directly from the studies included in this scoping review.

The primary component of this conceptual framework focuses on source reduction within the animal gut, the initial site of Salmonella colonization and genomic amplification. By prioritizing non-antibiotic interventions, such as probiotics and botanical antimicrobials together with proper and optimal animal nutrition to promote gut health and mucosal immunity, the framework aims to suppress Salmonella before it can proliferate, shed into the environment, or enter the food supply chain. Probiotic-based interventions align with One Health principles by minimizing the selective pressure exerted by synthetic antibiotics, thereby enabling pathogen suppression without expanding the AMR gene pool. Experimental trials demonstrate the efficacy of this approach, in which broiler feeds were supplemented with competitive exclusion probiotics (i.e., Lactic Acid Bacteria and Bacillus subtilis), thereby successfully occupying cecal adhesion sites. This significantly diminishes NTS colonization even when birds are actively challenged by environmental exposure [56,57,58]. Probiotics inhibit pathogens through competitive exclusion and immune modulation, cultivating a microbiome less permissive to colonization [57,59]. Studies assessing native Southeast Asian broiler models indicate that these multi-strain probiotic supplements not only reduce Salmonella loads in the ceca and crop but also improve the intestinal mucosal barrier [56].

Furthermore, botanical antimicrobials derived from indigenous plants (e.g., Voacanga globosa) provide a complementary, non-antibiotic strategy for livestock health management [54]. While these biological interventions theoretically mitigate environmental contamination by reducing fecal shedding, practical implementation in low-resource settings faces distinct challenges. Operationally, these biological alternatives face significant implementation hurdles. While potentially feasible for backyard producers, scaling them requires consistent supply chains and upfront capital investment. Furthermore, rigorous regulatory barriers exist; the widespread application of these alternatives requires standardized approval pathways through agencies such as the Bureau of Animal Industry (BAI) to ensure safety and optimize dosing.

To interrupt environmental transmission, the framework recommends the utilization of Integrated Pest Management (IPM). This multidimensional strategy disrupts transmission pathways through sustainable physical, biological, and chemical interventions, addressing the structural vulnerabilities identified in Section 5.1 [7]. A robust IPM strategy must prioritize environmental modifications to address structural vulnerabilities in Philippine farm infrastructure. Specifically, repairing fractured walls, fixing broken flooring, and clearing blocked drainage systems are vital physical controls that eliminate the moisture-rich microhabitats where vectors breed and persist. Empirical interventions confirm that standard sanitation protocols frequently fail when these synanthropic vectors are ignored; wild rodents act as biological bridges, harboring NTS at rates more than double that of the surrounding poultry house [60]. Given that rodents in Southeast Asian wet markets act as high-density Salmonella reservoirs with prevalence rates exceeding 70%, targeted habitat reduction and pest control are essential to prevent persistent cross-contamination of food supplies [31].

This requirement for structural and biological pest management extends directly into the retail sector. Traditional wet markets in developing regions frequently lack secure waste disposal and structural zoning, creating optimal microhabitats for flies and rodents to cross-contaminate raw meat products [61]. Integrating these repairs with environmentally responsible biological agents, such as entomopathogenic fungi, addresses the specific challenges of Philippine farm sanitation by minimizing the attraction of mechanical vectors to organic waste and mismanaged manure while reducing reliance on chemical disinfectants. By addressing these environmental factors, the framework offers comprehensive protection at the animal-environment interface. It increases the likelihood of effective control while reducing the risk of resistance development associated with any single intervention. However, the economic feasibility of comprehensive infrastructure repairs remains a major barrier for low-resource farmers. The initial capital required for structural infrastructure improvements (e.g., reinforcing walls, installing pest-proof flooring, and upgrading drainage systems) remains a major barrier for small-scale and backyard farmers who often operate with thin profit margins and are risk-averse toward non-traditional investments [62,63]. Successful IPM implementation requires a collective, community-wide action that is supported by sustained financial subsidies and technical training, elements that are often lacking in the Philippine rural agricultural sectors [63,64].

To strengthen food safety, the framework proposes adopting Loop-mediated Isothermal Amplification (LAMP) as a rapid, cost-effective monitoring tool. Targeting the invA gene, a highly conserved marker essential for Salmonella virulence, the LAMP assay addresses the limitations of traditional culture methods, which are often impractical for routine screening due to 5- to 7-day turnaround times. Recent validation of closed-tube, calcein-based LAMP assays using raw meat samples from Metro Manila wet markets has demonstrated a 10-fold higher sensitivity than conventional PCR [65], providing a viable, high-throughput solution for resource-limited settings such as Philippine wet markets, where conventional molecular diagnostics are often cost-prohibitive.

Deploying such rapid diagnostics at critical nodes, such as abattoirs and retail outlets, provides the timely data necessary for effective risk communication. In the informal sector, LAMP can serve as a public-facing validation tool to build consumer trust in food regulatory systems. However, rapid detection must be coupled with targeted behavioral interventions. Research suggests that consumer compliance in the Philippines is driven more by personal accountability and perceived regulatory legitimacy than by mere awareness of hygiene rules. Therefore, surveillance data must be integrated into educational programs that reinforce public trust and instill a sense of personal responsibility for food safety practices.

In summary, this One Health intervention framework employs a tripartite strategy: (1) reducing the animal source through probiotics and botanicals, (2) breaking environmental bridges via IPM and infrastructure repair, and (3) monitoring human spillover through rapid LAMP diagnostics and behavioral education. By addressing each stage of the transmission cycle, this multimodal approach offers a sustainable pathway to mitigate the burden of AMR-Salmonella in the Philippines.

4.4. Limitations of the Scoping Review

While this scoping review provides a comprehensive One Health synthesis of Salmonella dissemination pathways, several structural limitations inherent to the synthesized literature must be acknowledged. First, there is a notable scarcity of local primary data regarding synanthropic vectors. Although the association between rodent population density and Salmonella shedding in poultry has been documented in two local studies, no locally published literature provides phenotypic or molecular AMR data for insect vectors, such as flies and beetles, in Philippine livestock settings. To address this gap and the limited availability of historical local data prior to 2010, this review used key ASEAN-based studies from 1996 to 2009 as regional baselines. These studies provided the necessary context to complement the primary body of evidence (predominantly concentrated between 2010 and 2026), enabling a more robust structural mapping of transmission dynamics across the animal, environmental, and human interfaces, particularly for arthropod-mediated pathways, where local data remains sparse.

Moreover, significant heterogeneity is evident across the literature. The included studies vary considerably in diagnostic capacity, ranging from early-stage conventional culture and pulsed-field gel electrophoresis (PFGE) to high-resolution whole-genome sequencing (WGS) capable of detecting complex genomic structures, such as the 308,757 bp pESI megaplasmid. Furthermore, local research exhibits strong geographical clustering; most studies profiling swine, poultry, and retail meats are confined to Metro Manila, Laguna, and specific regions in Bukidnon and Davao. This concentration fails to account for the diverse biosecurity landscapes present across the rest of the Philippine archipelago. In accordance with PRISMA-ScR guidelines, the high degree of methodological and sampling heterogeneity precluded any formal meta-analysis or statistical pooling of data.

Finally, the findings are subject to inherent reporting biases within existing surveillance systems. Local foodborne outbreak data and published surveillance entries are often skewed toward high-prevalence resistance profiles and visible clusters of clinical morbidity. This selection bias in reporting likely underrepresents baseline environmental contamination or small-scale backyard operations, where Salmonella occurrence may remain low, self-limiting, or undetected. Rather than a limitation of the review itself, this pattern reflects a systematic gap in current public health monitoring. Acknowledging this identifies a clear path forward for implementing standardized, national-level surveillance protocols that encompass both clinical and subclinical reservoirs.

5. Conclusions

5.1. Summary

This scoping review underscores the need for a comprehensive, vector-aware One Health policy to address the spread of multidrug-resistant (MDR) Salmonella across the Philippine food supply chain. The gathered evidence suggests that integrating rapid diagnostic tools, such as LAMP, with targeted behavioral education could play a pivotal role in reducing human health risks. Simultaneously, interventions targeting the animal interface, specifically non-antibiotic strategies such as probiotics and botanical antimicrobials, show potential to minimize the selection and transmission of resistant strains. Furthermore, environmental management measures, including infrastructure maintenance and improved drainage systems, are critical to disrupting the pathways exploited by synanthropic vectors. The review highlights the value of shifting from reactive, fragmented monitoring toward a multi-modal framework that recognizes the intricate interconnections among humans, animals, and environmental reservoirs. Ultimately, an integrated approach that fosters cross-sectoral collaboration is essential to address systemic biosecurity gaps that contribute to Salmonella antimicrobial resistance, thereby strengthening the resilience and security of the national food system.

5.2. Policy Recommendation

Successfully addressing AMR Salmonella requires strong political commitment and sustained collaboration among diverse stakeholders across sectors, including the Department of Agriculture, the Department of Health, Local Government Units, and other pertinent government agencies. The suggested integrated One Health framework should be implemented instead of reactive, case-driven monitoring. It is recommended to:

• Use antibiotic substitutes, such as probiotics and botanical antimicrobials, to lessen livestock fecal shedding.
• Eliminate vector microhabitats on farms by standardizing infrastructure repairs and Integrated Pest Management (IPM).
• Enhance real-time risk surveillance at crucial food supply nodes by implementing affordable diagnostic tools like LAMP assays.

5.3. Future Research

Future studies should evaluate the long-term cost-effectiveness and economic viability of IPM techniques compared to conventional chemical disinfection, particularly for small-scale Filipino producers. To accurately map the transmission pathways of AMR genes among synanthropic vectors, environmental reservoirs, and clinical human cases, molecular tracing studies utilizing whole-genome sequencing (WGS) are required. In conjunction with these initiatives, the development of predictive risk models that incorporate tropical climatic variables, such as humidity and seasonal flooding, is essential for identifying and mitigating vector-borne contamination hotspots.